cartVersion cartVersion cartVersion cartVersion 0 -6 0 0 0 0 0 0 0 0 0 cartVersion cartVersion cartVersion 0 cartVersion 6 dbSnp155Composite dbSNP 155 bed 3 Short Genetic Variants from dbSNP release 155 3 0.8 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$

Description

\ This track shows short genetic variants\ (up to approximately 50 base pairs) from\ dbSNP\ build 155:\ single-nucleotide variants (SNVs),\ small insertions, deletions, and complex deletion/insertions (indels),\ relative to the reference genome assembly.\ Most variants in dbSNP are rare, not true polymorphisms,\ and some variants are known to be pathogenic.\

\ For hg38 (GRCh38), approximately 998 million distinct variants\ (RefSNP clusters with rs# ids)\ have been mapped to more than 1.06 billion genomic locations\ including alternate haplotype and fix patch sequences.\ dbSNP remapped variants from hg38 to hg19 (GRCh37);\ approximately 981 million distinct variants were mapped to\ more than 1.02 billion genomic locations\ including alternate haplotype and fix patch sequences (not\ all of which are included in UCSC's hg19).\

\ This track includes four subtracks of variants:\

All dbSNP (155): the entire set (1.02 billion for hg19, 1.06 billion for hg38)\
Common dbSNP (155): approximately 15 million variants with a minor allele\ frequency (MAF) of at least 1% (0.01) in the 1000 Genomes Phase 3 dataset.\ Variants in the Mult. subset (below) are excluded.\
ClinVar dbSNP (155): approximately 820,000 variants mentioned in ClinVar.\ Note: that includes both benign and pathogenic (as well as uncertain) variants.\ Variants in the Mult. subset (below) are excluded.\
Mult. dbSNP (155): variants that have been mapped to multiple chromosomes,\ for example chr1 and chr2,\ raising the question of whether the variant is really a variant or just a difference\ between duplicated sequences.\ There are some exceptions in which a variant is mapped to more than one reference\ sequence, but not culled into this set:\
- A variant may appear in both X and Y\ pseudo-autosomal regions (PARs) without being included in this set.\
- A variant may also appear in a main chromosome as well as an alternate haplotype\ or fix patch sequence assigned to that chromosome.\
\

\ A fifth subtrack highlights coordinate ranges to which dbSNP mapped a variant but with genomic\ coordinates that are not internally consistent, i.e. different coordinate ranges were provided\ when describing different alleles. This can occur due to a bug with mapping variants from one\ assembly sequence to another when there is an indel difference between the assembly sequences:\

Map Err (155): around 134,000 mappings of 88,000 distinct rsIDs for hg19\ and 178,000 mappings of 108,000 distinct rsIDs for hg38.\

\ \

Interpreting and Configuring the Graphical Display

\ SNVs and pure deletions are displayed as boxes covering the affected base(s).\ Pure insertions are drawn as single-pixel tickmarks between\ the base before and the base after the insertion.\

\ Insertions and/or deletions in repetitive regions may be represented by a half-height box\ showing uncertainty in placement, followed by a full-height box showing the number of deleted\ bases, or a full-height tickmark to indicate an insertion.\ When an insertion or deletion falls in a repetitive region, the placement may be ambiguous.\ For example, if the reference genome contains "TAAAG" but some\ individuals have "TAAG" at the same location, then the variant is a deletion of a single\ A relative to the reference genome.\ However, which A was deleted? There is no way to tell whether the first, second or third A\ was removed.\ Different variant mapping tools may place the deletion at different bases in the reference genome.\ To reduce errors in merging variant calls made with different left vs. right biases,\ dbSNP made a major change in its representation of deletion/insertion variants in build 152.\ Now, instead of assigning a single-base genomic location at one of the A's,\ dbSNP expands the coordinates to encompass the whole repetitive region,\ so the variant is represented as a deletion of 3 A's combined with an insertion of 2 A's.\ In the track display, there will be a half-height box covering the first two A's,\ followed by a full-height box covering the third A, to show a net loss of one base\ but an uncertain placement within the three A's.\

\ Variants are colored according to functional effect on genes annotated by dbSNP:\

\ \

Protein-altering variants and splice site variants are\ red.\
Synonymous codon variants are\ green.\
\ Non-coding transcript or Untranslated Region (UTR) variants are\ blue.\

\ On the track controls page, several variant properties can be included or excluded from\ the item labels:\ rs# identifier assigned by dbSNP,\ reference/alternate alleles,\ major/minor alleles (when available) and\ minor allele frequency (when available).\ Allele frequencies are reported independently by the project\ (some of which may have overlapping sets of samples):\

\ 1000Genomes:\ The 1000 Genomes dataset contains data for 2,504 individuals from 26 populations.\
\ dbGaP_PopFreq:\ The new source of dbGaP aggregated frequency data (>1 Million Subjects) provided by dbSNP.\
\ TOPMED:\ The TOPMED dataset contains freeze 8 panel that includes about 158,000 individuals. The approximate ethnic breakdown is European(41%), African (31%), Hispanic or Latino (15%), East Asian (9%), and unknown (4%) ancestry.\
\ KOREAN:\ The Korean Reference Genome Database contains data for 1,465 Korean individuals.\
\ SGDP_PRJ:\ The Simons Genome Diversity Project dataset contains 263 C-panel fully public samples and 16 B-panel\ fully public samples for a total of 279 samples.\
\ Qatari:\ The dataset contains initial mappings of the genomes of more than 1,000 Qatari nationals.\
\ NorthernSweden:\ The dataset contains 300 whole-genome sequenced human samples from the county of Vasterbotten in\ northern Sweden.\
\ Siberian:\ The dataset contains paired-end whole-genome sequencing data of 28 modern-day humans from Siberia\ and Western Russia.\
\ TWINSUK:\ The UK10K - TwinsUK project contains 1854 samples from the Department of Twin Research and Genetic Epidemiology (DTR). The dataset contains data obtained from the 11,000 identical and non-identical twins between the ages of 16 and 85 years old.\
\ TOMMO:\ The Tohoku Medical Megabank Project contains an allele frequency panel of 3552 Japanese individuals,\ including the X chromosome.\
\ ALSPAC:\ The UK10K - Avon Longitudinal Study of Parents and Children project contains 1927 sample including individuals obtained from the ALSPAC population. This population contains more than 14,000 mothers enrolled during pregnancy in 1991 and 1992.\
\ GENOME_DK:\ The dataset contains the sequencing of Danish parent-offspring trios to determine genomic variation\ within the Danish population.\
\ GnomAD:\ The gnomAD genome dataset includes a catalog containing 602M SNVs and 105M indels based on the\ whole-genome sequencing of 71,702 samples mapped to the GRCh38 build of the human reference genome.\
\ GoNL:\ The Genome of the Netherlands (GoNL) Project characterizes DNA sequence variation, common and rare,\ for SNVs and short insertions and deletions (indels) and large deletions in 769 individuals of Dutch\ ancestry selected from five biobanks under the auspices of the Dutch hub of the Biobanking and\ Biomolecular Research Infrastructure (BBMRI-NL).\
\ Estonian:\ The dataset contains genetic variation in the Estonian population: pharmacogenomics study of adverse\ drug effects using electronic health records.\
\ Vietnamese:\ The Kinh Vietnamese database contains 24.81 million variants (22.47 million single nucleotide\ polymorphisms (SNPs) and 2.34 million indels), of which 0.71 million variants are novel.\
\ Korea1K:\ The dataset contains 1,094 Korean personal genomes with clinical information.\
\ HapMap:\ (HapMap is being retired.) The International HapMap Project contains samples from African, Asian,\ or European populations.\
\ PRJEB36033:\ The dataset contains ancient Sardinia genome-wide 1240k capture data from 70 ancient Sardinians.\
\ HGDP_Stanford:\ The Stanford HGDP SNP genotyping data consists of ~660,918 tag SNPs in autosomes, chromosome X and\ Y, the pseudoautosomal region, and mitochondrial DNA, typed across 1043 individuals from all panel\ populations.\
\ Daghestan:\ The dataset contains genotypes of >550 000 autosomal single-nucleotide polymorphisms (SNPs) in a\ set of 14 population isolates speaking Nakh-Daghestanian (ND) languages.\
\ PAGE_STUDY:\ The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of Complex Traits.\
\ Chileans:\ The dataset consists of genetic variation on the Chileans using genotype data on ~685,944 SNPs from\ 313 individuals across the whole-continental country.\
\ MGP:\ MGP contains aggregated information on 267 healthy individuals, representative of the Spanish population that were used as controls in the MGP (Medical Genome Project).\
\ PRJEB37584:\ The dataset contains genome-wide genotype analysis that identified copy number variations in cranial\ meningiomas in Chinese patients, and demonstrated diverse CNV burdens among individuals with diverse clinical features.\
\ GoESP:\ The NHLBI Grand Opportunity Exome Sequencing Project (GO-ESP) dataset contains 6503 samples drawn from multiple ESP cohorts and represents all of the ESP exome variant data.\
\ ExAC:\ The Exome Aggregation Consortium (ExAC) dataset contains 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. Individuals affected by severe pediatric disease have been removed.\
\ GnomAD_exomes:\ The gnomAD v2.1 exome dataset comprises a total of 16 million SNVs and 1.2 million indels from\ 125,748 exomes in 14 populations.\
\ FINRISK:\ The FINRISK cohorts comprise the respondents of representative, cross-sectional population surveys\ that are carried out every 5 years since 1972, to assess the risk factors of chronic diseases (e.g.\ CVD, diabetes, obesity, cancer) and health behavior in the working age population.\
\ PharmGKB:\ The dataset contains aggregated frequency data for all PharmGKB submissions.\
\ PRJEB37766:\ The Mexican Genomic Database for Addiction Research.\

\ \ The project from which to take allele frequency data defaults to 1000 Genomes\ but can be set to any of those projects.\

\ Using the track controls, variants can be filtered by\ \

minimum minor allele frequency (MAF)\
variation class/type (e.g. SNV, insertion, deletion)\
functional effect on a gene (e.g. synonymous, frameshift, intron, upstream)\
assorted features and anomalies noted by UCSC during processing of dbSNP's data\

\ \ \

Interesting and anomalous conditions noted by UCSC

\ While processing the information downloaded from dbSNP,\ UCSC annotates some properties of interest.\ These are noted on the item details page,\ and may be useful to include or exclude affected variants.\ \

\ Some are purely informational:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

keyword in data file (dbSnp155.bb)	# in hg19	# in hg38	description
clinvar	627817	630503	Variant is in ClinVar.\
clinvarBenign	275541	276409	Variant is in ClinVar with clinical significance of benign and/or likely benign.\
clinvarConflicting	16925	16834	Variant is in ClinVar with reports of both benign and pathogenic significance.\
clinvarPathogenic	56373	56475	Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic.\
commonAll	14904503	15862783	Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all projects reporting frequencies.\
commonSome	59633864	62095091	Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all, projects reporting frequencies.\
diffMajor	12748733	13073288	Different frequency sources have different major alleles.\
overlapDiffClass	198945442	207101421	This variant overlaps another variant with a different type/class.\
overlapSameClass	29281958	30301090	This variant overlaps another with the same type/class but different start/end.\
rareAll	906113910	938985356	Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in all projects reporting frequencies, or has no frequency data.\
rareSome	950843271	985217664	Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in some, but not all, projects reporting frequencies, or has no frequency data.\
revStrand	5540864	6770772	Alleles are displayed on the + strand at the current position. dbSNP's alleles are displayed on the + strand of a different assembly sequence, so dbSNP's variant page shows alleles that are reverse-complemented with respect to the alleles displayed above.\

\ \

\ while others may indicate that the reference genome contains a rare variant or sequencing issue:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

keyword in data file (dbSnp155.bb)	# in hg19	# in hg38	description
refIsAmbiguous	19	41	The reference genome allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G', or 'N' for 'any base').\
refIsMinor	14950212	15386394	The reference genome allele is not the major allele in at least one project.\
refIsRare	793081	822757	The reference genome allele is rare (i.e. allele frequency < 1%).\
refIsSingleton	694310	712794	The reference genome allele has never been observed in a population sequencing project reporting frequencies.\
refMismatch	1	18	The reference genome allele reported by dbSNP differs from the GenBank assembly sequence. This is very rare and in all cases observed so far, the GenBank assembly has an 'N' while the RefSeq assembly used by dbSNP has a less ambiguous character such as 'R'.\

\ \

\ and others may indicate an anomaly or problem with the variant data:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

keyword in data file (dbSnp155.bb)	# in hg19	# in hg38	description
altIsAmbiguous	5294	5361	At least one alternate allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G'). For alleles containing more than one ambiguous base, this may create a combinatoric explosion of possible alleles.\
classMismatch	13289	18475	Variation class/type is inconsistent with alleles mapped to this genome assembly.\
clusterError	373258	459130	This variant has the same start, end and class as another variant; they probably should have been merged into one variant.\
freqIncomplete	0	0	At least one project reported counts for only one allele which implies that at least one allele is missing from the report; that project's frequency data are ignored.\
freqIsAmbiguous	4332	4399	At least one allele reported by at least one project that reports frequencies contains an IUPAC ambiguous base.\
freqNotMapped	1149972	1141935	At least one project reported allele frequencies relative to a different assembly; However, dbSNP does not include a mapping of this variant to that assembly, which implies a problem with mapping the variant across assemblies. The mapping on this assembly may have an issue; evaluate carefully vs. original submissions, which you can view by clicking through to dbSNP above.\
freqNotRefAlt	74139	110646	At least one allele reported by at least one project that reports frequencies does not match any of the reference or alternate alleles listed by dbSNP.\
multiMap	799777	286666	This variant has been mapped to more than one distinct genomic location.\
otherMapErr	91260	195051	At least one other mapping of this variant has erroneous coordinates. The mapping(s) with erroneous coordinates are excluded from this track and are included in the Map Err subtrack. Sometimes despite this mapping having legal coordinates, there may still be an issue with this mapping's coordinates and alleles; you may want to click through to dbSNP to compare the initial submission's coordinates and alleles. In hg19, 55454 distinct rsIDs are affected; in hg38, 86636. \

\ \

Data Sources and Methods

\ dbSNP has collected genetic variant reports from researchers worldwide for \ more than 20 years.\ Since the advent of next-generation sequencing methods and the population sequencing efforts\ that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline,\ web infrastructure, and download files.\ (Holmes et al.)\ The same challenges of exponential growth affected UCSC's presentation of dbSNP variants,\ so we have taken the opportunity to change our internal representation and import pipeline.\ Most notably, flanking sequences are no longer provided by dbSNP,\ because most submissions have been genomic variant calls in VCF format as opposed to\ independent sequences.\

\ We downloaded JSON files available from dbSNP at\ http://ftp.ncbi.nlm.nih.gov/snp/archive/b155/JSON/,\ extracted a subset of the information about each variant, and collated\ it into a bigBed file using the\ bigDbSnp.as schema with the information\ necessary for filtering and displaying the variants,\ as well as a separate file containing more detailed information to be\ displayed on each variant's details page\ (dbSnpDetails.as schema).\ \

Data Access

\ Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies,\ and more information about how to convert SNPs between assemblies can be found on the following\ FAQ entry.

\ Since dbSNP has grown to include over 1 billion variants, the size of the All dbSNP (155)\ subtrack can cause the\ Table Browser and\ Data Integrator\ to time out, leading to a blank page or truncated output,\ unless queries are restricted to a chromosomal region, to particular defined regions, to a specific set \ of rs# IDs (which can be pasted/uploaded into the Table Browser),\ or to one of the subset tracks such as Common (~15 million variants) or ClinVar (~0.8M variants).\

\ For automated analysis, the track data files can be downloaded from the downloads server for\ hg19 and\ hg38.\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
file format subtrack
dbSnp155.bb hg19 hg38 bigDbSnp (bigBed4+13) All dbSNP (155)
dbSnp155ClinVar.bb hg19 hg38 bigDbSnp (bigBed4+13) ClinVar dbSNP (155)
dbSnp155Common.bb hg19 hg38 bigDbSnp (bigBed4+13) Common dbSNP (155)
dbSnp155Mult.bb hg19 hg38 bigDbSnp (bigBed4+13) Mult. dbSNP (155)
dbSnp155BadCoords.bb hg19 hg38 bigBed4 Map Err (155)
\ dbSnp155Details.tab.gz\ gzip-compressed tab-separated text Detailed variant properties, independent of genome assembly version
\

file	format	subtrack
dbSnp155.bb	hg19	hg38	bigDbSnp (bigBed4+13)	All dbSNP (155)
dbSnp155ClinVar.bb	hg19	hg38	bigDbSnp (bigBed4+13)	ClinVar dbSNP (155)
dbSnp155Common.bb	hg19	hg38	bigDbSnp (bigBed4+13)	Common dbSNP (155)
dbSnp155Mult.bb	hg19	hg38	bigDbSnp (bigBed4+13)	Mult. dbSNP (155)
dbSnp155BadCoords.bb	hg19	hg38	bigBed4	Map Err (155)
\ dbSnp155Details.tab.gz\	gzip-compressed tab-separated text	Detailed variant properties, independent of genome assembly version

\ Several utilities for working with bigBed-formatted binary files can be downloaded\ here.\ Run a utility with no arguments to see a brief description of the utility and its options.\

bigBedInfo provides summary statistics about a bigBed file including the number of\ items in the file. With the -as option, the output includes an\ autoSql\ definition of data columns, useful for interpreting the column values.
bigBedToBed converts the binary bigBed data to tab-separated text.\ Output can be restricted to a particular region by using the -chrom, -start\ and -end options.
bigBedNamedItems extracts rows for one or more rs# IDs.

\ \

Example: retrieve all variants in the region chr1:200001-200400

\ \

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb -chrom=chr1 -start=200000 -end=200400 stdout

\ \

Example: retrieve variant rs6657048

\ \

bigBedNamedItems dbSnp155.bb rs6657048 stdout

\ \

Example: retrieve all variants with rs# IDs in a file (myIds.txt)\ and output to another file (dbSnp155.myIds.bed)

\ \

bigBedNamedItems -nameFile dbSnp155.bb myIds.txt dbSnp155.myIds.bed

\ \

\ The columns in the bigDbSnp/bigBed files and dbSnp155Details.tab.gz file are described in\ bigDbSnp.as and\ dbSnpDetails.as respectively.\ \ For columns that contain lists of allele frequency data, the order of projects\ providing the data listed is as follows:\

\ 1000Genomes\
\ dbGaP_PopFreq\
\ TOPMED\
\ KOREAN\
\ SGDP_PRJ\
\ Qatari\
\ NorthernSweden\
\ Siberian\
\ TWINSUK\
\ TOMMO\
\ ALSPAC\
\ GENOME_DK\
\ GnomAD\
\ GoNL\
\ Estonian\
\ Vietnamese\
\ Korea1K\
\ HapMap\
\ PRJEB36033\
\ HGDP_Stanford\
\ Daghestan\
\ PAGE_STUDY\
\ Chileans\
\ MGP\
\ PRJEB37584\
\ GoESP\
\ ExAC\
\ GnomAD_exomes\
\ FINRISK\
\ PharmGKB\
\ PRJEB37766\

\ The functional effect (maxFuncImpact) for each variant contains the\ Sequence\ Ontology (SO) ID for the greatest functional impact on the gene. This field\ contains a 0 when no SO terms are annotated on the variant.\

\ UCSC also has an\ API\ that can be used to retrieve values from a particular chromosome range.\

\ A list of rs# IDs can be pasted/uploaded in the\ Variant Annotation Integrator\ tool to find out which genes (if any) the variants are located in,\ as well as functional effect such as intron, coding-synonymous, missense, frameshift, etc.\

\ Please refer to our searchable\ mailing list archives\ for more questions and example queries, or our\ Data Access FAQ\ for more information.\

\ \

References

\ \

\ Holmes JB, Moyer E, Phan L, Maglott D, Kattman B.\ \ SPDI: Data Model for Variants and Applications at NCBI.\ Bioinformatics. 2019 Nov 18;.\ PMID: 31738401\

\ Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, Connor R, Fiorini N, Funk K,\ Hefferon T et al.\ \ Database resources of the National Center for Biotechnology Information.\ Nucleic Acids Res. 2019 Jan 8;47(D1):D23-D28.\ PMID: 30395293; PMC: PMC6323993\

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K.\ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122;\ PMC: PMC29783\

\ \ varRep 1 compositeTrack on\ group varRep\ longLabel Short Genetic Variants from dbSNP release 155\ maxWindowCoverage 4000000\ priority 0.8\ shortLabel dbSNP 155\ subGroup1 view Views variants=Variants errs=Mapping_Errors\ track dbSnp155Composite\ type bed 3\ url https://www.ncbi.nlm.nih.gov/snp/$$\ urlLabel dbSNP:\ visibility pack\ dbSnp155ViewErrs Mapping Errors bed 3 Short Genetic Variants from dbSNP release 155 1 0.8 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 longLabel Short Genetic Variants from dbSNP release 155\ parent dbSnp155Composite\ shortLabel Mapping Errors\ track dbSnp155ViewErrs\ view errs\ visibility dense\ dbSnp155ViewVariants Variants bigDbSnp Short Genetic Variants from dbSNP release 155 1 0.8 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 classFilterType multipleListOr\ classFilterValues snv,mnv,ins,del,delins,identity\ detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp155Details.tab.gz\ freqSourceOrder 1000Genomes,dbGaP_PopFreq,TOPMED,KOREAN,SGDP_PRJ,Qatari,NorthernSweden,Siberian,TWINSUK,TOMMO,ALSPAC,GENOME_DK,GnomAD,GoNL,Estonian,Vietnamese,Korea1K,HapMap,PRJEB36033,HGDP_Stanford,Daghestan,PAGE_STUDY,Chileans,MGP,PRJEB37584,GoESP,ExAC,GnomAD_exomes,FINRISK,PharmGKB,PRJEB37766\ longLabel Short Genetic Variants from dbSNP release 155\ maxFuncImpactFilterLabel Greatest functional impact on gene\ maxFuncImpactFilterType multipleListOr\ maxFuncImpactFilterValues 0|(not annotated),0865|frameshift,1587|stop_gained,1574|splice_acceptor_variant,1575|splice_donor_variant,1821|inframe_insertion,1583|missense_variant,1590|terminator_codon_variant,1819|synonymous_variant,1580|coding_sequence_variant,1623|5_prime_UTR_variant,1624|3_prime_UTR_variant,1619|nc_transcript_variant,2|genic_upstream_transcript_variant,1986|upstream_transcript_variant,2152|genic_downstream_transcript_variant,1987|downstream_transcript_variant,1627|intron_variant\ parent dbSnp155Composite\ shortLabel Variants\ track dbSnp155ViewVariants\ type bigDbSnp\ ucscNotesFilterType multipleListOr\ ucscNotesFilterValues altIsAmbiguous|Alternate allele contains IUPAC ambiguous base(s),classMismatch|Variant class/type is inconsistent with allele sizes,clinvar|Present in ClinVar,clinvarBenign|ClinVar significance of benign and/or likely benign,clinvarConflicting|ClinVar includes both benign and pathogenic reports,clinvarPathogenic|ClinVar significance of pathogenic and/or likely pathogenic,clusterError|Overlaps a variant with the same type/class and position,commonAll|MAF >= 1% in all projects that report frequencies,commonSome|MAF >= 1% in at least one project that reports frequencies,diffMajor|Different projects report different major alleles,freqIncomplete|Frequency reported with incomplete allele data,freqIsAmbiguous|Frequency reported for allele with IUPAC ambiguous base(s),freqNotMapped|Frequency reported on different assembly but not mapped by dbSNP,freqNotRefAlt|Reference genome allele is not major allele in at least one project,multiMap|Variant is placed in more than one genomic position,otherMapErr|Another mapping of this variant has illegal coords (indel mapping error?),overlapDiffClass|Variant overlaps other variant(s) of different type/class,overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,rareAll|MAF < 1% in all projects that report frequencies (or no frequency data),rareSome|MAF < 1% in at least one project that reports frequencies,refIsAmbiguous|Reference genome allele contains IUPAC ambiguous base(s),refIsMinor|Reference genome allele is minor allele in at least one project that reports frequencies,refIsRare|Reference genome allele frequency is <1% in at least one project,refIsSingleton|Reference genome frequency is 0 in all projects that report frequencies,refMismatch|Reference allele mismatches reference genome sequence,revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement\ view variants\ visibility dense\ dbSnp153Composite dbSNP 153 bed 6 + Short Genetic Variants from dbSNP release 153 3 0.908 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$

Description

\ This track shows short genetic variants\ (up to approximately 50 base pairs) from\ dbSNP\ build 153:\ single-nucleotide variants (SNVs),\ small insertions, deletions, and complex deletion/insertions (indels),\ relative to the reference genome assembly.\ Most variants in dbSNP are rare, not true polymorphisms,\ and some variants are known to be pathogenic.\

\ For hg38 (GRCh38), approximately 667 million distinct variants\ (RefSNP clusters with rs# ids)\ have been mapped to more than 702 million genomic locations\ including alternate haplotype and fix patch sequences.\ dbSNP remapped variants from hg38 to hg19 (GRCh37);\ approximately 658 million distinct variants were mapped to\ more than 683 million genomic locations\ including alternate haplotype and fix patch sequences (not\ all of which are included in UCSC's hg19).\

\ This track includes four subtracks of variants:\

All dbSNP (153): the entire set (683 million for hg19, 702 million for hg38)\
Common dbSNP (153): approximately 15 million variants with a minor allele\ frequency (MAF) of at least 1% (0.01) in the 1000 Genomes Phase 3 dataset.\ Variants in the Mult. subset (below) are excluded.\
ClinVar dbSNP (153): approximately 455,000 variants mentioned in ClinVar.\ Note: that includes both benign and pathogenic (as well as uncertain) variants.\ Variants in the Mult. subset (below) are excluded.\
Mult. dbSNP (153): variants that have been mapped to multiple chromosomes,\ for example chr1 and chr2,\ raising the question of whether the variant is really a variant or just a difference\ between duplicated sequences.\ There are some exceptions in which a variant is mapped to more than one reference\ sequence, but not culled into this set:\
- A variant may appear in both X and Y\ pseudo-autosomal regions (PARs) without being included in this set.\
- A variant may also appear in a main chromosome as well as an alternate haplotype\ or fix patch sequence assigned to that chromosome.\
\

Map Err (153): around 120,000 mappings of 55,000 distinct rsIDs for hg19\ and 149,000 mappings of 86,000 distinct rsIDs for hg38.\

\ \

Interpreting and Configuring the Graphical Display

\ SNVs and pure deletions are displayed as boxes covering the affected base(s).\ Pure insertions are drawn as single-pixel tickmarks between\ the base before and the base after the insertion.\

\ Variants are colored according to functional effect on genes annotated by dbSNP:\

\ \

Protein-altering variants and splice site variants are\ red.\
Synonymous codon variants are\ green.\
\ Non-coding transcript or Untranslated Region (UTR) variants are\ blue.\

\ On the track controls page, several variant properties can be included or excluded from\ the item labels:\ rs# identifier assigned by dbSNP,\ reference/alternate alleles,\ major/minor alleles (when available) and\ minor allele frequency (when available).\ Allele frequencies are reported independently by twelve projects\ (some of which may have overlapping sets of samples):\

1000Genomes:\ The 1000 Genomes Phase 3 dataset contains data for 2,504 individuals from 26 populations.\
GnomAD exomes:\ The gnomAD\ v2.1\ exome dataset comprises a total of 16 million SNVs and 1.2 million indels from 125,748 exomes\ in 14 populations.\
TOPMED:\ The TOPMED dataset contains phase 3 data from freeze 5 panel that include more than 60,000\ individuals. The approximate ethnic breakdown is European(52%), African (31%),\ Hispanic or Latino (10%), and East Asian (7%) ancestry.\
PAGE STUDY:\ The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of\ Complex Traits.\
GnomAD genomes:\ The gnomAD\ v2.1\ genome dataset includes 229 million SNVs and 33 million indels from 15,708 genomes\ in 9 populations.\
GoESP:\ The NHLBI Grand Opportunity Exome Sequencing Project (GO-ESP) dataset contains 6503 samples\ drawn from multiple ESP cohorts and represents all of the ESP exome variant data.\
Estonian:\ Genetic variation in the Estonian population: pharmacogenomics study of\ adverse drug effects using electronic health records.\
ALSPAC:\ The UK10K - Avon Longitudinal Study of Parents and Children project contains 1927 sample\ including individuals obtained from the\ ALSPAC population.\ This population contains more than 14,000 mothers enrolled during pregnancy in 1991 and 1992.\
TWINSUK:\ The UK10K - TwinsUK project contains 1854 samples from the\ Department of Twin Research and\ Genetic Epidemiology (DTR).\ The DTR dataset contains data obtained from the 11,000 identical and non-identical twins\ between the ages of 16 and 85 years old.\
NorthernSweden:\ Whole-genome sequenced control population in northern Sweden reveals subregional\ genetic differences. This population consists of 300 whole genome sequenced human samples\ selected from the county of Vasterbotten in northern Sweden. To be selected for inclusion\ into the population, the individuals had to have reached at least 80 years of age and have\ no diagnosed cancer.\
Vietnamese:\ The Vietnamese Genetic Variation Database includes about 25 million variants (SNVs and indels)\ from 406 genomes and 305 exomes of unrelated healthy Kinh Vietnamese (KHV) people.\

\ The project from which to take allele frequency data defaults to 1000 Genomes\ but can be set to any of those projects.\

\ Using the track controls, variants can be filtered by\ \

minimum minor allele frequency (MAF)\
variation class/type (e.g. SNV, insertion, deletion)\
functional effect on a gene (e.g. synonymous, frameshift, intron, upstream)\
assorted features and anomalies noted by UCSC during processing of dbSNP's data\

\ \ \

Interesting and anomalous conditions noted by UCSC

\ Some are purely informational:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

keyword in data file (dbSnp153.bb)	# in hg19	# in hg38	description
clinvar	454678	453996	Variant is in ClinVar.
clinvarBenign	143864	143736	Variant is in ClinVar with clinical significance of benign and/or likely benign.
clinvarConflicting	7932	7950	Variant is in ClinVar with reports of both benign and pathogenic significance.
clinvarPathogenic	96242	95262	Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic.
commonAll	12184521	12438655	Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all\ projects reporting frequencies.
commonSome	20541190	20902944	Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all,\ projects reporting frequencies.
diffMajor	1377831	1399109	Different frequency sources have different major alleles.
overlapDiffClass	107015341	110007682	This variant overlaps another variant with a different type/class.
overlapSameClass	16915239	17291289	This variant overlaps another with the same type/class but different start/end.
rareAll	662601770	681696398	Variant is "rare", i.e. has a Minor Allele Frequency of less than 1%\ in all projects reporting frequencies, or has no frequency data.
rareSome	670958439	690160687	Variant is "rare", i.e. has a Minor Allele Frequency of less than 1%\ in some, but not all, projects reporting frequencies, or has no frequency data.
revStrand	3813702	4532511	Alleles are displayed on the + strand at the current position.\ dbSNP's alleles are displayed on the + strand of a different assembly sequence,\ so dbSNP's variant page shows alleles that are reverse-complemented with respect to\ the alleles displayed above.

\ while others may indicate that the reference genome contains a rare variant or sequencing issue:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

keyword in data file (dbSnp153.bb)	# in hg19	# in hg38	description
refIsAmbiguous	101	111	The reference genome allele contains an IUPAC ambiguous base\ (e.g. 'R' for 'A or G', or 'N' for 'any base').
refIsMinor	3272116	3360435	The reference genome allele is not the major allele in at least one project.
refIsRare	136547	160827	The reference genome allele is rare (i.e. allele frequency < 1%).
refIsSingleton	37832	50927	The reference genome allele has never been observed in a population sequencing project\ reporting frequencies.
refMismatch	4	33	The reference genome allele reported by dbSNP differs from the GenBank assembly sequence.\ This is very rare and in all cases observed so far, the GenBank assembly has an 'N'\ while the RefSeq assembly used by dbSNP has a less ambiguous character such as 'R'.

\ and others may indicate an anomaly or problem with the variant data:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

keyword in data file (dbSnp153.bb)	# in hg19	# in hg38	description
altIsAmbiguous	10755	10888	At least one alternate allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G').\ For alleles containing more than one ambiguous base, this may create a\ combinatoric explosion of possible alleles.
classMismatch	5998	6216	Variation class/type is inconsistent with alleles mapped to this genome assembly.
clusterError	114826	128306	This variant has the same start, end and class as another variant;\ they probably should have been merged into one variant.
freqIncomplete	3922	4673	At least one project reported counts for only one allele which implies that at\ least one allele is missing from the report;\ that project's frequency data are ignored.
freqIsAmbiguous	7656	7756	At least one allele reported by at least one project that reports frequencies\ contains an IUPAC ambiguous base.
freqNotMapped	2685	6590	At least one project reported allele frequencies relative to a different assembly;\ However, dbSNP does not include a mapping of this variant to that assembly, which\ implies a problem with mapping the variant across assemblies. The mapping on this\ assembly may have an issue; evaluate carefully vs. original submissions, which you\ can view by clicking through to dbSNP above.
freqNotRefAlt	17694	32170	At least one allele reported by at least one project that reports frequencies\ does not match any of the reference or alternate alleles listed by dbSNP.
multiMap	562180	132123	This variant has been mapped to more than one distinct genomic location.
otherMapErr	114095	204219	At least one other mapping of this variant has erroneous coordinates.\ The mapping(s) with erroneous coordinates are excluded from this track\ and are included in the Map Err subtrack. Sometimes despite this mapping\ having legal coordinates, there may still be an issue with this mapping's\ coordinates and alleles; you may want to click through to dbSNP to compare\ the initial submission's coordinates and alleles.\ In hg19, 55454 distinct rsIDs are affected; in hg38, 86636.\

\ \ \

Data Sources and Methods

\ We downloaded JSON files available from dbSNP at\ ftp://ftp.ncbi.nlm.nih.gov/snp/archive/b153/JSON/,\ extracted a subset of the information about each variant, and collated\ it into a bigBed file using the\ bigDbSnp.as schema with the information\ necessary for filtering and displaying the variants,\ as well as a separate file containing more detailed information to be\ displayed on each variant's details page\ (dbSnpDetails.as schema).\ \

Data Access

\ Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies,\ and more information about how to convert SNPs between assemblies can be found on the following\ FAQ entry.

\ Since dbSNP has grown to include approximately 700 million variants, the size of the All dbSNP (153)\ subtrack can cause the\ Table Browser and\ Data Integrator\ to time out, leading to a blank page or truncated output,\ unless queries are restricted to a chromosomal region, to particular defined regions, to a specific set \ of rs# IDs (which can be pasted/uploaded into the Table Browser),\ or to one of the subset tracks such as Common (~15 million variants) or ClinVar (~0.5M variants).\

\ For automated analysis, the track data files can be downloaded from the downloads server for\ hg19 and\ hg38.\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
file format subtrack
dbSnp153.bb hg19 hg38 bigDbSnp (bigBed4+13) All dbSNP (153)
dbSnp153ClinVar.bb hg19 hg38 bigDbSnp (bigBed4+13) ClinVar dbSNP (153)
dbSnp153Common.bb hg19 hg38 bigDbSnp (bigBed4+13) Common dbSNP (153)
dbSnp153Mult.bb hg19 hg38 bigDbSnp (bigBed4+13) Mult. dbSNP (153)
dbSnp153BadCoords.bb hg19 hg38 bigBed4 Map Err (153)
\ dbSnp153Details.tab.gz\ gzip-compressed tab-separated text Detailed variant properties, independent of genome assembly version
\

file	format	subtrack
dbSnp153.bb	hg19	hg38	bigDbSnp (bigBed4+13)	All dbSNP (153)
dbSnp153ClinVar.bb	hg19	hg38	bigDbSnp (bigBed4+13)	ClinVar dbSNP (153)
dbSnp153Common.bb	hg19	hg38	bigDbSnp (bigBed4+13)	Common dbSNP (153)
dbSnp153Mult.bb	hg19	hg38	bigDbSnp (bigBed4+13)	Mult. dbSNP (153)
dbSnp153BadCoords.bb	hg19	hg38	bigBed4	Map Err (153)
\ dbSnp153Details.tab.gz\	gzip-compressed tab-separated text	Detailed variant properties, independent of genome assembly version

\ Several utilities for working with bigBed-formatted binary files can be downloaded\ here.\ Run a utility with no arguments to see a brief description of the utility and its options.\

bigBedInfo provides summary statistics about a bigBed file including the number of\ items in the file. With the -as option, the output includes an\ autoSql\ definition of data columns, useful for interpreting the column values.
bigBedToBed converts the binary bigBed data to tab-separated text.\ Output can be restricted to a particular region by using the -chrom, -start\ and -end options.
bigBedNamedItems extracts rows for one or more rs# IDs.

\ \

Example: retrieve all variants in the region chr1:200001-200400

\ \

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp153.bb -chrom=chr1 -start=200000 -end=200400 stdout

\ \

Example: retrieve variant rs6657048

\ \

bigBedNamedItems dbSnp153.bb rs6657048 stdout

\ \

Example: retrieve all variants with rs# IDs in file myIds.txt

\ \

bigBedNamedItems -nameFile dbSnp153.bb myIds.txt dbSnp153.myIds.bed

\ \

\ The columns in the bigDbSnp/bigBed files and dbSnp153Details.tab.gz file are described in\ bigDbSnp.as and\ dbSnpDetails.as respectively.\ For columns that contain lists of allele frequency data, the order of projects\ providing the data listed is as follows:\

\ UCSC also has an\ API\ that can be used to retrieve values from a particular chromosome range.\

\ Please refer to our searchable\ mailing list archives\ for more questions and example queries, or our\ Data Access FAQ\ for more information.\

\ \

References

\ \

\ Holmes JB, Moyer E, Phan L, Maglott D, Kattman B.\ \ SPDI: Data Model for Variants and Applications at NCBI.\ Bioinformatics. 2019 Nov 18;.\ PMID: 31738401\

\ \ varRep 1 compositeTrack on\ group varRep\ html ../dbSnp153Composite\ longLabel Short Genetic Variants from dbSNP release 153\ maxWindowCoverage 4000000\ parent dbSnpArchive on\ priority 0.908\ shortLabel dbSNP 153\ subGroup1 view Views variants=Variants errs=Mapping_Errors\ track dbSnp153Composite\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/snp/$$\ urlLabel dbSNP:\ visibility pack\ dbSnp153ViewErrs Mapping Errors bed 6 + Short Genetic Variants from dbSNP release 153 1 0.908 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 longLabel Short Genetic Variants from dbSNP release 153\ parent dbSnp153Composite\ shortLabel Mapping Errors\ track dbSnp153ViewErrs\ view errs\ visibility dense\ dbSnp153ViewVariants Variants bigDbSnp Short Genetic Variants from dbSNP release 153 1 0.908 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 classFilterType multipleListOr\ classFilterValues snv,mnv,ins,del,delins,identity\ detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz\ freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,ExAC,PAGE_STUDY,GnomAD,GoESP,Estonian,ALSPAC,TWINSUK,NorthernSweden,Vietnamese\ longLabel Short Genetic Variants from dbSNP release 153\ maxFuncImpactFilterLabel Greatest functional impact on gene\ maxFuncImpactFilterType multipleListOr\ maxFuncImpactFilterValues 0|(not annotated),0865|frameshift,1587|stop_gained,1574|splice_acceptor_variant,1575|splice_donor_variant,1821|inframe_insertion,1583|missense_variant,1590|terminator_codon_variant,1819|synonymous_variant,1580|coding_sequence_variant,1623|5_prime_UTR_variant,1624|3_prime_UTR_variant,1619|nc_transcript_variant,2153|genic_upstream_transcript_variant,1986|upstream_transcript_variant,2152|genic_downstream_transcript_variant,1987|downstream_transcript_variant,1627|intron_variant\ parent dbSnp153Composite\ shortLabel Variants\ showCfg on\ track dbSnp153ViewVariants\ type bigDbSnp\ ucscNotesFilterType multipleListOr\ ucscNotesFilterValues altIsAmbiguous|Alternate allele contains IUPAC ambiguous base(s),classMismatch|Variant class/type is inconsistent with allele sizes,clinvar|Present in ClinVar,clinvarBenign|ClinVar significance of benign and/or likely benign,clinvarConflicting|ClinVar includes both benign and pathogenic reports,clinvarPathogenic|ClinVar significance of pathogenic and/or likely pathogenic,clusterError|Overlaps a variant with the same type/class and position,commonAll|MAF >= 1% in all projects that report frequencies,commonSome|MAF >= 1% in at least one project that reports frequencies,diffMajor|Different projects report different major alleles,freqIncomplete|Frequency reported with incomplete allele data,freqIsAmbiguous|Frequency reported for allele with IUPAC ambiguous base(s),freqNotMapped|Frequency reported on different assembly but not mapped by dbSNP,freqNotRefAlt|Reference genome allele is not major allele in at least one project,multiMap|Variant is placed in more than one genomic position,otherMapErr|Another mapping of this variant has illegal coords (indel mapping error?),overlapDiffClass|Variant overlaps other variant(s) of different type/class,overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,rareAll|MAF < 1% in all projects that report frequencies (or no frequency data),rareSome|MAF < 1% in at least one project that reports frequencies,refIsAmbiguous|Reference genome allele contains IUPAC ambiguous base(s),refIsMinor|Reference genome allele is minor allele in at least one project that reports frequencies,refIsRare|Reference genome allele frequency is <1% in at least one project,refIsSingleton|Reference genome frequency is 0 in all projects that report frequencies,refMismatch|Reference allele mismatches reference genome sequence,revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement\ view variants\ visibility dense\ snp151Common Common SNPs(151) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples 0 0.909 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 151, available from\ ftp.ncbi.nlm.nih.gov/snp.\ Only SNPs that have a minor allele frequency (MAF) of at least 1% and\ are mapped to a single location in the reference genome assembly are\ included in this subset. Frequency data are not available for all SNPs,\ so this subset is incomplete.\ Allele counts from all submissions that include frequency data are combined\ when determining MAF, so for example the allele counts from\ the 1000 Genomes Project and an independent submitter may be combined for the\ same variant.\

\ dbSNP provides\ download files\ in the\ Variant Call Format (VCF)\ that include a "COMMON" flag in the INFO column. That is determined by a different method,\ and is generally a superset of the UCSC Common set.\ dbSNP uses frequency data from the\ 1000 Genomes Project\ only, and considers a variant COMMON if it has a MAF of at least 0.01 in any of the five\ super-populations:\

African (AFR)
Admixed American (AMR)
East Asian (EAS)
European (EUR)
South Asian (SAS)

\ In build 151, dbSNP marks approximately 38M variants as COMMON; 23M of those have a\ global MAF < 0.01. The remainder should be in agreement with UCSC's Common subset.\

\ The selection of SNPs with a minor allele frequency of 1% or greater\ is an attempt to identify variants that appear to be reasonably common\ in the general population. Taken as a set, common variants should be\ less likely to be associated with severe genetic diseases due to the\ effects of natural selection,\ following the view that deleterious variants are not likely to become\ common in the population.\ However, the significance of any particular variant should be interpreted\ only by a trained medical geneticist using all available information.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(151) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(151) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly.
All SNPs(151) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width\ of a single base, and multiple nucleotide variants are represented by a\ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by\ HapMap project
- By 1000Genomes (human only) - submitted by \ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors.\ If a SNP has more than one of these attributes, the stronger color will override \ the weaker color. The order of colors, from strongest to weakest, is red, green, \ blue, gray, and black.\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build\ 147, weight had values 1, 2 or 3, with 1 being the highest quality\ (mapped to a single genomic location). As of dbSNP build 147, dbSNP\ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to\ particular gene sets. Choose the gene sets from the list on the SNP\ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to.\ When one or more gene tracks are selected, the SNP details page\ lists all genes that the SNP hits (or is close to), with the same keywords\ used in the function category. The function usually\ agrees with NCBI's function, except when NCBI's functional annotation is\ relative to an XM_* predicted RefSeq (not included in the UCSC Genome\ Browser's RefSeq Genes track) and/or UCSC's functional annotation is\ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ dbSNP uses a class called 'in-del'. We compare the length of the\ reference allele to the length(s) of observed alleles; if the\ reference allele is shorter than all other observed alleles, we change\ 'in-del' to 'insertion'. Likewise, if the reference allele is longer\ than all other observed alleles, we change 'in-del' to 'deletion'.\

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking\ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences\ to the neighboring genomic sequence for display on SNP details pages.\ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period >= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b151_SNPContigLoc_N.bcp.gz and\ b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38)
b151_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b151_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp151*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies.\ We use our liftOver utility to identify the orthologous alleles.\ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the\ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use\ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ \ GRCh37/hg19, GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ \ varRep 1 chimpDb panTro5\ chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8\ codingAnnotations snp151CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp151Common\ longLabel Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples\ macaqueDb rheMac8\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.909\ shortLabel Common SNPs(151)\ snpExceptionDesc snp151ExceptionDesc\ snpSeq snp151Seq\ track snp151Common\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp151 All SNPs(151) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 151) 0 0.91 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 151, available from\ ftp.ncbi.nlm.nih.gov/snp.\

\ Three tracks contain subsets of the items in this track:\

Common SNPs(151): SNPs that have a minor allele frequency\ of at least 1% and are mapped to a single location in the reference\ genome assembly. Frequency data are not available for all SNPs,\ so this subset is incomplete.
Flagged SNPs(151): SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at least 1%.\ Frequency data are not available for all SNPs, so this subset may\ include some SNPs whose true minor allele frequency is 1% or greater.
Mult. SNPs(151): SNPs that have been mapped to multiple locations\ in the reference genome assembly. There are very few SNPs in this category\ because dbSNP has been filtering out almost all multiple-mapping SNPs since\ build 149.

\ The default maximum weight for this track is 1, so unless\ the setting is changed in the track controls, SNPs that map to multiple genomic\ locations will be omitted from display. When a SNP's flanking sequences\ map to multiple locations in the reference genome, it calls into question\ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(151) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(151) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly.
All SNPs(151) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by\ HapMap project
- By 1000Genomes (human only) - submitted by \ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors.\ If a SNP has more than one of these attributes, the stronger color will override \ the weaker color. The order of colors, from strongest to weakest, is red, green, \ blue, gray, and black.\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build\ 147, weight had values 1, 2 or 3, with 1 being the highest quality\ (mapped to a single genomic location). As of dbSNP build 147, dbSNP\ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro5\ chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8\ codingAnnotations snp151CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp151\ longLabel Simple Nucleotide Polymorphisms (dbSNP 151)\ macaqueDb rheMac8\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.910\ shortLabel All SNPs(151)\ track snp151\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp151Flagged Flagged SNPs(151) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc 0 0.911 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 151, available from\ ftp.ncbi.nlm.nih.gov/snp.\ Only SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at\ least 1%, are included in this subset.\ Frequency data are not available for all SNPs, so this subset probably\ includes some SNPs whose true minor allele frequency is 1% or greater.\

\ The significance of any particular variant in this track should be\ interpreted only by a trained medical geneticist using all available\ information. For example, some variants are included in this track\ because of their inclusion in a Locus-Specific Database (LSDB) or\ mention in OMIM, but are not thought to be disease-causing, so\ inclusion of a variant in this track is not necessarily an indicator\ of risk. Again, all available information must be carefully considered\ by a qualified professional.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(151) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(151) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly.
All SNPs(151) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by\ HapMap project
- By 1000Genomes (human only) - submitted by \ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors.\ If a SNP has more than one of these attributes, the stronger color will override \ the weaker color. The order of colors, from strongest to weakest, is red, green, \ blue, gray, and black.\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build\ 147, weight had values 1, 2 or 3, with 1 being the highest quality\ (mapped to a single genomic location). As of dbSNP build 147, dbSNP\ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro5\ chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8\ codingAnnotations snp151CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html snp151Flagged\ longLabel Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc\ macaqueDb rheMac8\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.911\ shortLabel Flagged SNPs(151)\ snpExceptionDesc snp151ExceptionDesc\ snpSeq snp151Seq\ track snp151Flagged\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp151Mult Mult. SNPs(151) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci 0 0.912 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 150, available from\ ftp.ncbi.nlm.nih.gov/snp.\ Only SNPs that have been mapped to multiple locations in the reference\ genome assembly are included in this subset. When a SNP's flanking sequences\ map to multiple locations in the reference genome, it calls into question\ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ Since build 149, dbSNP has been filtering out almost all such "SNPs" so\ there are very few items in this track.\

\ The default maximum weight for this track is 3,\ unlike the other dbSNP build 150 tracks which have a maximum weight of 1.\ That enables these multiply-mapped SNPs to appear in the display, while\ by default they will not appear in the All SNPs(150) track because of its\ maximum weight filter.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(150) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(150) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly.
All SNPs(150) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by \ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors.\ If a SNP has more than one of these attributes, the stronger color will override \ the weaker color. The order of colors, from strongest to weakest, is red, green, \ blue, gray, and black.\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build\ 147, weight had values 1, 2 or 3, with 1 being the highest quality\ (mapped to a single genomic location). As of dbSNP build 147, dbSNP\ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

References

\ \ varRep 1 chimpDb panTro5\ chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8\ codingAnnotations snp151CodingDbSnp,\ defaultGeneTracks knownGene\ defaultMaxWeight 3\ group varRep\ hapmapPhase III\ html ../snp150Mult\ longLabel Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci\ macaqueDb rheMac8\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.912\ shortLabel Mult. SNPs(151)\ snpExceptionDesc snp151ExceptionDesc\ snpSeq snp151Seq\ track snp151Mult\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp150Mult Mult. SNPs(150) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci 0 0.913 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 150, available from\ ftp.ncbi.nlm.nih.gov/snp.\ Only SNPs that have been mapped to multiple locations in the reference\ genome assembly are included in this subset. When a SNP's flanking sequences\ map to multiple locations in the reference genome, it calls into question\ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ Since build 149, dbSNP has been filtering out almost all such "SNPs" so\ there are very few items in this track.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(150) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(150) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly.
All SNPs(150) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by \ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors.\ If a SNP has more than one of these attributes, the stronger color will override \ the weaker color. The order of colors, from strongest to weakest, is red, green, \ blue, gray, and black.\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build\ 147, weight had values 1, 2 or 3, with 1 being the highest quality\ (mapped to a single genomic location). As of dbSNP build 147, dbSNP\ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b150_SNPContigLoc_N.bcp.gz and\ b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b150_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b150_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp150*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro5\ chimpOrangMacOrthoTable snp150OrthoPt5Pa2Rm8\ codingAnnotations snp150CodingDbSnp,\ defaultGeneTracks knownGene\ defaultMaxWeight 3\ group varRep\ hapmapPhase III\ html ../snp150Mult\ longLabel Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci\ macaqueDb rheMac8\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.913\ shortLabel Mult. SNPs(150)\ snpExceptionDesc snp150ExceptionDesc\ snpSeq snp150Seq\ track snp150Mult\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp150 All SNPs(150) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 150) 0 0.914 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ Three tracks contain subsets of the items in this track:\

Common SNPs(150): SNPs that have a minor allele frequency\ of at least 1% and are mapped to a single location in the reference\ genome assembly. Frequency data are not available for all SNPs,\ so this subset is incomplete.
Flagged SNPs(150): SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at least 1%.\ Frequency data are not available for all SNPs, so this subset may\ include some SNPs whose true minor allele frequency is 1% or greater.
Mult. SNPs(150): SNPs that have been mapped to multiple locations\ in the reference genome assembly. There are very few SNPs in this category\ because dbSNP has been filtering out almost all multiple-mapping SNPs since\ build 149.

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(150) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(150) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly.
All SNPs(150) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by \ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors.\ If a SNP has more than one of these attributes, the stronger color will override \ the weaker color. The order of colors, from strongest to weakest, is red, green, \ blue, gray, and black.\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build\ 147, weight had values 1, 2 or 3, with 1 being the highest quality\ (mapped to a single genomic location). As of dbSNP build 147, dbSNP\ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b150_SNPContigLoc_N.bcp.gz and\ b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b150_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b150_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp150*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro5\ chimpOrangMacOrthoTable snp150OrthoPt5Pa2Rm8\ codingAnnotations snp150CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp150\ longLabel Simple Nucleotide Polymorphisms (dbSNP 150)\ macaqueDb rheMac8\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.914\ shortLabel All SNPs(150)\ track snp150\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp150Common Common SNPs(150) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples 0 0.915 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 150, available from\ ftp.ncbi.nlm.nih.gov/snp.\ Only SNPs that have a minor allele frequency (MAF) of at least 1% and\ are mapped to a single location in the reference genome assembly are\ included in this subset. Frequency data are not available for all SNPs,\ so this subset is incomplete.\ Allele counts from all submissions that include frequency data are combined\ when determining MAF, so for example the allele counts from\ the 1000 Genomes Project and an independent submitter may be combined for the\ same variant.\

African (AFR)
Admixed American (AMR)
East Asian (EAS)
European (EUR)
South Asian (SAS)

\ In build 151 (which has replaced build 150 on the dbSNP web and download site),\ dbSNP marks approximately 38M variants as COMMON; 23M of those have a\ global MAF < 0.01. The remainder should be in agreement with UCSC's Common subset.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(150) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(150) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly.
All SNPs(150) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by \ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors.\ If a SNP has more than one of these attributes, the stronger color will override \ the weaker color. The order of colors, from strongest to weakest, is red, green, \ blue, gray, and black.\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build\ 147, weight had values 1, 2 or 3, with 1 being the highest quality\ (mapped to a single genomic location). As of dbSNP build 147, dbSNP\ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b150_SNPContigLoc_N.bcp.gz and\ b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b150_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b150_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp150*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro5\ chimpOrangMacOrthoTable snp150OrthoPt5Pa2Rm8\ codingAnnotations snp150CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp150Common\ longLabel Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples\ macaqueDb rheMac8\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.915\ shortLabel Common SNPs(150)\ snpExceptionDesc snp150ExceptionDesc\ snpSeq snp150Seq\ track snp150Common\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp150Flagged Flagged SNPs(150) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc 0 0.916 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 150, available from\ ftp.ncbi.nlm.nih.gov/snp.\ Only SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at\ least 1%, are included in this subset.\ Frequency data are not available for all SNPs, so this subset probably\ includes some SNPs whose true minor allele frequency is 1% or greater.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(150) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(150) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly.
All SNPs(150) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by \ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors.\ If a SNP has more than one of these attributes, the stronger color will override \ the weaker color. The order of colors, from strongest to weakest, is red, green, \ blue, gray, and black.\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build\ 147, weight had values 1, 2 or 3, with 1 being the highest quality\ (mapped to a single genomic location). As of dbSNP build 147, dbSNP\ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b150_SNPContigLoc_N.bcp.gz and\ b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b150_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b150_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp150*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro5\ chimpOrangMacOrthoTable snp150OrthoPt5Pa2Rm8\ codingAnnotations snp150CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp150Flagged\ longLabel Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc\ macaqueDb rheMac8\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.916\ shortLabel Flagged SNPs(150)\ snpExceptionDesc snp150ExceptionDesc\ snpSeq snp150Seq\ track snp150Flagged\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp147Mult Mult. SNPs(147) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci 0 0.921 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 147, available from\ ftp.ncbi.nlm.nih.gov/snp.\ Only SNPs that have been mapped to multiple locations in the reference\ genome assembly are included in this subset. When a SNP's flanking sequences\ map to multiple locations in the reference genome, it calls into question\ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ The default maximum weight for this track is 3,\ unlike the other dbSNP build 147 tracks which have a maximum weight of 1.\ That enables these multiply-mapped SNPs to appear in the display, while\ by default they will not appear in the All SNPs(147) track because of its\ maximum weight filter.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(147) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(147) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly.
All SNPs(147) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are always colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build \ \ 147, weight had values 1, 2 or 3, with 1 being the highest quality \ \ (mapped to a single genomic location). As of dbSNP build 147, dbSNP \ \ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b147_SNPContigLoc_N.bcp.gz and\ b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b147_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b147_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp147*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp147OrthoPt4Pa2Rm3\ codingAnnotations snp147CodingDbSnp,\ defaultGeneTracks knownGene\ defaultMaxWeight 3\ group varRep\ hapmapPhase III\ html ../snp147Mult\ longLabel Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.921\ shortLabel Mult. SNPs(147)\ snpExceptionDesc snp147ExceptionDesc\ snpSeq snp147Seq\ track snp147Mult\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp147Flagged Flagged SNPs(147) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc 0 0.922 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 147, available from\ ftp.ncbi.nlm.nih.gov/snp.\ Only SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at\ least 1%, are included in this subset.\ Frequency data are not available for all SNPs, so this subset probably\ includes some SNPs whose true minor allele frequency is 1% or greater.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(147) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(147) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly.
All SNPs(147) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are always colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build \ \ 147, weight had values 1, 2 or 3, with 1 being the highest quality \ \ (mapped to a single genomic location). As of dbSNP build 147, dbSNP \ \ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b147_SNPContigLoc_N.bcp.gz and\ b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b147_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b147_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp147*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp147OrthoPt4Pa2Rm3\ codingAnnotations snp147CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp147Flagged\ longLabel Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc\ macaqueDb rheMac3\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.922\ shortLabel Flagged SNPs(147)\ snpExceptionDesc snp147ExceptionDesc\ snpSeq snp147Seq\ track snp147Flagged\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp147Common Common SNPs(147) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples 0 0.923 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(147) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(147) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly.
All SNPs(147) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are always colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build \ \ 147, weight had values 1, 2 or 3, with 1 being the highest quality \ \ (mapped to a single genomic location). As of dbSNP build 147, dbSNP \ \ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b147_SNPContigLoc_N.bcp.gz and\ b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b147_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b147_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp147*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp147OrthoPt4Pa2Rm3\ codingAnnotations snp147CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp147Common\ longLabel Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.923\ shortLabel Common SNPs(147)\ snpExceptionDesc snp147ExceptionDesc\ snpSeq snp147Seq\ track snp147Common\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp147 All SNPs(147) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 147) 0 0.924 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ Three tracks contain subsets of the items in this track:\

Common SNPs(147): SNPs that have a minor allele frequency\ of at least 1% and are mapped to a single location in the reference\ genome assembly. Frequency data are not available for all SNPs,\ so this subset is incomplete.
Flagged SNPs(147): SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at least 1%.\ Frequency data are not available for all SNPs, so this subset may\ include some SNPs whose true minor allele frequency is 1% or greater.
Mult. SNPs(147): SNPs that have been mapped to multiple locations\ in the reference genome assembly.

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(147) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(147) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly.
All SNPs(147) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\ Non-coding (ncRNA):\ (nc_transcript_variant) are always colored blue.\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP. Before dbSNP build \ \ 147, weight had values 1, 2 or 3, with 1 being the highest quality \ \ (mapped to a single genomic location). As of dbSNP build 147, dbSNP \ \ now releases only the variants with weight 1.\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b147_SNPContigLoc_N.bcp.gz and\ b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b147_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b147_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp147*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp147OrthoPt4Pa2Rm3\ codingAnnotations snp147CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp147\ longLabel Simple Nucleotide Polymorphisms (dbSNP 147)\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.924\ shortLabel All SNPs(147)\ track snp147\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp146Mult Mult. SNPs(146) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci 0 0.925 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 146, available from\ ftp.ncbi.nih.gov/snp.\ Only SNPs that have been mapped to multiple locations in the reference\ genome assembly are included in this subset. When a SNP's flanking sequences\ map to multiple locations in the reference genome, it calls into question\ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ The default maximum weight for this track is 3,\ unlike the other dbSNP build 146 tracks which have a maximum weight of 1.\ That enables these multiply-mapped SNPs to appear in the display, while\ by default they will not appear in the All SNPs(146) track because of its\ maximum weight filter.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(146) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(146) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly.
All SNPs(146) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b146_SNPContigLoc_N.bcp.gz and\ b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b146_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b146_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp146*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp146OrthoPt4Pa2Rm3\ codingAnnotations snp146CodingDbSnp,\ defaultGeneTracks knownGene\ defaultMaxWeight 3\ group varRep\ hapmapPhase III\ html ../snp146Mult\ longLabel Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.925\ shortLabel Mult. SNPs(146)\ snpExceptionDesc snp146ExceptionDesc\ snpSeq snp146Seq\ track snp146Mult\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp146Flagged Flagged SNPs(146) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc 0 0.926 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 146, available from\ ftp.ncbi.nih.gov/snp.\ Only SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at\ least 1%, are included in this subset.\ Frequency data are not available for all SNPs, so this subset probably\ includes some SNPs whose true minor allele frequency is 1% or greater.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(146) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(146) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly.
All SNPs(146) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b146_SNPContigLoc_N.bcp.gz and\ b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b146_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b146_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp146*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp146OrthoPt4Pa2Rm3\ codingAnnotations snp146CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp146Flagged\ longLabel Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc\ macaqueDb rheMac3\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.926\ shortLabel Flagged SNPs(146)\ snpExceptionDesc snp146ExceptionDesc\ snpSeq snp146Seq\ track snp146Flagged\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp146Common Common SNPs(146) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples 0 0.927 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(146) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(146) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly.
All SNPs(146) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b146_SNPContigLoc_N.bcp.gz and\ b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b146_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b146_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp146*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp146OrthoPt4Pa2Rm3\ codingAnnotations snp146CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp146Common\ longLabel Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.927\ shortLabel Common SNPs(146)\ snpExceptionDesc snp146ExceptionDesc\ snpSeq snp146Seq\ track snp146Common\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp146 All SNPs(146) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 146) 0 0.928 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ Three tracks contain subsets of the items in this track:\

Common SNPs(146): SNPs that have a minor allele frequency\ of at least 1% and are mapped to a single location in the reference\ genome assembly. Frequency data are not available for all SNPs,\ so this subset is incomplete.
Flagged SNPs(146): SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at least 1%.\ Frequency data are not available for all SNPs, so this subset may\ include some SNPs whose true minor allele frequency is 1% or greater.
Mult. SNPs(146): SNPs that have been mapped to multiple locations\ in the reference genome assembly.

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(146) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(146) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly.
All SNPs(146) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b146_SNPContigLoc_N.bcp.gz and\ b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b146_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b146_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp146*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp146OrthoPt4Pa2Rm3\ codingAnnotations snp146CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp146\ longLabel Simple Nucleotide Polymorphisms (dbSNP 146)\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.928\ shortLabel All SNPs(146)\ track snp146\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp144Mult Mult. SNPs(144) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci 0 0.929 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 144, available from\ ftp.ncbi.nih.gov/snp.\ Only SNPs that have been mapped to multiple locations in the reference\ genome assembly are included in this subset. When a SNP's flanking sequences\ map to multiple locations in the reference genome, it calls into question\ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ The default maximum weight for this track is 3,\ unlike the other dbSNP build 144 tracks which have a maximum weight of 1.\ That enables these multiply-mapped SNPs to appear in the display, while\ by default they will not appear in the All SNPs(144) track because of its\ maximum weight filter.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(144) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(144) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly.
All SNPs(144) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b144_SNPContigLoc_N.bcp.gz and\ b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b144_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b144_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp144*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp144OrthoPt4Pa2Rm3\ codingAnnotations snp144CodingDbSnp,\ defaultGeneTracks knownGene\ defaultMaxWeight 3\ group varRep\ hapmapPhase III\ html ../snp144Mult\ longLabel Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.929\ shortLabel Mult. SNPs(144)\ snpExceptionDesc snp144ExceptionDesc\ snpSeq snp144Seq\ snpSeqFile /gbdb/hg38/snp/snp144.fa\ track snp144Mult\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp144Flagged Flagged SNPs(144) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc 0 0.93 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the\ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 144, available from\ ftp.ncbi.nih.gov/snp.\ Only SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at\ least 1%, are included in this subset.\ Frequency data are not available for all SNPs, so this subset probably\ includes some SNPs whose true minor allele frequency is 1% or greater.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(144) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(144) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly.
All SNPs(144) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b144_SNPContigLoc_N.bcp.gz and\ b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b144_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b144_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp144*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp144OrthoPt4Pa2Rm3\ codingAnnotations snp144CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp144Flagged\ longLabel Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc\ macaqueDb rheMac3\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.93\ shortLabel Flagged SNPs(144)\ snpExceptionDesc snp144ExceptionDesc\ snpSeq snp144Seq\ snpSeqFile /gbdb/hg38/snp/snp144.fa\ track snp144Flagged\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp144Common Common SNPs(144) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples 0 0.931 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(144) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(144) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly.
All SNPs(144) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b144_SNPContigLoc_N.bcp.gz and\ b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b144_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b144_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp144*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp144OrthoPt4Pa2Rm3\ codingAnnotations snp144CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp144Common\ longLabel Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.931\ shortLabel Common SNPs(144)\ snpExceptionDesc snp144ExceptionDesc\ snpSeq snp144Seq\ snpSeqFile /gbdb/hg38/snp/snp144.fa\ track snp144Common\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp144 All SNPs(144) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 144) 0 0.932 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ Three tracks contain subsets of the items in this track:\

Common SNPs(144): SNPs that have a minor allele frequency\ of at least 1% and are mapped to a single location in the reference\ genome assembly. Frequency data are not available for all SNPs,\ so this subset is incomplete.
Flagged SNPs(144): SNPs flagged as clinically associated by dbSNP,\ mapped to a single location in the reference genome assembly, and\ not known to have a minor allele frequency of at least 1%.\ Frequency data are not available for all SNPs, so this subset may\ include some SNPs whose true minor allele frequency is 1% or greater.
Mult. SNPs(144): SNPs that have been mapped to multiple locations\ in the reference genome assembly.

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(144) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(144) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly,\ flagged in dbSnp as "clinically associated"\ -- not necessarily a risk allele!
Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly.
All SNPs(144) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the\ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies\ that may indicate a problem with the mapping, and reports them in the\ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have\ \ been mapped to this location, with either the same inserted\ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences\ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele\ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic -\ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at\ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in\ \ Online Mendelian Inheritance in Man for\ \ human SNPs, or Online Mendelian Inheritance in Animals for\ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes\ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed -\ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have\ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in\ Computation of Average\ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic\ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include\ allele frequencies and the study's sample size\ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are\ clustered together into a reference SNP.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ Non-repetitive genomic sequence is shown in upper case like the flanking\ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files\ and headers of fasta files downloaded from NCBI.\ The database dump files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/\ for hg38.\ The fasta files were downloaded from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b144_SNPContigLoc_N.bcp.gz and\ b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38)
b144_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from\ b144_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and\ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document\ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp144*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

Masked FASTA Files (human assemblies only)

References

\ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp144OrthoPt4Pa2Rm3\ codingAnnotations snp144CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp144\ longLabel Simple Nucleotide Polymorphisms (dbSNP 144)\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.932\ shortLabel All SNPs(144)\ snpSeqFile /gbdb/hg38/snp/snp144.fa\ track snp144\ trackHandler snp125\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp142Mult Mult. SNPs(142) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci 0 0.933 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the \ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 142, available from\ ftp.ncbi.nih.gov/snp.\ Only SNPs that have been mapped to multiple locations in the reference\ genome assembly are included in this subset. When a SNP's flanking sequences \ map to multiple locations in the reference genome, it calls into question \ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ The default maximum weight for this track is 3,\ unlike the other dbSNP build 142 tracks which have a maximum weight of 1. \ That enables these multiply-mapped SNPs to appear in the display, while \ by default they will not appear in the All SNPs(142) track because of its \ maximum weight filter.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(142) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(142) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly, \ flagged in dbSnp as "clinically associated" \ -- not necessarily a risk allele!
Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly.
All SNPs(142) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ Computation of Average \ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/\ for hg38.\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b142_SNPContigLoc_N.bcp.gz and\ b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38)
b142_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from \ b142_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp142*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ GRCh37/hg19, \ GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

\ \ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp142OrthoPt4Pa2Rm3\ codingAnnotations snp142CodingDbSnp,\ defaultGeneTracks knownGene\ defaultMaxWeight 3\ group varRep\ hapmapPhase III\ html ../snp142Mult\ longLabel Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.933\ shortLabel Mult. SNPs(142)\ snpExceptionDesc snp142ExceptionDesc\ snpSeq snp142Seq\ snpSeqFile /gbdb/hg38/snp/snp142.fa\ track snp142Mult\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp142Flagged Flagged SNPs(142) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc 0 0.934 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the \ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 142, available from\ ftp.ncbi.nih.gov/snp.\ Only SNPs flagged as clinically associated by dbSNP, \ mapped to a single location in the reference genome assembly, and \ not known to have a minor allele frequency of at \ least 1%, are included in this subset.\ Frequency data are not available for all SNPs, so this subset probably\ includes some SNPs whose true minor allele frequency is 1% or greater.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(142) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(142) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly, \ flagged in dbSnp as "clinically associated" \ -- not necessarily a risk allele!
Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly.
All SNPs(142) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ Computation of Average \ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/\ for hg38.\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b142_SNPContigLoc_N.bcp.gz and\ b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38)
b142_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from \ b142_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp142*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ GRCh37/hg19, \ GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

\ \ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp142OrthoPt4Pa2Rm3\ codingAnnotations snp142CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp142Flagged\ longLabel Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc\ macaqueDb rheMac3\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.934\ shortLabel Flagged SNPs(142)\ snpExceptionDesc snp142ExceptionDesc\ snpSeq snp142Seq\ snpSeqFile /gbdb/hg38/snp/snp142.fa\ track snp142Flagged\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp142Common Common SNPs(142) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples 0 0.935 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(142) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(142) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly, \ flagged in dbSnp as "clinically associated" \ -- not necessarily a risk allele!
Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly.
All SNPs(142) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ Computation of Average \ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/\ for hg38.\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b142_SNPContigLoc_N.bcp.gz and\ b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38)
b142_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from \ b142_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp142*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ GRCh37/hg19, \ GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

\ \ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp142OrthoPt4Pa2Rm3\ codingAnnotations snp142CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp142Common\ longLabel Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.935\ shortLabel Common SNPs(142)\ snpExceptionDesc snp142ExceptionDesc\ snpSeq snp142Seq\ snpSeqFile /gbdb/hg38/snp/snp142.fa\ track snp142Common\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp142 All SNPs(142) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 142) 0 0.936 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ Three tracks contain subsets of the items in this track:\

Common SNPs(142): SNPs that have a minor allele frequency\ of at least 1% and are mapped to a single location in the reference\ genome assembly. Frequency data are not available for all SNPs,\ so this subset is incomplete.
Flagged SNPs(142): SNPs flagged as clinically associated by dbSNP, \ mapped to a single location in the reference genome assembly, and \ not known to have a minor allele frequency of at least 1%.\ Frequency data are not available for all SNPs, so this subset may\ include some SNPs whose true minor allele frequency is 1% or greater.
Mult. SNPs(142): SNPs that have been mapped to multiple locations\ in the reference genome assembly.

\ The default maximum weight for this track is 1, so unless\ the setting is changed in the track controls, SNPs that map to multiple genomic \ locations will be omitted from display. When a SNP's flanking sequences \ map to multiple locations in the reference genome, it calls into question \ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(142) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(142) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly, \ flagged in dbSnp as "clinically associated" \ -- not necessarily a risk allele!
Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly.
All SNPs(142) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ Computation of Average \ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/\ for hg19 and from\ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/\ for hg38.\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/\ for hg19 and from\ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/\ for hg38.\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b142_SNPContigLoc_N.bcp.gz and\ b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38)
b142_SNPMapInfo_N.bcp.gz provided the alignment weights.\
Functional classification was obtained from \ b142_SNPContigLocusId_N.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp142*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ GRCh37/hg19, \ GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

\ \ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp142OrthoPt4Pa2Rm3\ codingAnnotations snp142CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp142\ longLabel Simple Nucleotide Polymorphisms (dbSNP 142)\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.936\ shortLabel All SNPs(142)\ snpSeqFile /gbdb/hg38/snp/snp142.fa\ track snp142\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp141Mult Mult. SNPs(141) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 141) That Map to Multiple Genomic Loci 0 0.937 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the \ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 141, available from\ ftp.ncbi.nih.gov/snp.\ Only SNPs that have been mapped to multiple locations in the reference\ genome assembly are included in this subset. When a SNP's flanking sequences \ map to multiple locations in the reference genome, it calls into question \ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ The default maximum weight for this track is 3,\ unlike the other dbSNP build 141 tracks which have a maximum weight of 1. \ That enables these multiply-mapped SNPs to appear in the display, while \ by default they will not appear in the All SNPs(141) track because of its \ maximum weight filter.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(141) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(141) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly, \ flagged in dbSnp as "clinically associated" \ -- not necessarily a risk allele!
Mult. SNPs(141) - SNPs mapping in more than one place on reference assembly.
All SNPs(141) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ Computation of Average \ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/database/\ (for human, organism_tax_id = human_9606;\ for mouse, organism_tax_id = mouse_10090).\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/rs_fasta/\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b141_SNPContigLoc.bcp.gz and \ b141_ContigInfo.bcp.gz.
b141_SNPMapInfo.bcp.gz provided the alignment weights.\
Functional classification was obtained from \ b141_SNPContigLocusId.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp141*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ GRCh37/hg19, \ GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

\ \ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp141OrthoPt4Pa2Rm3\ codingAnnotations snp141CodingDbSnp,\ defaultGeneTracks knownGene\ defaultMaxWeight 3\ group varRep\ hapmapPhase III\ html ../snp141Mult\ longLabel Simple Nucleotide Polymorphisms (dbSNP 141) That Map to Multiple Genomic Loci\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.937\ shortLabel Mult. SNPs(141)\ snpExceptionDesc snp141ExceptionDesc\ snpSeq snp141Seq\ snpSeqFile /gbdb/hg38/snp/snp141.fa\ track snp141Mult\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ snp141Flagged Flagged SNPs(141) bed 6 + Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc 0 0.938 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This track contains information about a subset of the \ single nucleotide polymorphisms\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP\ build 141, available from\ ftp.ncbi.nih.gov/snp.\ Only SNPs flagged as clinically associated by dbSNP, \ mapped to a single location in the reference genome assembly, and \ not known to have a minor allele frequency of at \ least 1%, are included in this subset.\ Frequency data are not available for all SNPs, so this subset probably\ includes some SNPs whose true minor allele frequency is 1% or greater.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(141) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(141) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly, \ flagged in dbSnp as "clinically associated" \ -- not necessarily a risk allele!
Mult. SNPs(141) - SNPs mapping in more than one place on reference assembly.
All SNPs(141) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ Computation of Average \ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/database/\ (for human, organism_tax_id = human_9606;\ for mouse, organism_tax_id = mouse_10090).\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/rs_fasta/\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b141_SNPContigLoc.bcp.gz and \ b141_ContigInfo.bcp.gz.
b141_SNPMapInfo.bcp.gz provided the alignment weights.\
Functional classification was obtained from \ b141_SNPContigLocusId.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp141*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ GRCh37/hg19, \ GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

Description

\ \

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(141) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(141) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly, \ flagged in dbSnp as "clinically associated" \ -- not necessarily a risk allele!
Mult. SNPs(141) - SNPs mapping in more than one place on reference assembly.
All SNPs(141) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ Computation of Average \ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/database/\ (for human, organism_tax_id = human_9606;\ for mouse, organism_tax_id = mouse_10090).\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/rs_fasta/\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b141_SNPContigLoc.bcp.gz and \ b141_ContigInfo.bcp.gz.
b141_SNPMapInfo.bcp.gz provided the alignment weights.\
Functional classification was obtained from \ b141_SNPContigLocusId.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp141*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ GRCh37/hg19, \ GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

Description

\ \

\ Three tracks contain subsets of the items in this track:\

Common SNPs(141): SNPs that have a minor allele frequency\ of at least 1% and are mapped to a single location in the reference\ genome assembly. Frequency data are not available for all SNPs,\ so this subset is incomplete.
Flagged SNPs(141): SNPs flagged as clinically associated by dbSNP, \ mapped to a single location in the reference genome assembly, and \ not known to have a minor allele frequency of at least 1%.\ Frequency data are not available for all SNPs, so this subset may\ include some SNPs whose true minor allele frequency is 1% or greater.
Mult. SNPs(141): SNPs that have been mapped to multiple locations\ in the reference genome assembly.

\ The default maximum weight for this track is 1, so unless\ the setting is changed in the track controls, SNPs that map to multiple genomic \ locations will be omitted from display. When a SNP's flanking sequences \ map to multiple locations in the reference genome, it calls into question \ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ \ The remainder of this page is identical on the following tracks:\

Common SNPs(141) - SNPs with >= 1% minor allele frequency (MAF), mapping\ only once to reference assembly.
Flagged SNPs(141) - SNPs < 1% minor allele frequency (MAF) (or unknown),\ mapping only once to reference assembly, \ flagged in dbSnp as "clinically associated" \ -- not necessarily a risk allele!
Mult. SNPs(141) - SNPs mapping in more than one place on reference assembly.
All SNPs(141) - all SNPs from dbSNP mapping to reference assembly.

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is\ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is\ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ Computation of Average \ Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/database/\ (for human, organism_tax_id = human_9606;\ for mouse, organism_tax_id = mouse_10090).\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/rs_fasta/\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from b141_SNPContigLoc.bcp.gz and \ b141_ContigInfo.bcp.gz.
b141_SNPMapInfo.bcp.gz provided the alignment weights.\
Functional classification was obtained from \ b141_SNPContigLocusId.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser,\ Data Integrator, or Variant Annotation Integrator.\ For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and\ hg19 (snp141*.txt.gz) or the public MySQL server.\ Please refer to our mailing list archives\ for questions and example queries, or our Data Access FAQ for more information.\

\ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download:\ GRCh37/hg19, \ GRCh38/hg38.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exclude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

\ \ \ varRep 1 chimpDb panTro4\ chimpOrangMacOrthoTable snp141OrthoPt4Pa2Rm3\ codingAnnotations snp141CodingDbSnp,\ defaultGeneTracks knownGene\ group varRep\ hapmapPhase III\ html ../snp141\ longLabel Simple Nucleotide Polymorphisms (dbSNP 141)\ macaqueDb rheMac3\ maxWindowToDraw 10000000\ orangDb ponAbe2\ parent dbSnpArchive\ priority 0.94\ shortLabel All SNPs(141)\ snpSeqFile /gbdb/hg38/snp/snp141.fa\ track snp141\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ visibility hide\ chainMonDom5 Opossum Chain chain monDom5 Opossum (Oct. 2006 (Broad/monDom5)) Chained Alignments 3 1 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Opossum (Oct. 2006 (Broad/monDom5)) Chained Alignments\ otherDb monDom5\ parent vertebrateChainNetViewchain off\ shortLabel Opossum Chain\ subGroups view=chain species=s003 clade=c00\ track chainMonDom5\ type chain monDom5\ chainPanTro6 Chimp Chain chain panTro6 Chimp (Jan. 2018 (Clint_PTRv2/panTro6)) Chained Alignments 3 1 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Chimp (Jan. 2018 (Clint_PTRv2/panTro6)) Chained Alignments\ otherDb panTro6\ parent primateChainNetViewchain off\ shortLabel Chimp Chain\ subGroups view=chain species=s0025 clade=c00\ track chainPanTro6\ type chain panTro6\ chainCriGriChoV2 Chinese hamster Chain chain criGriChoV2 Chinese hamster (Jun. 2017 (CHOK1S_HZDv1/criGriChoV2)) Chained Alignments 3 1 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Chinese hamster (Jun. 2017 (CHOK1S_HZDv1/criGriChoV2)) Chained Alignments\ otherDb criGriChoV2\ parent placentalChainNetViewchain off\ shortLabel Chinese hamster Chain\ subGroups view=chain species=s004b clade=c00\ track chainCriGriChoV2\ type chain criGriChoV2\ tgpNA12878_1463_CEU 1463 CEU Trio vcfPhasedTrio 1000 Genomes Utah CEPH Trio 2 1 0 0 0 127 127 127 0 0 23 chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX, varRep 0 longLabel 1000 Genomes Utah CEPH Trio\ parent tgpTrios\ shortLabel 1463 CEU Trio\ track tgpNA12878_1463_CEU\ type vcfPhasedTrio\ vcfChildSample NA12878|child\ vcfParentSamples NA12892|mother,NA12891|father\ visibility full\ phyloP447wayBW 447 phyloP REV bigWig -20 11.936 447 mammals Basewise Conservation by PhyloP phyloFit REV model 2 1 60 60 140 140 60 60 0 0 0 compGeno 0 altColor 140,60,60\ autoScale off\ bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP447way/hg38.phyloP447way.bw\ color 60,60,140\ configurable on\ longLabel 447 mammals Basewise Conservation by PhyloP phyloFit REV model\ maxHeightPixels 100:50:11\ noInherit on\ parent cons447wayViewphyloP\ priority 1\ shortLabel 447 phyloP REV\ spanList 1\ subGroups view=phyloP\ track phyloP447wayBW\ type bigWig -20 11.936\ viewLimits -4.5:7.5\ windowingFunction mean\ encTfChipPkENCFF851UTY A549 ATF3 narrowPeak Transcription Factor ChIP-seq Peaks of ATF3 in A549 from ENCODE 3 (ENCFF851UTY) 0 1 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of ATF3 in A549 from ENCODE 3 (ENCFF851UTY)\ parent encTfChipPk off\ shortLabel A549 ATF3\ subGroups cellType=A549 factor=ATF3\ track encTfChipPkENCFF851UTY\ cloneEndABC10 ABC10 bed 12 Agencourt fosmid library 10 3 1 0 0 0 127 127 127 0 0 0 map 1 colorByStrand 0,0,128 0,128,0\ longLabel Agencourt fosmid library 10\ parent cloneEndSuper off\ priority 1\ shortLabel ABC10\ subGroups source=agencourt\ track cloneEndABC10\ type bed 12\ visibility pack\ gtexCovAdiposeSubcutaneous Adip Subcut bigWig Adipose Subcutaneous 0 1 255 165 79 255 210 167 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-NFK9-0326-SM-3MJGV.Adipose_Subcutaneous.RNAseq.bw\ color 255,165,79\ longLabel Adipose Subcutaneous\ parent gtexCov\ shortLabel Adip Subcut\ track gtexCovAdiposeSubcutaneous\ lincRNAsCTAdipose Adipose bed 5 + lincRNAs from adipose 1 1 0 60 120 127 157 187 1 0 0 genes 1 longLabel lincRNAs from adipose\ origAssembly hg19\ parent lincRNAsAllCellType on\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel Adipose\ subGroups view=lincRNAsRefseqExp tissueType=adipose\ track lincRNAsCTAdipose\ genetiSureCytoCghSnp Agilent GenetiSure Cyto CGH+SNP bigBed 4 Agilent GenetiSure Cyto CGH+SNP 4x180K 085591 20200302 3 1 0 0 0 127 127 127 0 0 0 varRep 1 bigDataUrl /gbdb/hg38/snpCnvArrays/agilent/hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bb\ longLabel Agilent GenetiSure Cyto CGH+SNP 4x180K 085591 20200302\ parent genotypeArrays on\ priority 1\ shortLabel Agilent GenetiSure Cyto CGH+SNP\ track genetiSureCytoCghSnp\ type bigBed 4\ visibility pack\ allCancer All Cancers bigLolly 12 + All TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33) 0 1 0 0 0 127 127 127 0 0 0 phenDis 1 autoScale on\ bigDataUrl /gbdb/hg38/gdcCancer/gdcCancer.bb\ configurable off\ group phenDis\ lollyField 13\ longLabel All TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)\ parent gdcCancer on\ priority 1\ shortLabel All Cancers\ track allCancer\ type bigLolly 12 +\ urls case_id=https://portal.gdc.cancer.gov/cases/$$\ alldifficultregions All difficult regions bigBed 3 Genome In a Bottle: all difficult regions 1 1 0 0 0 127 127 127 0 0 0 map 1 bigDataUrl /gbdb/hg38/problematic/GIAB/alldifficultregions.bb\ longLabel Genome In a Bottle: all difficult regions\ parent problematicGIAB on\ shortLabel All difficult regions\ track alldifficultregions\ type bigBed 3\ visibility dense\ AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_tpm_fwd AorticSmsToFgf2_00hr00minBr1+ bigWig Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_forward 1 1 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12642-134G5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr00min%2c%20biol_rep1%20%28LK1%29.CNhs13339.12642-134G5.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12642-134G5 sequence_tech=hCAGE\ parent TSS_activity_TPM on\ shortLabel AorticSmsToFgf2_00hr00minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12642-134G5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_ctss_fwd AorticSmsToFgf2_00hr00minBr1+ bigWig Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_forward 0 1 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12642-134G5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr00min%2c%20biol_rep1%20%28LK1%29.CNhs13339.12642-134G5.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12642-134G5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_00hr00minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12642-134G5\ urlLabel FANTOM5 Details:\ ashkenazimTrio Ashkenazim Trio vcfPhasedTrio Genome In a Bottle Ashkenazim Trio 0 1 0 0 0 127 127 127 0 0 0 varRep 0 bigDataUrl /gbdb/hg38/giab/AshkenazimTrio/merged.vcf.gz\ longLabel Genome In a Bottle Ashkenazim Trio\ maxWindowToDraw 5000000\ parent triosView\ shortLabel Ashkenazim Trio\ subGroups view=trios\ track ashkenazimTrio\ type vcfPhasedTrio\ vcfChildSample HG002|son\ vcfDoFilter off\ vcfDoMaf off\ vcfDoQual off\ vcfParentSamples HG003|father,HG004|mother\ vcfUseAltSampleNames on\ cons100wayViewphyloP Basewise Conservation (phyloP) bed 4 Vertebrate Multiz Alignment & Conservation (100 Species) 2 1 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Vertebrate Multiz Alignment & Conservation (100 Species)\ parent cons100way\ shortLabel Basewise Conservation (phyloP)\ track cons100wayViewphyloP\ view phyloP\ viewLimits -20.0:9.869\ viewLimitsMax -20:0.869\ visibility full\ wgEncodeGencodeBasicV20 Basic genePred Basic Gene Annotation Set from GENCODE Version 20 (Ensembl 76) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 20 (Ensembl 76)\ parent wgEncodeGencodeV20ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV20\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV22 Basic genePred Basic Gene Annotation Set from GENCODE Version 22 (Ensembl 79) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 22 (Ensembl 79)\ parent wgEncodeGencodeV22ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV22\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV23 Basic genePred Basic Gene Annotation Set from GENCODE Version 23 (Ensembl 81) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 23 (Ensembl 81)\ parent wgEncodeGencodeV23ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV23\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV24 Basic genePred Basic Gene Annotation Set from GENCODE Version 24 (Ensembl 83) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 24 (Ensembl 83)\ parent wgEncodeGencodeV24ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV24\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV25 Basic genePred Basic Gene Annotation Set from GENCODE Version 25 (Ensembl 85) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 25 (Ensembl 85)\ parent wgEncodeGencodeV25ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV25\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV26 Basic genePred Basic Gene Annotation Set from GENCODE Version 26 (Ensembl 88) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 26 (Ensembl 88)\ parent wgEncodeGencodeV26ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV26\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV27 Basic genePred Basic Gene Annotation Set from GENCODE Version 27 (Ensembl 90) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 27 (Ensembl 90)\ parent wgEncodeGencodeV27ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV27\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV28 Basic genePred Basic Gene Annotation Set from GENCODE Version 28 (Ensembl 92) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 28 (Ensembl 92)\ parent wgEncodeGencodeV28ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV28\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV29 Basic genePred Basic Gene Annotation Set from GENCODE Version 29 (Ensembl 94) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 29 (Ensembl 94)\ parent wgEncodeGencodeV29ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV29\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV30 Basic genePred Basic Gene Annotation Set from GENCODE Version 30 (Ensembl 96) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 30 (Ensembl 96)\ parent wgEncodeGencodeV30ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV30\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV31 Basic genePred Basic Gene Annotation Set from GENCODE Version 31 (Ensembl 97) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 31 (Ensembl 97)\ parent wgEncodeGencodeV31ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV31\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV32 Basic genePred Basic Gene Annotation Set from GENCODE Version 32 (Ensembl 98) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 32 (Ensembl 98)\ parent wgEncodeGencodeV32ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV32\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV33 Basic genePred Basic Gene Annotation Set from GENCODE Version 33 (Ensembl 99) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 33 (Ensembl 99)\ parent wgEncodeGencodeV33ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV33\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV34 Basic genePred Basic Gene Annotation Set from GENCODE Version 34 (Ensembl 100) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 34 (Ensembl 100)\ parent wgEncodeGencodeV34ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV34\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV35 Basic genePred Basic Gene Annotation Set from GENCODE Version 35 (Ensembl 101) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 35 (Ensembl 101)\ parent wgEncodeGencodeV35ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV35\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV36 Basic genePred Basic Gene Annotation Set from GENCODE Version 36 (Ensembl 102) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 36 (Ensembl 102)\ parent wgEncodeGencodeV36ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV36\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV37 Basic genePred Basic Gene Annotation Set from GENCODE Version 37 (Ensembl 103) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 37 (Ensembl 103)\ parent wgEncodeGencodeV37ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV37\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV38 Basic genePred Basic Gene Annotation Set from GENCODE Version 38 (Ensembl 104) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 38 (Ensembl 104)\ parent wgEncodeGencodeV38ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV38\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV39 Basic genePred Basic Gene Annotation Set from GENCODE Version 39 (Ensembl 105) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 39 (Ensembl 105)\ parent wgEncodeGencodeV39ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV39\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV40 Basic genePred Basic Gene Annotation Set from GENCODE Version 40 (Ensembl 106) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 40 (Ensembl 106)\ parent wgEncodeGencodeV40ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV40\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV41 Basic genePred Basic Gene Annotation Set from GENCODE Version 41 (Ensembl 107) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 41 (Ensembl 107)\ parent wgEncodeGencodeV41ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV41\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV42 Basic genePred Basic Gene Annotation Set from GENCODE Version 42 (Ensembl 108) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 42 (Ensembl 108)\ parent wgEncodeGencodeV42ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV42\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV43 Basic genePred Basic Gene Annotation Set from GENCODE Version 43 (Ensembl 109) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 43 (Ensembl 109)\ parent wgEncodeGencodeV43ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV43\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV44 Basic genePred Basic Gene Annotation Set from GENCODE Version 44 (Ensembl 110) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 44 (Ensembl 110)\ parent wgEncodeGencodeV44ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV44\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV45 Basic genePred Basic Gene Annotation Set from GENCODE Version 45 (Ensembl 111) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 45 (Ensembl 111)\ parent wgEncodeGencodeV45ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV45\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV46 Basic genePred Basic Gene Annotation Set from GENCODE Version 46 (Ensembl 112) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 46 (Ensembl 112)\ parent wgEncodeGencodeV46ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV46\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencodeBasicV47 Basic genePred Basic Gene Annotation Set from GENCODE Version 47 (Ensembl 113) 3 1 0 0 0 127 127 127 0 0 0 genes 1 longLabel Basic Gene Annotation Set from GENCODE Version 47 (Ensembl 113)\ parent wgEncodeGencodeV47ViewGenes on\ priority 1\ shortLabel Basic\ subGroups view=aGenes name=Basic\ track wgEncodeGencodeBasicV47\ trackHandler wgEncodeGencode\ type genePred\ bismap24Pos Bismap S24 + bigBed 6 Single-read mappability with 24-mers after bisulfite conversion (forward strand) 1 1 240 20 80 247 137 167 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k24.C2T-Converted.bb\ color 240,20,80\ longLabel Single-read mappability with 24-mers after bisulfite conversion (forward strand)\ parent bismapBigBed on\ priority 1\ shortLabel Bismap S24 +\ subGroups view=SR\ track bismap24Pos\ visibility dense\ cnvDevDelayCase Case gvf Copy Number Variation Morbidity Map of Developmental Delay - Case 3 1 0 0 0 127 127 127 0 0 0 phenDis 1 longLabel Copy Number Variation Morbidity Map of Developmental Delay - Case\ parent cnvDevDelay on\ priority 1\ shortLabel Case\ track cnvDevDelayCase\ type gvf\ visibility pack\ clinGenHaplo ClinGen Haploinsufficiency bigBed 9 + ClinGen Dosage Sensitivity Map - Haploinsufficiency 3 1 0 0 0 127 127 127 0 0 0 phenDis 1 bigDataUrl /gbdb/hg38/bbi/clinGen/clinGenHaplo.bb\ filterLabel.haploScore Dosage Sensitivity Score\ filterValues.haploScore 0|No evidence available,1|Little evidence for dosage pathogenicity,2|Some evidence for dosage pathogenicity,3|Sufficient evidence for dosage pathogenicity,30|Gene associated with autosomal recessive phenotype,40|Dosage sensitivity unlikely\ longLabel ClinGen Dosage Sensitivity Map - Haploinsufficiency\ mouseOverField _mouseOver\ parent clinGenComp on\ priority 1\ shortLabel ClinGen Haploinsufficiency\ showCfg on\ track clinGenHaplo\ type bigBed 9 +\ urls url="$$" PMID1="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID2="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID3="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID4="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID5="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" PMID6="https://pubmed.ncbi.nlm.nih.gov/$$/?from_single_result=$$&expanded_search_query=$$" mondoID="https://monarchinitiative.org/disease/$$"\ visibility pack\ clinvarMain ClinVar SNVs bigBed 12 + ClinVar Short Variants < 50bp 0 1 0 0 0 127 127 127 0 0 0 phenDis 1 bigDataUrl /gbdb/hg38/bbi/clinvar/clinvarMain.bb\ filter._varLen 0\ filterByRange._varLen on\ filterLabel._originCode Alelle Origin\ filterLimits._varLen 0:49\ filterType._allTypeCode multiple\ filterType._clinSignCode multiple\ filterType._originCode multiple\ filterValues._allTypeCode SUBST|single nucleotide variant - SUBST,STRUCT|translocation and fusion - STRUCT,LOSS|deletion and copy loss - LOSS,GAIN|duplication and copy gain - GAIN,INS|indel and insertion - INS,INV|inversion - INV,SEQALT|undetermined - SEQALT,SEQLEN|repeat change - SEQLEN\ filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,RF|risk factor,OT|other,VUS|vus\ filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,UNK|unknown\ filterValues.molConseq genic downstream transcript variant|genic downstream transcript variant,no sequence alteration|no sequence alteration,inframe indel|inframe indel,stop lost|stop lost,genic upstream transcript variant|genic upstream transcript variant,initiatior codon variant|initiatior codon variant,inframe insertion|inframe insertion,inframe deletion|inframe deletion,splice acceptor variant|splice acceptor variant,splice donor variant|splice donor variant,5 prime UTR variant|5 prime UTR variant,nonsense|nonsense,non-coding transcript variant|non-coding transcript variant,3 prime UTR variant|3 prime UTR variant,frameshift variant|frameshift variant,intron variant|intron variant,synonymous variant|synonymous variant,missense variant|missense variant,|unknown,initiator codon variant|initiator codon variant\ group phenDis\ itemRgb on\ longLabel ClinVar Short Variants < 50bp\ maxWindowCoverage 10000000\ mouseOverField _mouseOver\ noScoreFilter on\ parent clinvar\ priority 1\ searchIndex _dbVarSsvId\ shortLabel ClinVar SNVs\ showCfg on\ skipFields rcvAcc\ track clinvarMain\ type bigBed 12 +\ urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"\ visibility hide\ dbSnp153Common Common dbSNP(153) bigDbSnp Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153 1 1 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 bigDataUrl /gbdb/hg38/snp/dbSnp153Common.bb\ defaultGeneTracks knownGene\ longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153\ parent dbSnp153ViewVariants on\ priority 1\ shortLabel Common dbSNP(153)\ subGroups view=variants\ track dbSnp153Common\ dbSnp155Common Common dbSNP(155) bigDbSnp Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 155 1 1 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 bigDataUrl /gbdb/hg38/snp/dbSnp155Common.bb\ defaultGeneTracks knownGene\ longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 155\ parent dbSnp155ViewVariants on\ priority 1\ shortLabel Common dbSNP(155)\ showCfg on\ subGroups view=variants\ track dbSnp155Common\ cons100way Conservation bed 4 Vertebrate Multiz Alignment & Conservation (100 Species) 2 1 0 0 0 127 127 127 0 0 0

\ Downloads for data in this track are available:\

\ Multiz alignments (MAF format), and phylogenetic trees\
\ PhyloP conservation (WIG format)\
\ PhastCons conservation (WIG format)\

\ \

Description

\ This track shows multiple alignments of 100 vertebrate\ species and measurements of evolutionary conservation using\ two methods (phastCons and phyloP) from the\ \ PHAST package, for all species.\ The multiple alignments were generated using multiz and\ other tools in the UCSC/Penn State Bioinformatics\ comparative genomics alignment pipeline.\ Conserved elements identified by phastCons are also displayed in\ this track.\ PHAST/Multiz are built from chains ("alignable") and nets ("syntenic"), see the documentation of the Chain/Net tracks for a description of the complete\ alignment process.\

\ PhastCons is a hidden Markov model-based method that estimates the probability that each\ nucleotide belongs to a conserved element, based on the multiple alignment.\ It considers not just each individual alignment column, but also its\ flanking columns. By contrast, phyloP separately measures conservation at\ individual columns, ignoring the effects of their neighbors. As a\ consequence, the phyloP plots have a less smooth appearance than the\ phastCons plots, with more "texture" at individual sites. The two methods\ have different strengths and weaknesses. PhastCons is sensitive to "runs"\ of conserved sites, and is therefore effective for picking out conserved\ elements. PhyloP, on the other hand, is more appropriate for evaluating\ signatures of selection at particular nucleotides or classes of nucleotides\ (e.g., third codon positions, or first positions of miRNA target sites).\

\ Another important difference is that phyloP can measure acceleration\ (faster evolution than expected under neutral drift) as well as\ conservation (slower than expected evolution). In the phyloP plots, sites\ predicted to be conserved are assigned positive scores (and shown in blue),\ while sites predicted to be fast-evolving are assigned negative scores (and\ shown in red). The absolute values of the scores represent -log p-values\ under a null hypothesis of neutral evolution. The phastCons scores, by\ contrast, represent probabilities of negative selection and range between 0\ and 1.\

\ Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as\ missing data, and both were run with the same parameters.\

\ See also: lastz parameters and other details\ and chain minimum score and gap parameters used in these alignments.\

\ \

\ UCSC has repeatmasked and aligned all genome assemblies, and\ provides all the sequences for download. For genome assemblies\ not available in the genome browser, there are alternative assembly hub\ genome browsers. Missing sequence in any assembly\ is highlighted in the track display by regions of yellow when\ zoomed out and by Ns when displayed at base level (see Gap Annotation, below).

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Primate subset
Organism Species Release date UCSC version Alignment type
Baboon Papio hamadryas Mar 2012 Baylor Panu_2.0/papAnu2 Reciprocal best net
Bushbaby Otolemur garnettii Mar 2011 Broad/otoGar3 Syntenic net
Chimp Pan troglodytes Feb 2011 CSAC 2.1.4/panTro4 Syntenic net
Crab-eating macaque Macaca fascicularis Jun 2013 Macaca_fascicularis_5.0/macFas5 Syntenic net
Gibbon Nomascus leucogenys Oct 2012 GGSC Nleu3.0/nomLeu3 Syntenic net
Gorilla Gorilla gorilla gorilla May 2011 gorGor3.1/gorGor3 Reciprocal best net
Green monkey Chlorocebus sabaeus Mar 2014 Chlorocebus_sabeus 1.1/chlSab2 Syntenic net
Human Homo sapiens Dec 2013 GRCh38/hg38 reference species
Marmoset Callithrix jacchus Mar 2009 WUGSC 3.2/calJac3 Syntenic net
Orangutan Pongo pygmaeus abelii July 2007 WUGSC 2.0.2/ponAbe2 Reciprocal best net
Rhesus Macaca mulatta Oct 2010 BGI CR_1.0/rheMac3 Syntenic net
Squirrel monkey Saimiri boliviensis Oct 2011 Broad/saiBol1 Syntenic net
Euarchontoglires subset
Brush-tailed rat Octodon degus Apr 2012 OctDeg1.0/octDeg1 Syntenic net
Chinchilla Chinchilla lanigera May 2012 ChiLan1.0/chiLan1 Syntenic net
Chinese hamster Cricetulus griseus Jul 2013 C_griseus_v1.0/criGri1 Syntenic net
Chinese tree shrew Tupaia chinensis Jan 2013 TupChi_1.0/tupChi1 Syntenic net
Golden hamster Mesocricetus auratus Mar 2013 MesAur1.0/mesAur1 Syntenic net
Guinea pig Cavia porcellus Feb 2008 Broad/cavPor3 Syntenic net
Lesser Egyptian jerboa Jaculus jaculus May 2012 JacJac1.0/jacJac1 Syntenic net
Mouse Mus musculus Dec 2011 GRCm38/mm10 Syntenic net
Naked mole-rat Heterocephalus glaber Jan 2012 Broad HetGla_female_1.0/hetGla2 Syntenic net
Pika Ochotona princeps May 2012 OchPri3.0/ochPri3 Syntenic net
Prairie vole Microtus ochrogaster Oct 2012 MicOch1.0/micOch1 Syntenic net
Rabbit Oryctolagus cuniculus Apr 2009 Broad/oryCun2 Syntenic net
Rat Rattus norvegicus Jul 2014 RGSC 6.0/rn6 Syntenic net
Squirrel Spermophilus tridecemlineatus Nov 2011 Broad/speTri2 Syntenic net
Laurasiatheria subset
Alpaca Vicugna pacos Mar 2013 Vicugna_pacos-2.0.1/vicPac2 Syntenic net
Bactrian camel Camelus ferus Dec 2011 CB1/camFer1 Syntenic net
Big brown bat Eptesicus fuscus Jul 2012 EptFus1.0/eptFus1 Syntenic net
Black flying-fox Pteropus alecto Aug 2012 ASM32557v1/pteAle1 Syntenic net
Cat Felis catus Nov 2014 ICGSC Felis_catus 8.0/felCat8 Syntenic net
Cow Bos taurus Jun 2014 Bos_taurus_UMD_3.1.1/bosTau8 Syntenic net
David's myotis bat Myotis davidii Aug 2012 ASM32734v1/myoDav1 Syntenic net
Dog Canis lupus familiaris Sep 2011 Broad CanFam3.1/canFam3 Syntenic net
Dolphin Tursiops truncatus Oct 2011 Baylor Ttru_1.4/turTru2 Reciprocal best net
Domestic goat Capra hircus May 2012 CHIR_1.0/capHir1 Syntenic net
Ferret Mustela putorius furo Apr 2011 MusPutFur1.0/musFur1 Syntenic net
Hedgehog Erinaceus europaeus May 2012 EriEur2.0/eriEur2 Syntenic net
Horse Equus caballus Sep 2007 Broad/equCab2 Syntenic net
Killer whale Orcinus orca Jan 2013 Oorc_1.1/orcOrc1 Syntenic net
Megabat Pteropus vampyrus Jul 2008 Broad/pteVam1 Reciprocal best net
Little brown bat Myotis lucifugus Jul 2010 Broad Institute Myoluc2.0/myoLuc2 Syntenic net
Pacific walrus Odobenus rosmarus divergens Jan 2013 Oros_1.0/odoRosDiv1 Syntenic net
Panda Ailuropoda melanoleuca Dec 2009 BGI-Shenzhen 1.0/ailMel1 Syntenic net
Pig Sus scrofa Aug 2011 SGSC Sscrofa10.2/susScr3 Syntenic net
Sheep Ovis aries Aug 2012 ISGC Oar_v3.1/oviAri3 Syntenic net
Shrew Sorex araneus Aug 2008 Broad/sorAra2 Syntenic net
Star-nosed mole Condylura cristata Mar 2012 ConCri1.0/conCri1 Syntenic net
Tibetan antelope Pantholops hodgsonii May 2013 PHO1.0/panHod1 Syntenic net
Weddell seal Leptonychotes weddellii Mar 2013 LepWed1.0/lepWed1 Reciprocal best net
White rhinoceros Ceratotherium simum May 2012 CerSimSim1.0/cerSim1 Syntenic net
Afrotheria subset
Aardvark Orycteropus afer afer May 2012 OryAfe1.0/oryAfe1 Syntenic net
Cape elephant shrew Elephantulus edwardii Aug 2012 EleEdw1.0/eleEdw1 Syntenic net
Cape golden mole Chrysochloris asiatica Aug 2012 ChrAsi1.0/chrAsi1 Syntenic net
Elephant Loxodonta africana Jul 2009 Broad/loxAfr3 Syntenic net
Manatee Trichechus manatus latirostris Oct 2011 Broad v1.0/triMan1 Syntenic net
Tenrec Echinops telfairi Nov 2012 Broad/echTel2 Syntenic net
Mammal subset
Armadillo Dasypus novemcinctus Dec 2011 Baylor/dasNov3 Syntenic net
Opossum Monodelphis domestica Oct 2006 Broad/monDom5 Net
Platypus Ornithorhynchus anatinus Mar 2007 WUGSC 5.0.1/ornAna1 Reciprocal best net
Tasmanian devil Sarcophilus harrisii Feb 2011 WTSI Devil_ref v7.0/sarHar1 Net
Wallaby Macropus eugenii Sep 2009 TWGS Meug_1.1/macEug2 Reciprocal best net
Aves subset
Budgerigar Melopsittacus undulatus Sep 2011 WUSTL v6.3/melUnd1 Net
Chicken Gallus gallus Nov 2011 ICGSC Gallus_gallus-4.0/galGal4 Net
Collared flycatcher Ficedula albicollis Jun 2013 FicAlb1.5/ficAlb2 Net
Mallard duck Anas platyrhynchos Apr 2013 BGI_duck_1.0/anaPla1 Net
Medium ground finch Geospiza fortis Apr 2012 GeoFor_1.0/geoFor1 Net
Parrot Amazona vittata Jan 2013 AV1/amaVit1 Net
Peregrine falcon Falco peregrinus Feb 2013 F_peregrinus_v1.0/falPer1 Net
Rock pigeon Columba livia Feb 2013 Cliv_1.0/colLiv1 Net
Saker falcon Falco cherrug Feb 2013 F_cherrug_v1.0/falChe1 Net
Scarlet macaw Ara macao Jun 2013 SMACv1.1/araMac1 Net
Tibetan ground jay Pseudopodoces humilis Jan 2013 PseHum1.0/pseHum1 Net
Turkey Meleagris gallopavo Dec 2009 TGC Turkey_2.01/melGal1 Net
White-throated sparrow Zonotrichia albicollis Apr 2013 ASM38545v1/zonAlb1 Net
Zebra finch Taeniopygia guttata Feb 2013 WashU taeGut324/taeGut2 Net
Sarcopterygii subset
American alligator Alligator mississippiensis Aug 2012 allMis0.2/allMis1 Net
Chinese softshell turtle Pelodiscus sinensis Oct 2011 PelSin_1.0/pelSin1 Net
Coelacanth Latimeria chalumnae Aug 2011 Broad/latCha1 Net
Green seaturtle Chelonia mydas Mar 2013 CheMyd_1.0/cheMyd1 Net
Lizard Anolis carolinensis May 2010 Broad AnoCar2.0/anoCar2 Net
Painted turtle Chrysemys picta bellii Mar 2014 v3.0.3/chrPic2 Net
Spiny softshell turtle Apalone spinifera May 2013 ASM38561v1/apaSpi1 Net
X. tropicalis Xenopus tropicalis Sep 2012 JGI 7.0/xenTro7 Net
Fish subset
Atlantic cod Gadus morhua May 2010 Genofisk GadMor_May2010/gadMor1 Net
Burton's mouthbreeder Haplochromis burtoni Oct 2011 AstBur1.0/hapBur1 Net
Fugu Takifugu rubripes Oct 2011 FUGU5/fr3 Net
Lamprey Petromyzon marinus Sep 2010 WUGSC 7.0/petMar2 Net
Medaka Oryzias latipes Oct 2005 NIG/UT MEDAKA1/oryLat2 Net
Mexican tetra (cavefish) Astyanax mexicanus Apr 2013 Astyanax_mexicanus-1.0.2/astMex1 Net
Nile tilapia Oreochromis niloticus Jan 2011 Broad oreNil1.1/oreNil2 Net
Princess of Burundi Neolamprologus brichardi May 2011 NeoBri1.0/neoBri1 Net
Pundamilia nyererei Pundamilia nyererei Oct 2011 PunNye1.0/punNye1 Net
Southern platyfish Xiphophorus maculatus Jan 2012 Xiphophorus_maculatus-4.4.2/xipMac1 Net
Spotted gar Lepisosteus oculatus Dec 2011 LepOcu1/lepOcu1 Net
Stickleback Gasterosteus aculeatus Feb 2006 Broad/gasAcu1 Net
Tetraodon Tetraodon nigroviridis Mar 2007 Genoscope 8.0/tetNig2 Net
Yellowbelly pufferfish Takifugu flavidus May 2013 version 1 of Takifugu flavidus genome/takFla1 Net
Zebra mbuna Maylandia zebra Mar 2012 MetZeb1.1/mayZeb1 Net
Zebrafish Danio rerio Sep 2014 GRCz10/danRer10 Net

\ Table 1. Genome assemblies included in the 100-way Conservation track.
\

Primate subset
Organism	Species	Release date	UCSC version	Alignment type
Baboon	Papio hamadryas	Mar 2012	Baylor Panu_2.0/papAnu2	Reciprocal best net
Bushbaby	Otolemur garnettii	Mar 2011	Broad/otoGar3	Syntenic net
Chimp	Pan troglodytes	Feb 2011	CSAC 2.1.4/panTro4	Syntenic net
Crab-eating macaque	Macaca fascicularis	Jun 2013	Macaca_fascicularis_5.0/macFas5	Syntenic net
Gibbon	Nomascus leucogenys	Oct 2012	GGSC Nleu3.0/nomLeu3	Syntenic net
Gorilla	Gorilla gorilla gorilla	May 2011	gorGor3.1/gorGor3	Reciprocal best net
Green monkey	Chlorocebus sabaeus	Mar 2014	Chlorocebus_sabeus 1.1/chlSab2	Syntenic net
Human	Homo sapiens	Dec 2013	GRCh38/hg38	reference species
Marmoset	Callithrix jacchus	Mar 2009	WUGSC 3.2/calJac3	Syntenic net
Orangutan	Pongo pygmaeus abelii	July 2007	WUGSC 2.0.2/ponAbe2	Reciprocal best net
Rhesus	Macaca mulatta	Oct 2010	BGI CR_1.0/rheMac3	Syntenic net
Squirrel monkey	Saimiri boliviensis	Oct 2011	Broad/saiBol1	Syntenic net
Euarchontoglires subset
Brush-tailed rat	Octodon degus	Apr 2012	OctDeg1.0/octDeg1	Syntenic net
Chinchilla	Chinchilla lanigera	May 2012	ChiLan1.0/chiLan1	Syntenic net
Chinese hamster	Cricetulus griseus	Jul 2013	C_griseus_v1.0/criGri1	Syntenic net
Chinese tree shrew	Tupaia chinensis	Jan 2013	TupChi_1.0/tupChi1	Syntenic net
Golden hamster	Mesocricetus auratus	Mar 2013	MesAur1.0/mesAur1	Syntenic net
Guinea pig	Cavia porcellus	Feb 2008	Broad/cavPor3	Syntenic net
Lesser Egyptian jerboa	Jaculus jaculus	May 2012	JacJac1.0/jacJac1	Syntenic net
Mouse	Mus musculus	Dec 2011	GRCm38/mm10	Syntenic net
Naked mole-rat	Heterocephalus glaber	Jan 2012	Broad HetGla_female_1.0/hetGla2	Syntenic net
Pika	Ochotona princeps	May 2012	OchPri3.0/ochPri3	Syntenic net
Prairie vole	Microtus ochrogaster	Oct 2012	MicOch1.0/micOch1	Syntenic net
Rabbit	Oryctolagus cuniculus	Apr 2009	Broad/oryCun2	Syntenic net
Rat	Rattus norvegicus	Jul 2014	RGSC 6.0/rn6	Syntenic net
Squirrel	Spermophilus tridecemlineatus	Nov 2011	Broad/speTri2	Syntenic net
Laurasiatheria subset
Alpaca	Vicugna pacos	Mar 2013	Vicugna_pacos-2.0.1/vicPac2	Syntenic net
Bactrian camel	Camelus ferus	Dec 2011	CB1/camFer1	Syntenic net
Big brown bat	Eptesicus fuscus	Jul 2012	EptFus1.0/eptFus1	Syntenic net
Black flying-fox	Pteropus alecto	Aug 2012	ASM32557v1/pteAle1	Syntenic net
Cat	Felis catus	Nov 2014	ICGSC Felis_catus 8.0/felCat8	Syntenic net
Cow	Bos taurus	Jun 2014	Bos_taurus_UMD_3.1.1/bosTau8	Syntenic net
David's myotis bat	Myotis davidii	Aug 2012	ASM32734v1/myoDav1	Syntenic net
Dog	Canis lupus familiaris	Sep 2011	Broad CanFam3.1/canFam3	Syntenic net
Dolphin	Tursiops truncatus	Oct 2011	Baylor Ttru_1.4/turTru2	Reciprocal best net
Domestic goat	Capra hircus	May 2012	CHIR_1.0/capHir1	Syntenic net
Ferret	Mustela putorius furo	Apr 2011	MusPutFur1.0/musFur1	Syntenic net
Hedgehog	Erinaceus europaeus	May 2012	EriEur2.0/eriEur2	Syntenic net
Horse	Equus caballus	Sep 2007	Broad/equCab2	Syntenic net
Killer whale	Orcinus orca	Jan 2013	Oorc_1.1/orcOrc1	Syntenic net
Megabat	Pteropus vampyrus	Jul 2008	Broad/pteVam1	Reciprocal best net
Little brown bat	Myotis lucifugus	Jul 2010	Broad Institute Myoluc2.0/myoLuc2	Syntenic net
Pacific walrus	Odobenus rosmarus divergens	Jan 2013	Oros_1.0/odoRosDiv1	Syntenic net
Panda	Ailuropoda melanoleuca	Dec 2009	BGI-Shenzhen 1.0/ailMel1	Syntenic net
Pig	Sus scrofa	Aug 2011	SGSC Sscrofa10.2/susScr3	Syntenic net
Sheep	Ovis aries	Aug 2012	ISGC Oar_v3.1/oviAri3	Syntenic net
Shrew	Sorex araneus	Aug 2008	Broad/sorAra2	Syntenic net
Star-nosed mole	Condylura cristata	Mar 2012	ConCri1.0/conCri1	Syntenic net
Tibetan antelope	Pantholops hodgsonii	May 2013	PHO1.0/panHod1	Syntenic net
Weddell seal	Leptonychotes weddellii	Mar 2013	LepWed1.0/lepWed1	Reciprocal best net
White rhinoceros	Ceratotherium simum	May 2012	CerSimSim1.0/cerSim1	Syntenic net
Afrotheria subset
Aardvark	Orycteropus afer afer	May 2012	OryAfe1.0/oryAfe1	Syntenic net
Cape elephant shrew	Elephantulus edwardii	Aug 2012	EleEdw1.0/eleEdw1	Syntenic net
Cape golden mole	Chrysochloris asiatica	Aug 2012	ChrAsi1.0/chrAsi1	Syntenic net
Elephant	Loxodonta africana	Jul 2009	Broad/loxAfr3	Syntenic net
Manatee	Trichechus manatus latirostris	Oct 2011	Broad v1.0/triMan1	Syntenic net
Tenrec	Echinops telfairi	Nov 2012	Broad/echTel2	Syntenic net
Mammal subset
Armadillo	Dasypus novemcinctus	Dec 2011	Baylor/dasNov3	Syntenic net
Opossum	Monodelphis domestica	Oct 2006	Broad/monDom5	Net
Platypus	Ornithorhynchus anatinus	Mar 2007	WUGSC 5.0.1/ornAna1	Reciprocal best net
Tasmanian devil	Sarcophilus harrisii	Feb 2011	WTSI Devil_ref v7.0/sarHar1	Net
Wallaby	Macropus eugenii	Sep 2009	TWGS Meug_1.1/macEug2	Reciprocal best net
Aves subset
Budgerigar	Melopsittacus undulatus	Sep 2011	WUSTL v6.3/melUnd1	Net
Chicken	Gallus gallus	Nov 2011	ICGSC Gallus_gallus-4.0/galGal4	Net
Collared flycatcher	Ficedula albicollis	Jun 2013	FicAlb1.5/ficAlb2	Net
Mallard duck	Anas platyrhynchos	Apr 2013	BGI_duck_1.0/anaPla1	Net
Medium ground finch	Geospiza fortis	Apr 2012	GeoFor_1.0/geoFor1	Net
Parrot	Amazona vittata	Jan 2013	AV1/amaVit1	Net
Peregrine falcon	Falco peregrinus	Feb 2013	F_peregrinus_v1.0/falPer1	Net
Rock pigeon	Columba livia	Feb 2013	Cliv_1.0/colLiv1	Net
Saker falcon	Falco cherrug	Feb 2013	F_cherrug_v1.0/falChe1	Net
Scarlet macaw	Ara macao	Jun 2013	SMACv1.1/araMac1	Net
Tibetan ground jay	Pseudopodoces humilis	Jan 2013	PseHum1.0/pseHum1	Net
Turkey	Meleagris gallopavo	Dec 2009	TGC Turkey_2.01/melGal1	Net
White-throated sparrow	Zonotrichia albicollis	Apr 2013	ASM38545v1/zonAlb1	Net
Zebra finch	Taeniopygia guttata	Feb 2013	WashU taeGut324/taeGut2	Net
Sarcopterygii subset
American alligator	Alligator mississippiensis	Aug 2012	allMis0.2/allMis1	Net
Chinese softshell turtle	Pelodiscus sinensis	Oct 2011	PelSin_1.0/pelSin1	Net
Coelacanth	Latimeria chalumnae	Aug 2011	Broad/latCha1	Net
Green seaturtle	Chelonia mydas	Mar 2013	CheMyd_1.0/cheMyd1	Net
Lizard	Anolis carolinensis	May 2010	Broad AnoCar2.0/anoCar2	Net
Painted turtle	Chrysemys picta bellii	Mar 2014	v3.0.3/chrPic2	Net
Spiny softshell turtle	Apalone spinifera	May 2013	ASM38561v1/apaSpi1	Net
X. tropicalis	Xenopus tropicalis	Sep 2012	JGI 7.0/xenTro7	Net
Fish subset
Atlantic cod	Gadus morhua	May 2010	Genofisk GadMor_May2010/gadMor1	Net
Burton's mouthbreeder	Haplochromis burtoni	Oct 2011	AstBur1.0/hapBur1	Net
Fugu	Takifugu rubripes	Oct 2011	FUGU5/fr3	Net
Lamprey	Petromyzon marinus	Sep 2010	WUGSC 7.0/petMar2	Net
Medaka	Oryzias latipes	Oct 2005	NIG/UT MEDAKA1/oryLat2	Net
Mexican tetra (cavefish)	Astyanax mexicanus	Apr 2013	Astyanax_mexicanus-1.0.2/astMex1	Net
Nile tilapia	Oreochromis niloticus	Jan 2011	Broad oreNil1.1/oreNil2	Net
Princess of Burundi	Neolamprologus brichardi	May 2011	NeoBri1.0/neoBri1	Net
Pundamilia nyererei	Pundamilia nyererei	Oct 2011	PunNye1.0/punNye1	Net
Southern platyfish	Xiphophorus maculatus	Jan 2012	Xiphophorus_maculatus-4.4.2/xipMac1	Net
Spotted gar	Lepisosteus oculatus	Dec 2011	LepOcu1/lepOcu1	Net
Stickleback	Gasterosteus aculeatus	Feb 2006	Broad/gasAcu1	Net
Tetraodon	Tetraodon nigroviridis	Mar 2007	Genoscope 8.0/tetNig2	Net
Yellowbelly pufferfish	Takifugu flavidus	May 2013	version 1 of Takifugu flavidus genome/takFla1	Net
Zebra mbuna	Maylandia zebra	Mar 2012	MetZeb1.1/mayZeb1	Net
Zebrafish	Danio rerio	Sep 2014	GRCz10/danRer10	Net

\ \

Display Conventions and Configuration

\ In full and pack display modes, conservation scores are displayed as a\ wiggle track (histogram) in which the height reflects the\ size of the score.\ The conservation wiggles can be configured in a variety of ways to\ highlight different aspects of the displayed information.\ Click the Graph configuration help link for an explanation\ of the configuration options.

\ Pairwise alignments of each species to the human genome are\ displayed below the conservation histogram as a grayscale density plot (in\ pack mode) or as a wiggle (in full mode) that indicates alignment quality.\ In dense display mode, conservation is shown in grayscale using\ darker values to indicate higher levels of overall conservation\ as scored by phastCons.

\ Checkboxes on the track configuration page allow selection of the\ species to include in the pairwise display.\ Note that excluding species from the pairwise display does not alter the\ the conservation score display.

\ To view detailed information about the alignments at a specific\ position, zoom the display in to 30,000 or fewer bases, then click on\ the alignment.

\ \

Gap Annotation

Single line: No bases in the aligned species. Possibly due to a\ lineage-specific insertion between the aligned blocks in the human genome\ or a lineage-specific deletion between the aligned blocks in the aligning\ species.\
Double line: Aligning species has one or more unalignable bases in\ the gap region. Possibly due to excessive evolutionary distance between\ species or independent indels in the region between the aligned blocks in both\ species.\
Pale yellow coloring: Aligning species has Ns in the gap region.\ Reflects uncertainty in the relationship between the DNA of both species, due\ to lack of sequence in relevant portions of the aligning species.\

\ \

Genomic Breaks

\ Discontinuities in the genomic context (chromosome, scaffold or region) of the\ aligned DNA in the aligning species are shown as follows:\

\ Vertical blue bar: Represents a discontinuity that persists indefinitely\ on either side, e.g. a large region of DNA on either side of the bar\ comes from a different chromosome in the aligned species due to a large scale\ rearrangement.\
\ Green square brackets: Enclose shorter alignments consisting of DNA from\ one genomic context in the aligned species nested inside a larger chain of\ alignments from a different genomic context. The alignment within the\ brackets may represent a short misalignment, a lineage-specific insertion of a\ transposon in the human genome that aligns to a paralogous copy somewhere\ else in the aligned species, or other similar occurrence.\

\ \

Base Level

\ When zoomed-in to the base-level display, the track shows the base\ composition of each alignment. The numbers and symbols on the Gaps\ line indicate the lengths of gaps in the human sequence at those\ alignment positions relative to the longest non-human sequence.\ If there is sufficient space in the display, the size of the gap is shown.\ If the space is insufficient and the gap size is a multiple of 3, a\ "*" is displayed; other gap sizes are indicated by "+".

\ Codon translation is available in base-level display mode if the\ displayed region is identified as a coding segment. To display this annotation,\ select the species for translation from the pull-down menu in the Codon\ Translation configuration section at the top of the page. Then, select one of\ the following modes:\

\ No codon translation: The gene annotation is not used; the bases are\ displayed without translation.\
\ Use default species reading frames for translation: The annotations from\ the genome displayed in the Default species to establish reading frame\ pull-down menu are used to translate all the aligned species present in the\ alignment.\
\ Use reading frames for species if available, otherwise no translation:\ Codon translation is performed only for those species where the region is\ annotated as protein coding.\
Use reading frames for species if available, otherwise use default species:\ Codon translation is done on those species that are annotated as being protein\ coding over the aligned region using species-specific annotation; the remaining\ species are translated using the default species annotation.\

\ Codon translation uses the following gene tracks as the basis for translation:\ \

\ \ \ \ \ \
Gene Track Species
UCSC Genes Human, Mouse
RefSeq Genes Cow, Frog (X. tropicalis)
Ensembl Genes v73 Atlantic cod, Bushbaby, Cat, Chicken, Chimp, Coelacanth, Dog, Elephant, Ferret, Fugu, Gorilla, Horse, Lamprey, Little brown bat, Lizard, Mallard duck, Marmoset, Medaka, Megabat, Orangutan, Panda, Pig, Platypus, Rat, Soft-shell Turtle, Southern platyfish, Squirrel, Tasmanian devil, Tetraodon, Zebrafish
no annotation Aardvark, Alpaca, American alligator, Armadillo, Baboon, Bactrian camel, Big brown bat, Black flying-fox, Brush-tailed rat, Budgerigar, Burton's mouthbreeder, Cape elephant shrew, Cape golden mole, Chinchilla, Chinese hamster, Chinese tree shrew, Collared flycatcher, Crab-eating macaque, David's myotis (bat), Dolphin, Domestic goat, Gibbon, Golden hamster, Green monkey, Green seaturtle, Hedgehog, Killer whale, Lesser Egyptian jerboa, Manatee, Medium ground finch, Mexican tetra (cavefish), Naked mole-rat, Nile tilapia, Pacific walrus, Painted turtle, Parrot, Peregrine falcon, Pika, Prairie vole, Princess of Burundi, Pundamilia nyererei, Rhesus, Rock pigeon, Saker falcon, Scarlet Macaw, Sheep, Shrew, Spiny softshell turtle, Spotted gar, Squirrel monkey, Star-nosed mole, Tawny puffer fish, Tenrec, Tibetan antelope, Tibetan ground jay, Wallaby, Weddell seal, White rhinoceros, White-throated sparrow, Zebra Mbuna, Zebra finch
\ Table 2. Gene tracks used for codon translation.\

\ \

Methods

\ Pairwise alignments with the human genome were generated for\ each species using lastz from repeat-masked genomic sequence.\ Pairwise alignments were then linked into chains using a dynamic programming\ algorithm that finds maximally scoring chains of gapless subsections\ of the alignments organized in a kd-tree.\ The scoring matrix and parameters for pairwise alignment and chaining\ were tuned for each species based on phylogenetic distance from the reference.\ High-scoring chains were then placed along the genome, with\ gaps filled by lower-scoring chains, to produce an alignment net.\ For more information about the chaining and netting process and\ parameters for each species, see the description pages for the Chain and Net\ tracks.

\ An additional filtering step was introduced in the generation of the 100-way\ conservation track to reduce the number of paralogs and pseudogenes from the\ high-quality assemblies and the suspect alignments from the low-quality\ assemblies:\ the pairwise alignments of high-quality mammalian\ sequences (placental and marsupial) were filtered based on synteny;\ those for 2X mammalian genomes were filtered to retain only\ alignments of best quality in both the target and query ("reciprocal\ best").

\ The resulting best-in-genome pairwise alignments\ were progressively aligned using multiz/autoMZ,\ following the tree topology diagrammed above, to produce multiple alignments.\ The multiple alignments were post-processed to\ add annotations indicating alignment gaps, genomic breaks,\ and base quality of the component sequences.\ The annotated multiple alignments, in MAF format, are available for\ bulk download.\ An alignment summary table containing an entry for each\ alignment block in each species was generated to improve\ track display performance at large scales.\ Framing tables were constructed to enable\ visualization of codons in the multiple alignment display.

\ \

Phylogenetic Tree Model

\ Both phastCons and phyloP are phylogenetic methods that rely\ on a tree model containing the tree topology, branch lengths representing\ evolutionary distance at neutrally evolving sites, the background distribution\ of nucleotides, and a substitution rate matrix.\ The\ all-species tree model for this track was\ generated using the phyloFit program from the PHAST package\ (REV model, EM algorithm, medium precision) using multiple alignments of\ 4-fold degenerate sites extracted from the 100-way alignment\ (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene\ set, filtered to select single-coverage long transcripts.\

\ This same tree model was used in the phyloP calculations; however, the\ background frequencies were modified to maintain reversibility.\ The resulting tree model:\ all species.\

PhastCons Conservation

\ The phastCons program computes conservation scores based on a phylo-HMM, a\ type of probabilistic model that describes both the process of DNA\ substitution at each site in a genome and the way this process changes from\ one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and\ Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for\ conserved regions and a state for non-conserved regions. The value plotted\ at each site is the posterior probability that the corresponding alignment\ column was "generated" by the conserved state of the phylo-HMM. These\ scores reflect the phylogeny (including branch lengths) of the species in\ question, a continuous-time Markov model of the nucleotide substitution\ process, and a tendency for conservation levels to be autocorrelated along\ the genome (i.e., to be similar at adjacent sites). The general reversible\ (REV) substitution model was used. Unlike many conservation-scoring programs,\ phastCons does not rely on a sliding window\ of fixed size; therefore, short highly-conserved regions and long moderately\ conserved regions can both obtain high scores.\ More information about\ phastCons can be found in Siepel et al. 2005.

\ Felsenstein J, Churchill GA.\ A Hidden Markov Model approach to variation among sites in rate of\ evolution. Mol Biol Evol. 1996 Jan;13(1):93-104.\ PMID: 8583911\

\ \

\ Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.\ \ Detection of nonneutral substitution rates on mammalian phylogenies.\ Genome Res. 2010 Jan;20(1):110-21.\ PMID: 19858363; PMC: PMC2798823\

\ \

\ Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,\ Clawson H, Spieth J, Hillier LW, Richards S, et al.\ Evolutionarily conserved elements in vertebrate, insect, worm,\ and yeast genomes.\ Genome Res. 2005 Aug;15(8):1034-50.\ PMID: 16024819; PMC: PMC1182216\

\ \

\ Siepel A, Haussler D.\ Phylogenetic Hidden Markov Models.\ In: Nielsen R, editor. Statistical Methods in Molecular Evolution.\ New York: Springer; 2005. pp. 325-351.\ DOI: 10.1007/0-387-27733-1_12\

\ \

\ Yang Z.\ A space-time process model for the evolution of DNA\ sequences.\ Genetics. 1995 Feb;139(2):993-1005.\ PMID: 7713447; PMC: PMC1206396\

\ \

Chain/Net:

\ Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\ Evolution's cauldron:\ duplication, deletion, and rearrangement in the mouse and human genomes.\ Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.\ PMID: 14500911; PMC: PMC208784\

\ \

Multiz:

\ Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,\ Baertsch R, Rosenbloom K, Clawson H, Green ED, et al.\ Aligning multiple genomic sequences with the threaded blockset aligner.\ Genome Res. 2004 Apr;14(4):708-15.\ PMID: 15060014; PMC: PMC383317\

\ \

Lastz (formerly Blastz):

\ Chiaromonte F, Yap VB, Miller W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput. 2002:115-26.\ PMID: 11928468\

\ \

\ Harris RS.\ Improved pairwise alignment of genomic DNA.\ Ph.D. Thesis. Pennsylvania State University, USA. 2007.\

\ \

\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\ Haussler D, Miller W.\ Human-mouse alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.\ PMID: 12529312; PMC: PMC430961\

\ \ \

Phylogenetic Tree:

\ Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E,\ Ryder OA, Stanhope MJ, de Jong WW, Springer MS.\ Resolution of the early placental mammal radiation using Bayesian phylogenetics.\ Science. 2001 Dec 14;294(5550):2348-51.\ PMID: 11743200\

\ compGeno 1 compositeTrack on\ dragAndDrop subTracks\ group compGeno\ longLabel Vertebrate Multiz Alignment & Conservation (100 Species)\ priority 1\ shortLabel Conservation\ subGroup1 view Views align=Multiz_Alignments phyloP=Basewise_Conservation_(phyloP) phastcons=Element_Conservation_(phastCons) elements=Conserved_Elements\ track cons100way\ type bed 4\ visibility full\ cons100wayViewelements Conserved Elements bed 4 Vertebrate Multiz Alignment & Conservation (100 Species) 0 1 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Vertebrate Multiz Alignment & Conservation (100 Species)\ parent cons100way\ shortLabel Conserved Elements\ track cons100wayViewelements\ view elements\ visibility hide\ covidHgiGwasC2 COVID GWAS bigLolly 9 + COVID GWAS from the COVID-19 Host Genetics Initiative (6696 cases, 18 studies) 0 1 0 0 0 127 127 127 0 0 22 chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, phenDis 1 bigDataUrl /gbdb/hg38/covidHgiGwas/covidHgiGwasC2.hg38.bb\ longLabel COVID GWAS from the COVID-19 Host Genetics Initiative (6696 cases, 18 studies)\ parent covidHgiGwas on\ shortLabel COVID GWAS\ track covidHgiGwasC2\ cpgIslandExt CpG Islands bed 4 + CpG Islands (Islands < 300 Bases are Light Green) 3 1 0 100 0 128 228 128 0 0 0

Description

\ \

CpG islands are associated with genes, particularly housekeeping\ genes, in vertebrates. CpG islands are typically common near\ transcription start sites and may be associated with promoter\ regions. Normally a C (cytosine) base followed immediately by a \ G (guanine) base (a CpG) is rare in\ vertebrate DNA because the Cs in such an arrangement tend to be\ methylated. This methylation helps distinguish the newly synthesized\ DNA strand from the parent strand, which aids in the final stages of\ DNA proofreading after duplication. However, over evolutionary time,\ methylated Cs tend to turn into Ts because of spontaneous\ deamination. The result is that CpGs are relatively rare unless\ there is selective pressure to keep them or a region is not methylated\ for some other reason, perhaps having to do with the regulation of gene\ expression. CpG islands are regions where CpGs are present at\ significantly higher levels than is typical for the genome as a whole.

\ \

\ The unmasked version of the track displays potential CpG islands\ that exist in repeat regions and would otherwise not be visible\ in the repeat masked version.\

\ \

\ By default, only the masked version of the track is displayed. To view the\ unmasked version, change the visibility settings in the track controls at\ the top of this page.\

\ \

Methods

\ \

CpG islands were predicted by searching the sequence one base at a\ time, scoring each dinucleotide (+17 for CG and -1 for others) and\ identifying maximally scoring segments. Each segment was then\ evaluated for the following criteria:\ \

GC content of 50% or greater
length greater than 200 bp
ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the \ \ basis of the number of Gs and Cs in the segment

\ The entire genome sequence, masking areas included, was\ used for the construction of the track Unmasked CpG.\ The track CpG Islands is constructed on the sequence after\ all masked sequence is removed.\

\ \

The CpG count is the number of CG dinucleotides in the island. \ The Percentage CpG is the ratio of CpG nucleotide bases\ (twice the CpG count) to the length. The ratio of observed to expected \ CpG is calculated according to the formula (cited in \ Gardiner-Garden et al. (1987)):\ \

    Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)

\ \ where N = length of sequence.

\ The calculation of the track data is performed by the following command sequence:\

\
twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\\
  | cpg_lh /dev/stdin 2> cpg_lh.err \\\
    |  awk '{$2 = $2 - 1; width = $3 - $2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\\
     | sort -k1,1 -k2,2n > cpgIsland.bed\

\ The unmasked track data is constructed from\ twoBitToFa -noMask output for the twoBitToFa command.\

\ \

Data access

\ CpG islands and its associated tables can be explored interactively using the\ REST API, the\ Table Browser or the\ Data Integrator.\ All the tables can also be queried directly from our public MySQL\ servers, with more information available on our\ help page as well as on\ our blog.

\ The source for the cpg_lh program can be obtained from\ src/utils/cpgIslandExt/.\ The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file")\

\ \

Credits

\ \

This track was generated using a modification of a program developed by G. Miklem and L. Hillier \ (unpublished).

\ \

References

\ \

\ Gardiner-Garden M, Frommer M.\ \ CpG islands in vertebrate genomes.\ J Mol Biol. 1987 Jul 20;196(2):261-82.\ PMID: 3656447\

\ regulation 1 html cpgIslandSuper\ longLabel CpG Islands (Islands < 300 Bases are Light Green)\ parent cpgIslandSuper pack\ priority 1\ shortLabel CpG Islands\ track cpgIslandExt\ cq56Vcf CQ-56 Variants vcfTabix CQ-56 Variants 0 1 0 0 0 127 127 127 0 0 0 map 1 bigDataUrl /gbdb/hg38/problematic/highRepro/CQ-56.sort.vcf.gz\ longLabel CQ-56 Variants\ parent highReproVcfs\ shortLabel CQ-56 Variants\ subGroups view=vcfs\ track cq56Vcf\ type vcfTabix\ crossTissueMapsTissueCellType Cross Tissue Nuclei bigBarChart Cross tissue nuclei RNA by tissue and cell type 3 1 0 0 0 127 127 127 0 0 0 https://cells.ucsc.edu/?ds=tabula-sapiens+all&gene=$

\ Description

\ This track collection shows data from \ Single-nucleus cross-tissue molecular reference maps toward\ understanding disease gene function. The dataset covers ~200,000 single nuclei\ from a total of 16 human donors across 25 samples, using 4 different sample preparation\ protocols followed by droplet based single-cell RNA-seq. The samples were obtained from\ frozen tissue as part of the Genotype-Tissue Expression (GTEx) project.\ Samples were taken from the esophagus, skeletal muscle, heart, lung, prostate, breast,\ and skin. The dataset includes 43 broad cell classes, some specific to certain tissues\ and some shared across all tissue types.\

\ \

\ This track collection contains three bar chart tracks of RNA expression. The first track,\ Cross Tissue Nuclei, allows\ cells to be grouped together and faceted on up to 4 categories: tissue, cell class, cell subclass,\ and cell type. The second track,\ Cross Tissue Details, allows\ cells to be grouped together and faceted on up to 7 categories: tissue, cell class, cell subclass,\ cell type, granular cell type, sex, and donor. The third track,\ GTEx Immune Atlas,\ allows cells to be grouped together and faceted on up to 5 categories: tissue, cell type, cell\ class, sex, and donor.\

\ \

\ Please see the\ GTEx portal\ for further interactive displays and additional data.

\ \

Display Conventions and Configuration

\ Tissue-cell type combinations in the Full and Combined tracks are\ colored by which cell type they belong to in the below table:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Color Cell Type
Endothelial
Epithelial
Glia
Immune
Neuron
Stromal
Other
\

Color	Cell Type
	Endothelial
	Epithelial
	Glia
	Immune
	Neuron
	Stromal
	Other

\ \

\ Tissue-cell type combinations in the Immune Atlas track are shaded according\ to the below table:\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Color Cell Type
Inflammatory Macrophage
Lung Macrophage
Monocyte/Macrophage FCGR3A High
Monocyte/Macrophage FCGR3A Low
Macrophage HLAII High
Macrophage LYVE1 High
Proliferating Macrophage
Dendritic Cell 1
Dendritic Cell 2
Mature Dendritic Cell
Langerhans
CD14+ Monocyte
CD16+ Monocyte
LAM-like
Other
\

Color	Cell Type
	Inflammatory Macrophage
	Lung Macrophage
	Monocyte/Macrophage FCGR3A High
	Monocyte/Macrophage FCGR3A Low
	Macrophage HLAII High
	Macrophage LYVE1 High
	Proliferating Macrophage
	Dendritic Cell 1
	Dendritic Cell 2
	Mature Dendritic Cell
	Langerhans
	CD14+ Monocyte
	CD16+ Monocyte
	LAM-like
	Other

\ \

Methods

\ Using the previously collected tissue samples from the Genotype-Tissue Expression\ project, nuclei were isolated using four different protocols and sequenced\ using droplet based single cell RNA-seq. CellBender v2.1 and other standard quality\ control techniques were applied, resulting in 209,126 nuclei profiles across eight\ tissues, with a mean of 918 genes and 1519 transcripts per profile.\

\ \

\ Data from all samples was integrated with a conditional variation autoencoder\ in order to correct for multiple sources of variation like sex, and protocol\ while preserving tissue and cell type specific effects.\

\ \

\ \ \ \

Display Conventions and Configuration

\ CCREs are colored and labeled according to classification by regulatory signature:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Color UCSC label ENCODE classification ENCODE label
red prom promoter-like signature PLS
orange enhP proximal enhancer-like signature pELS
yellow enhD distal enhancer-like signature dELS
pink K4m3 DNase-H3K4me3 DNase-H3K4me3
blue CTCF CTCF-only CTCF-only
\

	UCSC label	ENCODE classification	ENCODE label
red	prom	promoter-like signature	PLS
orange	enhP	proximal enhancer-like signature	pELS
yellow	enhD	distal enhancer-like signature	dELS
pink	K4m3	DNase-H3K4me3	DNase-H3K4me3
blue	CTCF	CTCF-only	CTCF-only

\ The DNase-H3K4me3 elements are those with promoter-like biochemical signature that\ are not within 200bp of an annotated TSS.\

\ \

Methods

\ All individual DNase hypsersensitive sites (DHSs) identified from 706 DNase-seq experiments\ in humans (a total of 93 million sites from 706 experiments) were iteratively clustered\ and filtered for the highest signal across all experiments, producing \ representative DHSs (rDHSs), with a total of 2.2 million such sites in human.\ The highest signal elements from this set that were also supported by high H3K4me3, H3K27ac \ and/or CTCF ChIP-seq signals were designated cCRE's (a total of 926,535 in human).\

\ Classification of cCRE's was performed based on the following criteria:\

cCREs with promoter-like signatures (cCRE-PLS) fall within 200 bp of an annotated GENCODE TSS\ and have high DNase and H3K4me3 signals.
cCREs with enhancer-like signatures (cCRE-ELS) have high DNase and H3K27ac with low H3K4me3\ max-Z score if they are within 200 bp of an annotated TSS. The subset of cCREs-ELS within 2 kb\ of a TSS is denoted proximal (cCRE-pELS), while the remaining subset is denoted distal\ (cCRE-dELS).
DNase-H3K4me3 cCREs have high H3K4me3 max-Z scores but low H3K27ac max-Z scores and do not\ fall within 200 bp of a TSS.
CTCF-only cCREs have high DNase and CTCF and low H3K4me3 and H3K27ac.

\ \

\ \

\ The GENCODE V24 (Ensembl 33) basic gene annotation set was used in this analysis.\ For further detail about the identification and classification of ENCODE cCREs see \ the About page of the\ SCREEN web tool.\

\ \

Data Access

\ The ENCODE accession numbers of the constituent datasets at the\ ENCODE Portal\ are available from the cCRE details page.\

\ The data in this track can be interactively explored with the \ Table Browser or the \ Data Integrator. \ The data can be accessed from scripts through our \ API, the track name is "encodeCcreCombined".\ \

\ For automated download and analysis, this annotation is stored in a bigBed file that\ can be downloaded from\ our download server.\ The file for this track is called encodeCcreCombined.bb. \ Individual regions or the whole genome annotation can be obtained using our tool \ bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. \ Instructions for downloading source code and binaries can be found\ here.\ The tool can also be used to obtain only features within a given range, e.g.

\ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/encode3/ccre/encodeCcreCombined.bb -chrom=chr21 -start=0 -end=100000000 stdout

\ \

Release Notes

\ This annotation is based on ENCODE data released on or before September 14, 2018.

\ Data from the Common fund supported\ Roadmap Epigenomics Mapping Consortium\ (REMC) were included for building the ENCODE cCREs. Please see the 2015 paper on their analysis\ of reference human genomes for more information.

\ \

Credits

\ This dataset was produced by the\ ENCODE Data Analysis Center\ (ZLab at UMass Medical Center). Please check the\ ZLab ENCODE Public Hubs\ for the most updated data.\ Thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI for providing\ this data.\ Thanks also to the ENCODE Consortium, the ENCODE production laboratories, \ and the ENCODE Data Coordination Center for generating and processing the datasets used here.\

\ \

References

\ ENCODE Project Consortium.\ \ Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes.\ Nature. 2020 July 30;583(7818):699-710

\ \

\ ENCODE Project Consortium.\ \ An integrated encyclopedia of DNA elements in the human genome.\ Nature. 2012 Sep 6;489(7414):57-74.\ PMID: 22955616; PMC: PMC3439153\

\ \ ENCODE Project Consortium.\ \ A user's guide to the encyclopedia of DNA elements (ENCODE).\ PLoS Biol. 2011 Apr;9(4):e1001046.\ PMID: 21526222; PMC: PMC3079585\

\ \ regulation 1 bedNameLabel ENCODE Accession\ bigDataUrl /gbdb/hg38/encode3/ccre/encodeCcreCombined.bb\ darkerLabels on\ defaultLabelFields accessionLabel,ucscLabel\ filterLabel.ucscLabel cCRE classification\ filterValues.ucscLabel prom|promoter-like signature (PLS/prom),enhP|proximal enhancer-like signature (pELS/enhP),enhD|distal enhancer-like signature (dELS/enhD),CTCF|CTCF only (CTCF/CTCF-only),K4m3|DNase-H3K4me3 (DNase-H3K4me3/k4m3)\ group regulation\ itemRgb On\ labelFields accessionLabel,ucscLabel,encodeLabel\ longLabel ENCODE Candidate Cis-Regulatory Elements (cCREs) combined from all cell types\ mouseOverField description\ priority 1\ shortLabel ENCODE cCREs\ skipFields encodeLabel,ucscLabel,accessionLabel,description\ track encodeCcreCombined\ type bigBed 9 +\ url https://screen-v2.wenglab.org/search/?q=$$&assembly=GRCh38\ urlLabel cCRE details at ENCODE SCREEN:\ visibility dense\ wgEncodeReg ENCODE Regulation Integrated Regulation from ENCODE 0 1 0 0 0 127 127 127 0 0 0

Description

\ These tracks contain information relevant to the regulation of transcription from the\ ENCODE Project.\ \

The Transcription track shows transcription\ levels assayed by sequencing of polyadenylated RNA from a variety of cell types.
The Layered H3K4Me1 and Layered H3K27Ac tracks show where modification of histone proteins\ is suggestive of enhancer and, to a lesser extent, other regulatory activity. These histone \ modifications, particularly H3K4Me1, are quite broad. The actual enhancers are typically just a \ small portion of the area marked by these histone modifications.
The Layered H3K4Me3 \ track shows a histone mark associated with promoters.
The DNase I Hypersensitivity tracks indicate\ where chromatin is hypersensitive to cutting by the DNase enzyme, which has \ been assayed in a large number of cell types. Regulatory regions, in general, tend to be \ DNase-sensitive, and promoters are particularly DNase-sensitive.
The Txn Factor ChIP\ tracks show DNA regions where transcription factors, proteins responsible for \ modulating gene transcription, bind as assayed by chromatin immunoprecipitation with antibodies \ specific to the transcription factor followed by sequencing of the precipitated DNA (ChIP-seq).

\ \

\ These tracks complement each other and together can shed much light on regulatory DNA. The histone\ marks are informative at a high level, but they have a resolution of just ~200 bases and do not\ provide much in the way of functional detail. The DNase hypersensitivity assay is higher in\ resolution at the DNA level and can be done on a large number of cell types since it's just \ a single assay. At the functional level, DNase hypersensitivity suggests that a \ region is very likely to be regulatory in nature, but provides little information beyond that.\ The transcription factor ChIP assay has a high resolution at the DNA level and, due to the very\ specific nature of the transcription factors, is often informative with respect to functional\ detail. However, since each transcription factor must be assayed separately, the information is\ only available for a limited number of transcription factors on a limited number of cell lines. \ Though each assay has its strengths and weaknesses, the fact that all of these assays are \ relatively independent of each other gives increased confidence when multiple tracks are \ suggesting a regulatory function for a region.\

\ \

\ For additional information, please click on the hyperlinks for the individual tracks above.\ Also note that additional histone marks and transcription information is available in other\ ENCODE tracks. This integrative supertrack just shows a selection of the most informative data of\ most general interest.\

\ \

Display Conventions

\ By default, the transcription and histone mark displays use a transparent overlay method of \ displaying data from a number of cell lines in a single track. Each of the cell lines in this track\ is associated with a particular color, and these colors are relatively light and saturated so\ as to work best with the transparent overlay. The color of the transcription and histone mark tracks\ match their versions from their lifted source on the hg19 assembly.

\ The DNase tracks, which were not lifted from hg19, are colored differently \ to reflect similarity of cell types. There are three DNase tracks starting with a transparent\ overlay DNase Signal Track to allow viewing signals from all 95 cell types in one track.\ The individual signals and the same coloring scheme can also be found in the DNase HS Track\ where processed peaks and hotspots are also called out as gray boxes with the darkness of\ each box reflecting the underlying signal value. Lastly, in the DNase Clusters track all observed\ hypersensitive regions in the different cell lines at the same location were clustered into a single box\ where a number to the left of the box indicates how many cell types showed a hypersensitivity \ region and the darkness of the grey box is proportional to the the maximum value seen from one of\ the underlying cell lines. Clicking on these item takes you to a details page where\ additional information displays, such as the list of cell types that combined to form\ the cluster in the DNase Clusters track.\

\ \

Data Access

\ The raw data for ENCODE 3 Regulation tracks can be accessed from \ \ Table Browser or combined with other data-sets through \ Data Integrator. For automated analysis and downloads, the track data files can be downloaded \ from our downloads server or queried\ using the JSON API or the \ Public SQL Individual regions or the whole genome \ annotation can be accessed as text using our utility bigBedToBed. Instructions for downloading \ the utility can be found \ here. That \ utility can also be used to obtain features within a given range, e.g. \ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/wgEncodeRegDnase/wgEncodeRegDnaseUwA549Hotspot.broadPeak.bb -chrom=chr21 -start=0 -end=100000000 stdout

\ For sorting transcription factor binding sites by cell type, we recommend you use the following\ download \ file for hg38.\

\ \ \

\ \

\ Each item in the track is a representation of the promoter sequence identified by EPD. The\ "thin" part of the element represents the 49 bp upstream of the annotated transcription\ start site (TSS) whereas the "thick" part represents the TSS plus 10 bp downstream. The\ relative position of the thick and thin parts define the orientation of the promoter.

\ Note that the EPD team has created a public track hub containing\ promoter and supporting annotations for human, mouse, and other vertebrate and model organism\ genomes.

\ \

Methods

\ Briefly, gene transcript coordinates were obtained from multiple sources (HGNC, GENCODE, Ensembl,\ RefSeq) and validated using data from CAGE and RAMPAGE experimental studies obtained from FANTOM 5,\ UCSC, and ENCODE. Peak calling, clustering and filtering based on relative expression were applied\ to identify the most expressed promoters and those present in the largest number of samples.

\ For the methodology and principles used by EPD to predict TSSs, refer to Dreos et al.\ (2013) in the References section below. A more detailed description of how this data was\ generated can be found at the following links:\ \

\ Human promoter pipelines: \ coding,\ non-coding\
\ Mouse promoter pipelines:\ coding,\ non-coding\

\ \

Credits

\ \

\ Data was generated by the EPD team at the \ Swiss Institute of Bioinformatics. \ For inquiries, contact the EPD team using this on-line form \ or email \ \ philipp.\ bucher@epfl.\ ch\ \ .\

\ \

References

\ \

\ Dreos R, Ambrosini G, Perier RC, Bucher P.\ \ EPD and EPDnew, high-quality promoter resources in the\ next-generation sequencing era. Nucleic Acids\ Res. 2013 Jan 1;41(D1):D157-64. PMID: 23193273.\

\ \ expression 1 bigDataUrl /gbdb/hg38/bbi/epdNewHuman006.hg38.bb\ color 50,50,200\ dataVersion EPDNew Human Version 006 (May 2018)\ longLabel Promoters from EPDnew human version 006\ parent epdNew on\ priority 1\ shortLabel EPDnew v6\ track epdNewPromoter\ url https://epd.epfl.ch/cgi-bin/get_doc?db=hgEpdNew&format=genome&entry=$$\ fixSeqLiftOverPsl Fix Patches psl Reference Assembly Fix Patch Sequence Alignments 3 1 231 203 21 243 229 138 0 0 0

Description

\ \

\ This track shows alignments of fix patch sequences to\ main chromosome sequences in the reference genome assembly.\ When errors are corrected in the reference genome assembly, the\ Genome Reference Consortium\ (GRC) adds fix patch sequences containing the corrected regions.\ This strikes a balance between providing the most complete and correct genome\ sequence, while maintaining stable chromosome coordinates for the original assembly\ sequences.\

\ Fix patches are often associated with incident reports displayed in the GRC Incidents\ track.\

\ \

Display Conventions and Configuration

\ \

\ This track follows the display conventions for\ \ PSL alignment tracks.\ Mismatching bases are highlighted in red.\ Several types of alignment gap may also be colored;\ for more information, see\ \ Alignment Insertion/Deletion Display Options.\

\ \

Credits

\ The alignments were provided by NCBI as GFF files and translated into the PSL\ representation for browser display by UCSC.\

\ map 1 baseColorDefault diffBases\ baseColorUseSequence db\ color 231,203,21\ darkerLabels on\ group map\ indelDoubleInsert on\ indelQueryInsert on\ longLabel Reference Assembly Fix Patch Sequence Alignments\ pennantIcon p14 black https://genome-blog.gi.ucsc.edu/blog/patches/ "Includes annotations on GRCh38.p14 patch sequences"\ priority 1\ shortLabel Fix Patches\ showCdsAllScales .\ showCdsMaxZoom 10000.0\ showDiffBasesAllScales .\ showDiffBasesMaxZoom 10000.0\ track fixSeqLiftOverPsl\ type psl\ visibility pack\ knownGene GENCODE V47 bigGenePred knownGenePep knownGeneMrna GENCODE V47 3 1 0 0 0 127 127 127 0 0 0

Description

\ The GENCODE Genes track (version 47, October 2024) shows high-quality manual\ annotations merged with evidence-based automated annotations across the entire\ human genome generated by the\ GENCODE project.\ By default, only the basic gene set is\ displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts\ that GENCODE believes will be useful to the majority of users.

\ \

\ The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes\ are not displayed by default. It contains annotations on the reference chromosomes as well as\ assembly patches and alternative loci (haplotypes).

\ \

\ The v47 release was derived from the GTF file that contains annotations only on the main\ chromosomes. Statistics for this build and information on how they were generated can be found on\ the GENCODE site.

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes.\ It includes options to display the entire GENCODE set and pseudogenes. To customize these\ options, the respective boxes can be checked or unchecked at the top of this description page. \ \

\ This track also includes a variety of labels which identify the transcripts when visibility is set\ to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but\ additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID\ (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene\ and transcript names can be found in our\ FAQ.

\ \

\ This track, in general, follows the display conventions for gene prediction tracks. The exons for\ putative non-coding genes and untranslated regions are represented by relatively thin blocks, while\ those for coding open reading frames are thicker. \

Coloring for the gene annotations is mostly based on the annotation type:

MANE: MANE Select Plus Clinical transcripts.\ For non-MANE transcripts, the following conventions apply.\
coding: protein coding transcripts, including polymorphic\ pseudogenes\
non-coding: non-protein coding transcripts\
pseudogene: pseudogene transcript annotations\
problem: problem transcripts (Biotypes of\ retained_intron, TEC, or disrupted_domain)

\ \

\ This track contains an optional codon coloring feature that allows users to\ quickly validate and compare gene predictions. There is also an option to display the data as\ a density graph, which\ can be helpful for visualizing the distribution of items over a region.

\ \ \

Squishy-pack Display

\ Within a gene using the pack display mode, transcripts below a specified rank will be\ condensed into a view similar to squish mode. The transcript ranking approach is\ preliminary and will change in future releases. The transcripts rankings are defined by the\ following criteria for protein-coding and non-coding genes:

\ Protein_coding genes\

MANE or Ensembl canonical\
- 1st: MANE Select / Ensembl canonical
- 2nd: MANE Plus Clinical
\
Coding biotypes\
- 1st: protein_coding and protein_coding_LoF
- 2nd: NMDs and NSDs
- 3rd: retained intron and protein_coding_CDS_not_defined
\
Completeness\
- 1st: full length
- 2nd: CDS start/end not found
\
CARS score (only for coding transcripts)
Transcript genomic span and length (only for non-coding transcripts)

\ Non-coding genes\

Transcript biotype\
- 1st: transcript biotype identical to gene biotype
\
Ensembl canonical
GENCODE basic
Transcript genomic span
Transcript length

\ The gnomAD v3.1 track shows variants from 76,156 whole genomes (and no exomes), all mapped to the\ GRCh38/hg38 reference sequence. 4,454 genomes were added to the number of genomes in the previous\ v3 release. For more detailed information on gnomAD v3.1, see the related blog post.

\ \

\ The gnomAD v3.1.1 track contains the same underlying data as v3.1, but\ with minor corrections to the VEP annotations and dbSNP rsIDs. On the UCSC side, we have now\ included the mitochondrial chromosome data that was released as part of gnomAD v3.1 (but after\ the UCSC version of the track was released). For more information about gnomAD v3.1.1, please\ see the related\ changelog.

\ \

GnomAD Genome Mutational Constraint is based on v3.1.2 and is available only on hg38. \ It shows the reduced variation caused by purifying\ natural selection. This is similar to negative selection on loss-of-function\ (LoF) for genes, but can be calculated for non-coding regions too. \ Positive values are red and reflect stronger mutation constraint (and less variation), indicating \ higher natural selection pressure in a region. Negative values are green and \ reflect lower mutation constraint \ (and more variation), indicating less selection pressure and less functional effect.\ Briefly, for any 1kbp window in\ the genome, a model based on trinucleotide sequence context, base-level\ methylation, and regional genomic features predicts expected number of mutations,\ and compares this number to the observed number of mutations using a Z-score (see preprint\ in the Reference section for details). The chrX scores were added as received from the authors,\ as there are no de novo mutation data available on chrX (for estimating the effects of regional \ genomic features on mutation rates), they are more speculative than the ones on the autosomes.

\ \

\ The gnomAD Predicted Constraint Metrics track contains metrics of pathogenicity per-gene as \ predicted for gnomAD v2.1.1 and identifies genes subject to strong selection against various \ classes of mutation. This includes data on both the gene and transcript level.

\ \

\ The gnomAD v2 tracks show variants from 125,748 exomes and 15,708 whole genomes, all mapped to\ the GRCh37/hg19 reference sequence and lifted to the GRCh38/hg38 assembly. The data originate\ from 141,456 unrelated individuals sequenced as part of various population-genetic and\ disease-specific studies\ collected by the Genome Aggregation Database (gnomAD), release 2.1.1.\ Raw data from all studies have been reprocessed through a unified pipeline and jointly\ variant-called to increase consistency across projects. For more information on the processing\ pipeline and population annotations, see the following blog post\ and the 2.1.1 README.

\ gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the\ GRCh38/hg38 lift-over provided by gnomAD on their downloads site.\

\ \

On hg38 only, a subtrack "Gnomad mutational constraint" aka "Genome\ non-coding constraint of haploinsufficient variation (Gnocchi)" captures the\ depletion of variation caused by purifying natural selection.\ This is similar to negative selection on loss-of-function (LoF) for genes, but\ can be calculated for non-coding regions, too. Briefly, for any 1kbp window in\ the genome, a model based on trinucleotide sequence context, base-level\ methylation, and regional genomic features predicts expected number of mutations,\ and compares this number to the observed number of mutations using a Z-score (see Chen et al 2024 \ in the Reference section for details). The chrX scores were added as received from the authors, \ as there are no mutations available for chrX, they are more speculative than the ones on the autosomes.

\ \

\ For questions on the gnomAD data, also see the gnomAD FAQ.

\ More details on the Variant type(s) can be found on the Sequence Ontology page.

\ \

Display Conventions and Configuration

gnomAD v4.1

\ The gnomAD v4.1 track version follows the same conventions and configuration as the v3.1.1 track,\ except for mouse hovering items. Mouse hover on an item will display the following details about\ each variant:

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

\ \

gnomAD v3.1.1

\ The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,\ except as noted below.

\ \

There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).\
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one\ variant, with additional information available on the details page, which has roughly halved the\ number of items in the bigBed.\
The bigBed has been split into two files, one with the information necessary for the track\ display, and one with the information necessary for the details page. For more information on\ this data format, please see the Data Access section below.\
The VEP annotation is shown as a table instead of spread across multiple fields.\
Intergenic variants have not been pre-filtered.\

\ \

gnomAD v3.1

\ By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters\ described below), before the track switches to dense display mode.\

\ \

\ Mouse hover on an item will display many details about each variant, including the affected gene(s),\ the variant type, and annotation (missense, synonymous, etc).\

\ \

\ Clicking on an item will display additional details on the variant, including a population frequency\ table showing allele count in each sub-population.\

\ \

\ Following the conventions on the gnomAD browser, items are shaded according to their Annotation\ type:\ \ \ \ \ \
pLoF
Missense
Synonymous
Other
\

\ \

Label Options

\ To maintain consistency with the gnomAD website, variants are by default labeled according\ to their chromosomal start position followed by the reference and alternate alleles,\ for example "chr1-1234-T-CAG". dbSNP rsID's are also available as an additional\ label, if the variant is present in dbSnp.\

\ \

Filtering Options

\ Three filters are available for these tracks:\

FILTER: Used to exclude/include variants that failed Random Forest\ (RF), Inbreeding Coefficient (Inbreeding Coeff), or Allele Count (AC0) filters. The\ PASS option is used to include/exclude variants that pass all of the RF,\ InbreedingCoeff, and AC0 filters, as denoted in the original VCF.\
Annotation type: Used to exclude/include variants that are annotated as\ Probability Loss of Function (pLoF), Missense, Synonymous, or Other, as\ annotated by VEP version 85 (GENCODE v19).\
Variant Type: Used to exclude/include variants according to the type of\ variation, as annotated by VEP v85.\

\ There is one additional configurable filter on the minimum minor allele frequency.\ \

gnomAD v2.1.1

\ The gnomAD v2.1.1 track follows the standard display and configuration options available for\ VCF tracks, briefly explained below.\

In mode, a vertical line is drawn at the position of\ each variant.
In mode, "ref" and "alt" alleles are\ displayed to the left of a vertical line with colored portions corresponding to allele counts.\ Hovering the mouse pointer over a variant pops up a display of alleles and counts.

\ \

Filtering Options

\ Four filters are available for these tracks, the same as the underlying VCF:\

AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))\
InbreedingCoeff: Inbreeding Coefficient < -0.3\
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)\
Pass: Variant passes all 3 filters\

\ \

\ There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.\

\ \ \

UCSC Methods

\ The gnomAD v3.1.1 and v4.1 data is unfiltered.

\ For the v3.1 update only, in order to cut \ down on the amount of displayed data, the following variant\ types have been filtered out, but are still viewable in the gnomAD browser:\

Regulatory Region Variants\
Downstream/Upstream Gene Variants\
Transcription Factor Binding Site Variants\

\ \

\ For the full steps used to create the gnomAD tracks at UCSC, please see the\ hg38 gnomad makedoc.\

\ \ \

Data Access

\ \

\ The raw data can be explored interactively with the \ Table Browser, or the Data Integrator. For\ automated analysis, the data may be queried from our REST API, and the genome annotations are stored in files that\ can be downloaded from our download server, subject\ to the conditions set forth by the gnomAD consortium (see below). Variant VCFs can be found in the\ vcf\ subdirectory. The\ v3.1,\ v3.1.1, and\ v4.1 variants can\ be found in a special directory as they have been transformed from the underlying VCF.

\ \

\ For the v3.1.1 and v4.1 variants in particular, the underlying bigBed only contains enough information\ necessary to use the track in the browser. The extra data like VEP annotations and CADD scores are\ available in the same directory\ as the bigBed but in the files details.tab.gz and details.tab.gz.gzi. The\ details.tab.gz contains the gzip compressed extra data in JSON format, and the .gzi file is\ available to speed searching of this data. Each variant has an associated md5sum in the name field\ of the bigBed which can be used along with the _dataOffset and _dataLen fields to get the\ associated external data, as show below:\

\
# find item of interest:\
bigBedToBed genomes.bb stdout | head -4 | tail -1\
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted for brevity..]    chr1-12417-G-A    67293    902\
\
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:\
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz\
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant",  [..omitted for brevity..]\

\ \

\ The data can also be found directly from the gnomAD downloads page. Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.

\ \

The mutational constraints score was updated in October 2022 from a previous,\ now deprecated, pre-publication version. The old version can be found in our\ archive\ directory on the download server. It can be loaded by copying the URL into\ our "Custom tracks" input box.

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.\

\ \

\ Please note that some annotations within the provided files may have restrictions on usage. See here for more information. \

\ \

References

\ \

\ Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, Collins RL, Laricchia KM,\ Ganna A, Birnbaum DP et al.\ Variation across\ 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human\ protein-coding genes. doi: https://doi.org/10.1101/531210.\

\ Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill\ AJ, Cummings BB et al.\ Analysis of protein-coding\ genetic variation in 60,706 humans. Nature. 2016 Aug 17;536(7616):285-91.\ PMID: 27535533;\ PMC: PMC5018207\

\ Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C,\ Gauthier LD et al.\ \ A genomic mutational constraint map using variation in 76,156 human genomes.\ Nature. 2024 Jan;625(7993):92-100.\ PMID: 38057664
\ (We added the data in 2021, then later referenced the 2022 Biorxiv preprint, in which the track was not called "Gnocchi" yet)\

\ varRep 1 compositeTrack on\ configureByPopup off\ dataVersion Release v4.1 (April 19, 2024)\ html gnomadV4.1\ longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1\ maxItems 50000\ maxWindowCoverage 200000\ parent gnomadVariants\ pennantIcon New red ../goldenPath/newsarch.html#093024 "September 30, 2024"\ priority 1\ shortLabel gnomAD v4.1\ track gnomadVariantsV4.1\ type bigBed 9 +\ visibility squish\ gnomadGenomesVariantsV4_1 gnomAD v4.1 Genomes bigBed 9 + Genome Aggregation Database (gnomAD) Genome Variants v4.1 4 1 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$-$?dataset=gnomad_r4

Description

\ \

\ gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the\ GRCh38/hg38 lift-over provided by gnomAD on their downloads site.\

\ \

\ For questions on the gnomAD data, also see the gnomAD FAQ.

\ More details on the Variant type(s) can be found on the Sequence Ontology page.

\ \

Display Conventions and Configuration

gnomAD v4.1

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

\ \

gnomAD v3.1.1

\ The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,\ except as noted below.

\ \

There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).\
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one\ variant, with additional information available on the details page, which has roughly halved the\ number of items in the bigBed.\
The bigBed has been split into two files, one with the information necessary for the track\ display, and one with the information necessary for the details page. For more information on\ this data format, please see the Data Access section below.\
The VEP annotation is shown as a table instead of spread across multiple fields.\
Intergenic variants have not been pre-filtered.\

\ \

gnomAD v3.1

\ By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters\ described below), before the track switches to dense display mode.\

\ \

\ Mouse hover on an item will display many details about each variant, including the affected gene(s),\ the variant type, and annotation (missense, synonymous, etc).\

\ \

\ Clicking on an item will display additional details on the variant, including a population frequency\ table showing allele count in each sub-population.\

\ \

\ Following the conventions on the gnomAD browser, items are shaded according to their Annotation\ type:\ \ \ \ \ \
pLoF
Missense
Synonymous
Other
\

\ Four filters are available for these tracks, the same as the underlying VCF:\

AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))\
InbreedingCoeff: Inbreeding Coefficient < -0.3\
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)\
Pass: Variant passes all 3 filters\

\ \

\ There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.\

\ \ \

UCSC Methods

\ The gnomAD v3.1.1 and v4.1 data is unfiltered.

\ For the v3.1 update only, in order to cut \ down on the amount of displayed data, the following variant\ types have been filtered out, but are still viewable in the gnomAD browser:\

Regulatory Region Variants\
Downstream/Upstream Gene Variants\
Transcription Factor Binding Site Variants\

\ \

\ For the full steps used to create the gnomAD tracks at UCSC, please see the\ hg38 gnomad makedoc.\

\ \ \

Data Access

\ \

\
# find item of interest:\
bigBedToBed genomes.bb stdout | head -4 | tail -1\
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted for brevity..]    chr1-12417-G-A    67293    902\
\
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:\
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz\
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant",  [..omitted for brevity..]\

\ \

\ The data can also be found directly from the gnomAD downloads page. Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.\

\ \

\ Please note that some annotations within the provided files may have restrictions on usage. See here for more information. \

\ \

References

\ \

\ varRep 1 bigDataUrl /gbdb/hg38/gnomAD/v4.1/genomes/genomes.bb\ dataVersion Release v4.1 (April 19, 2024)\ defaultLabelFields _displayName\ detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies\ detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1/genomes/gnomad.v4.1.genomes.details.tab.gz\ filter.AF 0.0\ filterLabel.AF Minor Allele Frequency Filter\ filterType.FILTER multipleListAnd\ filterType.variation_type multipleListOr\ filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only)\ filterValues.annot pLoF,missense,synonymous,other\ filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation\ filterValuesDefault.FILTER PASS\ filterValuesDefault.annot pLoF,missense,synonymous\ html gnomadV4.1\ itemRgb on\ labelFields rsId,_displayName\ longLabel Genome Aggregation Database (gnomAD) Genome Variants v4.1\ mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt)
TotalAF: ${AF} (${AC}/${AN})
Genes: $genes
Annotation: $annot
FILTER: ${FILTER}
PopMaxAF: ${grpmax}
Homozygous Individuals: ${nhomalt}
Hemizygous Individuals (only in chrX & chrY): ${nhemi}\ parent gnomadVariantsV4.1 on\ priority 1\ searchIndex name,_displayName,rsId\ shortLabel gnomAD v4.1 Genomes\ skipEmptyFields on\ skipFields _displayName\ track gnomadGenomesVariantsV4_1\ type bigBed 9 +\ url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$-$?dataset=gnomad_r4\ urlLabel View this variant at gnomAD\ visibility squish\ gtexEqtlCaviar GTEx CAVIAR eQTLs bigBed 12 + GTEx High-Confidence cis-eQTLs from CAVIAR (no chrX) 3 1 0 0 0 127 127 127 0 0 0 regulation 1 bigDataUrl /gbdb/hg38/gtex/eQtl/gtexCaviar.bb\ filter.cpp 0\ filterLabel.cpp CPP (Causal Posterior Probability)\ filterLabel.geneName Gene Symbol\ filterLabel.tissue Tissue\ filterText.geneName *\ filterValues.tissue Adipose_Subcutaneous,Adipose_Visceral_Omentum,Adrenal_Gland,Artery_Aorta,Artery_Coronary,Artery_Tibial,Brain_Amygdala,Brain_Anterior_cingulate_cortex_BA24,Brain_Caudate_basal_ganglia,Brain_Cerebellar_Hemisphere,Brain_Cerebellum,Brain_Cortex,Brain_Frontal_Cortex_BA9,Brain_Hippocampus,Brain_Hypothalamus,Brain_Nucleus_accumbens_basal_ganglia,Brain_Putamen_basal_ganglia,Brain_Spinal_cord_cervical_c-1,Brain_Substantia_nigra,Breast_Mammary_Tissue,Cells_Cultured_fibroblasts,Cells_EBV-transformed_lymphocytes,Colon_Sigmoid,Colon_Transverse,Esophagus_Gastroesophageal_Junction,Esophagus_Mucosa,Esophagus_Muscularis,Heart_Atrial_Appendage,Heart_Left_Ventricle,Kidney_Cortex,Liver,Lung,Minor_Salivary_Gland,Muscle_Skeletal,Nerve_Tibial,Ovary,Pancreas,Pituitary,Prostate,Skin_Not_Sun_Exposed_Suprapubic,Skin_Sun_Exposed_Lower_leg,Small_Intestine_Terminal_Ileum,Spleen,Stomach,Testis,Thyroid,Uterus,Vagina,Whole_Blood\ itemRgb on\ longLabel GTEx High-Confidence cis-eQTLs from CAVIAR (no chrX)\ maxItems 100000\ mergeSpannedItems on\ mouseOver $name; CPP: $cpp\ noParentConfig on\ parent gtexEqtlHighConf\ shortLabel GTEx CAVIAR eQTLs\ showCfg on\ track gtexEqtlCaviar\ type bigBed 12 +\ urls eqtlName="https://gtexportal.org/home/snp/$$" geneName="https://gtexportal.org/home/locusBrowserPage/$$" eqtlPos="hgTracks?db=$D&position=$$" genePos="hgTracks?db=$D&position=$$" geneId="https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=$$"\ visibility pack\ gtexGeneV8 GTEx Gene V8 bed 6 + Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019) 3 1 0 0 0 127 127 127 1 0 0

Description

\ The\ \ NIH Genotype-Tissue Expression (GTEx) project\ was created to establish a sample and data resource for studies on the relationship between \ genetic variation and gene expression in multiple human tissues. \ This track shows median gene expression levels in 52 tissues and 2 cell lines, \ based on RNA-seq data from the GTEx final data release (V8, August 2019).\ This release is based on data from 17,382 tissue samples obtained from 948 adult \ post-mortem individuals.

\ \

Display Conventions

\ In Full and Pack display modes, expression for each gene is represented by a colored bargraph,\ where the height of each bar represents the median expression level across all samples for a \ tissue, and the bar color indicates the tissue.\ Tissue colors were assigned to conform to the GTEx Consortium publication conventions.\

\ The bargraph display has the same width and tissue order for all genes.\ Mouse hover over a bar will show the tissue and median expression level.\ The Squish display mode draws a rectangle for each gene, colored to indicate the tissue\ with highest expression level if it contributes more than 10% to the overall expression\ (and colored black if no tissue predominates).\ In Dense mode, the darkness of the grayscale rectangle displayed for the gene reflects the total\ median expression level across all tissues.

\ The GTEx transcript model used to quantify expression level is displayed below the graph,\ colored to indicate the transcript class \ (coding, \ noncoding, \ pseudogene, \ problem), \ following GENCODE conventions.\

\ Click-through on a graph displays a boxplot of expression level quartiles with outliers, \ per tissue, along with a link to the corresponding gene page on the GTEx Portal.

\ \

\ DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G.\ \ RNA-SeQC: RNA-seq metrics for quality control and process optimization.\ Bioinformatics. 2012 Jun 1;28(11):1530-2.\ PMID: 22539670; PMC: PMC3356847

\ \ expression 1 group expression\ longLabel Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019)\ maxItems 200\ priority 1\ shortLabel GTEx Gene V8\ spectrum on\ track gtexGeneV8\ type bed 6 +\ visibility pack\ h1hescInsitu H1-hESC In situ hic In situ Hi-C Chromatin Structure on H1-hESC 0 1 0 0 0 127 127 127 0 0 0 regulation 1 bigDataUrl /gbdb/hg38/bbi/hic/4DNFIQYQWPF5.hic\ longLabel In situ Hi-C Chromatin Structure on H1-hESC\ parent hicAndMicroC off\ shortLabel H1-hESC In situ\ track h1hescInsitu\ type hic\ chainHprcGCA_018466845v1 HG02257.mat chain GCA_018466845.1 HG02257.mat HG02257.pri.mat.f1_v2 (May 2021 GCA_018466845.1_HG02257.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 1 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02257.mat HG02257.pri.mat.f1_v2 (May 2021 GCA_018466845.1_HG02257.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018466845.1\ parent hprcChainNetViewchain off\ priority 18\ shortLabel HG02257.mat\ subGroups view=chain sample=s018 population=afr subpop=acb hap=mat\ track chainHprcGCA_018466845v1\ type chain GCA_018466845.1\ platinumHybrid hybrid vcfTabix Platinum genome hybrid 3 1 0 0 0 127 127 127 0 0 23 chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX, varRep 1 bigDataUrl /gbdb/hg38/platinumGenomes/hg38.hybrid.vcf.gz\ chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX\ configureByPopup off\ group varRep\ longLabel Platinum genome hybrid\ maxWindowToDraw 200000\ parent platinumGenomes\ shortLabel hybrid\ showHardyWeinberg on\ track platinumHybrid\ type vcfTabix\ vcfDoFilter off\ vcfDoMaf off\ visibility pack\ xGen_Research_Probes_V1 IDT xGen V1 P bigBed IDT - xGen Exome Research Panel V1 Probes 0 1 100 143 255 177 199 255 0 0 0 map 1 bigDataUrl /gbdb/hg38/exomeProbesets/xgen-exome-research-panel-probes-hg38.bb\ color 100,143,255\ longLabel IDT - xGen Exome Research Panel V1 Probes\ parent exomeProbesets off\ shortLabel IDT xGen V1 P\ track xGen_Research_Probes_V1\ type bigBed\ jarvis JARVIS bigWig JARVIS: score to prioritize non-coding regions for disease relevance 1 1 150 130 160 202 192 207 0 0 0

Description

\ \

\ The "Constraint scores" container track includes several subtracks showing the results of\ constraint prediction algorithms. These try to find regions of negative\ selection, where variations likely have functional impact. The algorithms do\ not use multi-species alignments to derive evolutionary constraint, but use\ primarily human variation, usually from variants collected by gnomAD (see the\ gnomAD V2 or V3 tracks on hg19 and hg38) or TOPMED (contained in our dbSNP\ tracks and available as a filter). One of the subtracks is based on UK Biobank\ variants, which are not available publicly, so we have no track with the raw data.\ The number of human genomes that are used as the input for these scores are\ 76k, 53k and 110k for gnomAD, TOPMED and UK Biobank, respectively.\

\ \

Note that another important constraint score, gnomAD\ constraint, is not part of this container track but can be found in the hg38 gnomAD\ track.\

\ \ The algorithms included in this track are:\

\ JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: \ JARVIS scores were created by first scanning the entire genome with a\ sliding-window approach (using a 1-nucleotide step), recording the number of\ all TOPMED variants and common variants, irrespective of their predicted effect,\ within each window, to eventually calculate a single-nucleotide resolution\ genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS\ was then combined with primary genomic sequence context, and additional genomic\ annotations with a multi-module deep learning framework to infer\ pathogenicity of noncoding regions that still remains naive to existing\ phylogenetic conservation metrics. The higher the score, the more deleterious\ the prediction. This score covers the entire genome, except the gaps.\ \
\ HMC - Homologous Missense Constraint:\ Homologous Missense Constraint (HMC) is a amino acid level measure\ of genetic intolerance of missense variants within human populations.\ For all assessable amino-acid positions in Pfam domains, the number of\ missense substitutions directly observed in gnomAD (Observed) was counted\ and compared to the expected value under a neutral evolution\ model (Expected). The upper limit of a 95% confidence interval for the\ Observed/Expected ratio is defined as the HMC score. Missense variants\ disrupting the amino-acid positions with HMC<0.8 are predicted to be\ likely deleterious. This score only covers PFAM domains within coding regions.\ \
\ MetaDome - Tolerance Landscape Score (hg19 only):\ MetaDome Tolerance Landscape scores are computed as a missense over synonymous \ variant count ratio, which is calculated in a sliding window (with a size of 21 \ codons/residues) to provide \ a per-position indication of regional tolerance to missense variation. The \ variant database was gnomAD and the score corrected for codon composition. Scores \ <0.7 are considered intolerant. This score covers only coding regions.\ \
\ MTR - Missense Tolerance Ratio (hg19 only):\ Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying \ selection acting specifically on missense variants in a given window of \ protein-coding sequence. It is estimated across sliding windows of 31 codons \ (default) and uses observed standing variation data from the WES component of \ gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores\ were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here\ is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), \ but this score only covers coding regions.\ \
\ UK Biobank depletion rank score (hg38 only):\ Halldorsson et al. tabulated the number of UK Biobank variants in each\ 500bp window of the genome and compared this number to an expected number\ given the heptamer nucleotide composition of the window and the fraction of\ heptamers with a sequence variant across the genome and their mutational\ classes. A variant depletion score was computed for every overlapping set\ of 500-bp windows in the genome with a 50-bp step size. They then assigned\ a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least\ depletion) for each 500-bp window. Since the windows are overlapping, we\ plot the value only in the central 50bp of the 500bp window, following\ advice from the author of the score,\ Hakon Jonsson, deCODE Genetics. He suggested that the value of the central\ window, rather than the worst possible score of all overlapping windows, is\ the most informative for a position. This score covers almost the entire genome,\ only very few regions were excluded, where the genome sequence had too many gap characters.

\ \

Display Conventions and Configuration

\ \

JARVIS

\ JARVIS scores are shown as a signal ("wiggle") track, with one score per genome position.\ Mousing over the bars displays the exact values. The scores were downloaded and converted to a single bigWig file.\ Move the mouse over the bars to display the exact values. A horizontal line is shown at the 0.733\ value which signifies the 90th percentile.

\ See hg19 makeDoc and\ hg38 makeDoc.

\ Interpretation: The authors offer a suggested guideline of > 0.9998 for identifying\ higher confidence calls and minimizing false positives. In addition to that strict threshold, the \ following two more relaxed cutoffs can be used to explore additional hits. Note that these\ thresholds are offered as guidelines and are not necessarily representative of pathogenicity.

\ \

\ \ \ \ \ \ \ \ \ \
Percentile JARVIS score threshold
99th 0.9998
95th 0.9826
90th 0.7338
\

Percentile	JARVIS score threshold
99th	0.9998
95th	0.9826
90th	0.7338

\ \

HMC

\ HMC scores are displayed as a signal ("wiggle") track, with one score per genome position.\ Mousing over the bars displays the exact values. The highly-constrained cutoff\ of 0.8 is indicated with a line.

\ Interpretation: \ A protein residue with HMC score <1 indicates that missense variants affecting\ the homologous residues are significantly under negative selection (P-value <\ 0.05) and likely to be deleterious. A more stringent score threshold of HMC<0.8\ is recommended to prioritize predicted disease-associated variants.\

\ \

MetaDome

\ MetaDome data can be found on two tracks, MetaDome and MetaDome All Data.\ The MetaDome track should be used by default for data exploration. In this track\ the raw data containing the MetaDome tolerance scores were converted into a signal ("wiggle")\ track. Since this data was computed on the proteome, there was a small amount of coordinate\ overlap, roughly 0.42%. In these regions the lowest possible score was chosen for display\ in the track to maintain sensitivity. For this reason, if a protein variant is being evaluated,\ the MetaDome All Data track can be used to validate the score. More information\ on this data can be found in the MetaDome FAQ.

\ Interpretation: The authors suggest the following guidelines for evaluating\ intolerance. By default, the MetaDome track displays a horizontal line at 0.7 which \ signifies the first intolerant bin. For more information see the MetaDome publication.

\ \

\ \ \ \ \ \ \ \ \ \
Classification MetaDome Tolerance Score
Highly intolerant ≤ 0.175
Intolerant ≤ 0.525
Slightly intolerant ≤ 0.7
\

Classification	MetaDome Tolerance Score
Highly intolerant	≤ 0.175
Intolerant	≤ 0.525
Slightly intolerant	≤ 0.7

\ \

MTR

\ MTR data can be found on two tracks, MTR All data and MTR Scores. In the\ MTR Scores track the data has been converted into 4 separate signal tracks\ representing each base pair mutation, with the lowest possible score shown when\ multiple transcripts overlap at a position. Overlaps can happen since this score\ is derived from transcripts and multiple transcripts can overlap. \ A horizontal line is drawn on the 0.8 score line\ to roughly represent the 25th percentile, meaning the items below may be of particular\ interest. It is recommended that the data be explored using\ this version of the track, as it condenses the information substantially while\ retaining the magnitude of the data.

\ \

Any specific point mutations of interest can then be researched in the \ MTR All data track. This track contains all of the information from\ \ MTRV2 including more than 3 possible scores per base when transcripts overlap.\ A mouse-over on this track shows the ref and alt allele, as well as the MTR score\ and the MTR score percentile. Filters are available for MTR score, False Discovery Rate\ (FDR), MTR percentile, and variant consequence. By default, only items in the bottom\ 25 percentile are shown. Items in the track are colored according\ to their MTR percentile:

Green items MTR percentiles over 75\
Black items MTR percentiles between 25 and 75\
Red items MTR percentiles below 25\
Blue items No MTR score\

\ Interpretation: Regions with low MTR scores were seen to be enriched with\ pathogenic variants. For example, ClinVar pathogenic variants were seen to\ have an average score of 0.77 whereas ClinVar benign variants had an average score\ of 0.92. Further validation using the FATHMM cancer-associated training dataset saw\ that scores less than 0.5 contained 8.6% of the pathogenic variants while only containing\ 0.9% of neutral variants. In summary, lower scores are more likely to represent\ pathogenic variants whereas higher scores could be pathogenic, but have a higher chance\ to be a false positive. For more information see the MTR-Viewer publication.

\ \

Methods

\ \

JARVIS

\ Scores were downloaded and converted to a single bigWig file. See the\ hg19 makeDoc and the\ hg38 makeDoc for more info.\

\ \

HMC

\ Scores were downloaded and converted to .bedGraph files with a custom Python \ script. The bedGraph files were then converted to bigWig files, as documented in our \ makeDoc hg19 build log.

\ \

MetaDome

\ The authors provided a bed file containing codon coordinates along with the scores. \ This file was parsed with a python script to create the two tracks. For the first track\ the scores were aggregated for each coordinate, then the lowest score chosen for any\ overlaps and the result written out to bedGraph format. The file was then converted\ to bigWig with the bedGraphToBigWig utility. For the second track the file\ was reorganized into a bed 4+3 and conveted to bigBed with the bedToBigBed\ utility.

\ See the hg19 makeDoc for details including the build script.

\ The raw MetaDome data can also be accessed via their Zenodo handle.

\ \

MTR

\ V2\ file was downloaded and columns were reshuffled as well as itemRgb added for the\ MTR All data track. For the MTR Scores track the file was parsed with a python\ script to pull out the highest possible MTR score for each of the 3 possible mutations\ at each base pair and 4 tracks built out of these values representing each mutation.

\ See the hg19 makeDoc entry on MTR for more info.

\ \

Data Access

\ \

\ For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed\ files that can be downloaded from\ our download server.\ Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig\ or bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\

\ bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/hmc/hmc.bw stdout\
\

\ \

\ Please refer to our\ Data Access FAQ\ for more information.\

\ \ \

Credits

\ \

\ Thanks to Jean-Madeleine Desainteagathe (APHP Paris, France) for suggesting the JARVIS, MTR, HMC tracks. Thanks to Xialei Zhang for providing the HMC data file and to Dimitrios Vitsios and Slave Petrovski for helping clean up the hg38 JARVIS files for providing guidance on interpretation. Additional\ thanks to Laurens van de Wiel for providing the MetaDome data as well as guidance on the track development and interpretation. \

\ \

References

\ \

\ Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S.\ \ Prioritizing non-coding regions based on human genomic constraint and sequence context with deep\ learning.\ Nat Commun. 2021 Mar 8;12(1):1504.\ PMID: 33686085; PMC: PMC7940646\

\ \

\ Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline F. Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware\ \ Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery.\ Medrxiv 2022.02.16.22271023\

\ \

\ Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C.\ \ MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein\ domains.\ Hum Mutat. 2019 Aug;40(8):1030-1038.\ PMID: 31116477; PMC: PMC6772141\

\ \

\ Silk M, Petrovski S, Ascher DB.\ \ MTR-Viewer: identifying regions within genes under purifying selection.\ Nucleic Acids Res. 2019 Jul 2;47(W1):W121-W126.\ PMID: 31170280; PMC: PMC6602522\

\ \

\ Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G,\ Hardarson MT, Oddsson A, Jensson BO et al.\ \ The sequences of 150,119 genomes in the UK Biobank.\ Nature. 2022 Jul;607(7920):732-740.\ PMID: 35859178; PMC: PMC9329122\

\ \ phenDis 0 bigDataUrl /gbdb/hg38/jarvis/jarvis.bw\ color 150,130,160\ group phenDis\ html constraintSuper\ longLabel JARVIS: score to prioritize non-coding regions for disease relevance\ maxHeightPixels 8:40:128\ maxWindowToDraw 10000000\ mouseOverFunction noAverage\ parent constraintSuper\ priority 1\ shortLabel JARVIS\ track jarvis\ type bigWig\ viewLimits 0.0:1.0\ visibility dense\ yLineMark 0.73\ yLineOnOff on\ jaspar2024 JASPAR 2024 TFBS bigBed 6 + JASPAR CORE 2024 - Predicted Transcription Factor Binding Sites 3 1 0 0 0 127 127 127 1 0 0 http://jaspar.genereg.net/search?q=$$&collection=all&tax_group=all&tax_id=all&type=all&class=all&family=all&version=all regulation 1 bigDataUrl /gbdb/hg38/jaspar/JASPAR2024.bb\ filter.score 400\ filterByRange.score 0:1000\ filterValues.TFName Ahr::Arnt,Alx1,ALX3,Alx4,Ar,ARGFX,Arid3a,Arid3b,Arid5a,Arnt,ARNT2,ARNT::HIF1A,Arntl,Arx,ASCL1,ASCL1,Ascl2,Atf1,ATF2,Atf3,ATF3,ATF4,ATF6,ATF7,Atoh1,Atoh1,ATOH7,BACH1,Bach1::Mafk,BACH2,BACH2,BARHL1,BARHL2,BARX1,BARX2,BATF,BATF3,BATF::JUN,BCL11A,Bcl11B,BCL6,BCL6B,Bhlha15,BHLHA15,BHLHE22,BHLHE22,BHLHE23,BHLHE40,BHLHE41,BNC2,BSX,CDX1,CDX2,CDX4,CEBPA,CEBPB,CEBPD,CEBPE,CEBPG,CEBPG,CLOCK,CREB1,CREB3,CREB3L1,Creb3l2,CREB3L4,CREB3L4,Creb5,CREM,Crx,CTCF,CTCF,CTCF,CTCFL,CUX1,CUX2,DBP,Ddit3::Cebpa,DLX1,Dlx2,Dlx3,Dlx4,Dlx5,DLX6,Dmbx1,Dmrt1,DMRT3,DMRTA1,DMRTA2,DMRTC2,DPRX,DRGX,Dux,DUX4,DUXA,E2F1,E2F2,E2F3,E2F4,E2F6,E2F7,E2F8,EBF1,Ebf2,EBF3,Ebf4,EGR1,EGR2,EGR3,EGR4,EHF,ELF1,ELF2,ELF3,ELF4,Elf5,ELK1,ELK1::HOXA1,ELK1::HOXB13,ELK1::SREBF2,ELK3,ELK4,EMX1,EMX2,EN1,EN2,EOMES,EPAS1,ERF,ERF::FIGLA,ERF::FOXI1,ERF::FOXO1,ERF::HOXB13,ERF::NHLH1,ERF::SREBF2,Erg,ESR1,ESR2,ESRRA,ESRRB,Esrrg,ESX1,ETS1,ETS2,ETV1,ETV2,ETV2::DRGX,ETV2::FIGLA,ETV2::FOXI1,ETV2::HOXB13,ETV3,ETV4,ETV5,ETV5::DRGX,ETV5::FIGLA,ETV5::FOXI1,ETV5::FOXO1,ETV5::HOXA2,ETV6,ETV7,EVX1,EVX2,EWSR1-FLI1,FERD3L,FEV,FEZF2,FIGLA,FLI1,FLI1::DRGX,FLI1::FOXI1,FOS,FOS,FOSB::JUN,FOSB::JUNB,FOSB::JUNB,FOS::JUN,FOS::JUN,FOS::JUNB,FOS::JUND,FOSL1,FOSL1::JUN,FOSL1::JUN,FOSL1::JUNB,FOSL1::JUND,FOSL1::JUND,FOSL2,FOSL2::JUN,FOSL2::JUN,FOSL2::JUNB,FOSL2::JUNB,FOSL2::JUND,FOSL2::JUND,FOXA1,FOXA2,FOXA3,FOXB1,FOXC1,FOXC2,FOXD1,FOXD2,FOXD3,FOXE1,Foxf1,FOXF2,FOXG1,FOXH1,FOXI1,Foxj2,FOXJ2::ELF1,Foxj3,FOXK1,FOXK2,FOXL1,Foxl2,Foxn1,FOXN3,Foxo1,FOXO1::ELF1,FOXO1::ELK1,FOXO1::ELK3,FOXO1::FLI1,Foxo3,FOXO4,FOXO6,FOXP1,FOXP2,FOXP3,FOXP4,Foxq1,FOXS1,GABPA,GATA1,GATA1::TAL1,GATA2,Gata3,GATA4,GATA5,GATA6,GBX1,GBX2,GCM1,GCM2,GFI1,Gfi1B,Gli1,Gli2,GLI3,GLIS1,GLIS2,GLIS3,Gmeb1,GMEB2,GRHL1,GRHL2,GSC,GSC2,GSX1,GSX2,Hand1,Hand1::Tcf3,HAND2,HES1,HES2,HES5,HES6,HES7,HESX1,HEY1,HEY2,Hic1,HIC2,HIF1A,HINFP,HLF,HMBOX1,Hmga1,Hmx1,Hmx2,Hmx3,Hnf1A,HNF1A,HNF1B,HNF4A,HNF4A,HNF4G,HOXA1,HOXA10,Hoxa11,Hoxa13,HOXA2,HOXA3,HOXA4,HOXA5,HOXA6,HOXA7,HOXA9,HOXB1,HOXB13,HOXB2,HOXB2::ELK1,HOXB3,HOXB4,HOXB5,HOXB6,HOXB7,HOXB8,HOXB9,HOXC10,HOXC11,HOXC12,HOXC13,HOXC4,HOXC8,HOXC9,HOXD10,HOXD11,HOXD12,HOXD12::ELK1,Hoxd13,HOXD3,HOXD4,HOXD8,HOXD9,HSF1,HSF2,HSF4,IKZF1,IKZF2,Ikzf3,INSM1,Irf1,IRF2,IRF3,IRF4,IRF5,IRF6,IRF7,IRF8,IRF9,Isl1,ISL2,ISX,JDP2,JDP2,Jun,JUN,JUNB,JUNB,JUND,JUND,JUN::JUNB,JUN::JUNB,KLF1,KLF10,KLF11,KLF12,KLF13,KLF14,KLF15,KLF16,KLF17,KLF2,KLF3,KLF4,KLF5,KLF6,KLF7,KLF9,LBX1,LBX2,Lef1,Lhx1,LHX2,Lhx3,Lhx4,LHX5,LHX6,Lhx8,LHX9,LIN54,LMX1A,LMX1B,MAF,MAFA,Mafb,MAFF,Mafg,MAFG::NFE2L1,MAFK,MAF::NFE2,MAX,MAX::MYC,MAZ,Mecom,MEF2A,MEF2B,MEF2C,MEF2D,MEIS1,MEIS1,MEIS2,MEIS2,MEIS3,MEOX1,MEOX2,MGA,MGA::EVX1,MITF,mix-a,MIXL1,MLX,Mlxip,MLXIPL,MNT,MNX1,MSANTD3,MSC,Msgn1,MSX1,MSX2,Msx3,MTF1,MXI1,MYB,MYBL1,MYBL2,MYC,MYCN,MYF5,MYF6,MYOD1,MYOG,MZF1,Nanog,NEUROD1,Neurod2,Neurod2,NEUROG1,NEUROG2,NEUROG2,Nfat5,Nfatc1,Nfatc2,NFATC3,NFATC4,NFE2,Nfe2l2,NFIA,NFIB,NFIC,NFIC,NFIC::TLX1,NFIL3,NFIX,NFIX,NFKB1,NFKB2,NFYA,NFYB,NFYC,NHLH1,NHLH2,Nkx2-1,NKX2-2,NKX2-3,NKX2-4,NKX2-5,NKX2-8,Nkx3-1,Nkx3-2,NKX6-1,NKX6-2,NKX6-3,Nobox,NOTO,Npas2,Npas4,NR1D1,NR1D2,Nr1H2,NR1H2::RXRA,Nr1h3,Nr1h3::Rxra,Nr1H4,NR1H4::RXRA,NR1I2,NR1I3,NR2C1,NR2C2,NR2C2,Nr2e1,Nr2e3,NR2F1,NR2F1,NR2F1,NR2F2,Nr2f6,Nr2F6,NR2F6,NR3C1,NR3C2,NR4A1,NR4A2,NR4A2::RXRA,NR5A1,Nr5A2,NR6A1,Nrf1,NRL,OLIG1,Olig2,OLIG2,OLIG3,ONECUT1,ONECUT2,ONECUT3,OSR1,OSR2,OTX1,OTX2,OVOL1,OVOL2,PATZ1,PAX1,PAX2,PAX3,PAX3,PAX4,PAX5,PAX6,Pax7,PAX8,PAX9,PBX1,PBX2,PBX3,PDX1,Pgr,PGR,PHOX2A,PHOX2B,PITX1,PITX2,PITX3,PKNOX1,PKNOX2,PLAG1,Plagl1,PLAGL2,POU1F1,POU2F1,POU2F1::SOX2,POU2F2,POU2F3,POU3F1,POU3F2,POU3F3,POU3F4,POU4F1,POU4F2,POU4F3,POU5F1,POU5F1B,Pou5f1::Sox2,POU6F1,POU6F1,POU6F2,Ppara,PPARA::RXRA,PPARD,PPARG,Pparg::Rxra,PRDM1,Prdm14,Prdm15,Prdm4,Prdm5,PRDM9,PROP1,PROX1,PRRX1,PRRX2,Ptf1A,Ptf1A,Ptf1A,RARA,RARA,RARA::RXRA,RARA::RXRG,Rarb,Rarb,RARB,Rarg,Rarg,RARG,RAX,RAX2,RBPJ,REL,RELA,RELB,REST,RFX1,RFX2,RFX3,RFX4,RFX5,Rfx6,RFX7,Rhox11,RHOXF1,RORA,RORA,RORB,RORC,RREB1,Runx1,RUNX2,RUNX3,Rxra,RXRA::VDR,RXRB,RXRB,RXRG,RXRG,SATB1,SCRT1,SCRT2,SHOX,Shox2,SIX1,SIX2,Six3,Six4,SMAD2,SMAD3,Smad4,SMAD5,SNAI1,SNAI2,SNAI3,SOHLH2,Sox1,SOX10,Sox11,SOX12,SOX13,SOX14,SOX15,Sox17,SOX18,SOX2,SOX21,Sox3,SOX4,Sox5,Sox6,Sox7,SOX8,SOX9,SP1,SP2,SP3,SP4,SP5,SP8,SP9,SPDEF,Spi1,SPIB,SPIC,Spz1,SREBF1,SREBF1,SREBF2,SREBF2,SRF,SRY,STAT1,STAT1::STAT2,Stat2,STAT3,Stat4,Stat5a,Stat5a::Stat5b,Stat5b,Stat6,TAL1::TCF3,TBP,TBR1,TBX1,TBX15,TBX18,TBX19,TBX2,TBX20,TBX21,TBX3,TBX4,TBX5,Tbx6,TBXT,Tcf12,TCF12,Tcf21,TCF21,TCF3,TCF4,TCF7,TCF7L1,TCF7L2,TCFL5,TEAD1,TEAD2,TEAD3,TEAD4,TEF,TFAP2A,TFAP2A,TFAP2A,TFAP2B,TFAP2B,TFAP2B,TFAP2C,TFAP2C,TFAP2C,TFAP2E,TFAP4,TFAP4,TFAP4::ETV1,TFAP4::FLI1,TFCP2,Tfcp2l1,TFDP1,TFE3,TFEB,TFEC,TGIF1,TGIF2,TGIF2LX,TGIF2LY,THAP1,Thap11,THRA,THRB,THRB,THRB,TLX2,TP53,TP63,TP73,TRPS1,TWIST1,Twist2,UNCX,USF1,USF2,VAX1,VAX2,Vdr,VENTX,VEZF1,VSX1,VSX2,Wt1,XBP1,Yy1,YY2,ZBED1,ZBED2,ZBED4,ZBTB11,ZBTB12,ZBTB14,ZBTB17,ZBTB18,Zbtb2,ZBTB24,ZBTB26,ZBTB32,ZBTB33,ZBTB6,ZBTB7A,ZBTB7B,ZBTB7C,ZEB1,ZFP14,Zfp335,ZFP42,ZFP57,Zfp809,Zfp961,Zfx,ZIC1,Zic1::Zic2,Zic2,Zic3,ZIC4,ZIC5,ZIM3,ZKSCAN1,ZKSCAN3,ZKSCAN5,ZNF135,ZNF136,ZNF140,ZNF143,ZNF148,ZNF157,ZNF16,ZNF175,ZNF184,ZNF189,ZNF211,ZNF213,ZNF214,ZNF24,ZNF257,ZNF263,ZNF274,ZNF281,ZNF282,ZNF317,ZNF320,ZNF324,ZNF331,ZNF341,ZNF343,ZNF35,ZNF354A,ZNF354C,ZNF382,ZNF384,ZNF410,ZNF416,ZNF417,ZNF418,Znf423,ZNF449,ZNF454,ZNF460,ZNF524,ZNF528,ZNF530,ZNF547,ZNF549,ZNF558,ZNF574,ZNF582,ZNF610,ZNF652,ZNF667,ZNF669,ZNF675,ZNF677,ZNF680,ZNF682,ZNF684,ZNF692,ZNF701,ZNF707,ZNF708,ZNF740,ZNF75A,ZNF75D,ZNF76,ZNF766,ZNF768,ZNF770,ZNF784,ZNF8,ZNF816,ZNF85,ZNF93,ZSCAN16,ZSCAN21,ZSCAN29,ZSCAN31,ZSCAN4\ labelFields TFName\ longLabel JASPAR CORE 2024 - Predicted Transcription Factor Binding Sites\ maxItems 100000\ motifPwmTable hgFixed.jasparCore2024\ parent jaspar on\ priority 1\ shortLabel JASPAR 2024 TFBS\ track jaspar2024\ type bigBed 6 +\ visibility pack\ wgEncodeRegDnaseUwK562Peak K562 Pk narrowPeak K562 lymphoblast chronic myeloid leukemia cell line DNaseI Peaks from ENCODE 1 1 255 85 85 255 170 170 1 0 0 regulation 1 color 255,85,85\ longLabel K562 lymphoblast chronic myeloid leukemia cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak on\ shortLabel K562 Pk\ subGroups view=a_Peaks cellType=K562 treatment=n_a tissue=bone_marrow cancer=cancer\ track wgEncodeRegDnaseUwK562Peak\ wgEncodeRegDnaseUwK562Wig K562 Sg bigWig 0 38914.2 K562 lymphoblast chronic myeloid leukemia cell line DNaseI Signal from ENCODE 0 1 255 85 85 255 170 170 0 0 0 regulation 1 color 255,85,85\ longLabel K562 lymphoblast chronic myeloid leukemia cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig on\ priority 1\ shortLabel K562 Sg\ subGroups cellType=K562 treatment=n_a tissue=bone_marrow cancer=cancer\ table wgEncodeRegDnaseUwK562Signal\ track wgEncodeRegDnaseUwK562Wig\ type bigWig 0 38914.2\ lovdShort LOVD Variants < 50 bp + ins bigBed 4 + LOVD: Leiden Open Variation Database, short < 50 bp variants and insertions of any length 0 1 0 0 0 127 127 127 0 0 0 phenDis 1 bigDataUrl /gbdb/hg38/lovd/lovd.hg38.short.bb\ group phenDis\ longLabel LOVD: Leiden Open Variation Database, short < 50 bp variants and insertions of any length\ noScoreFilter on\ parent lovdComp\ shortLabel LOVD Variants < 50 bp + ins\ track lovdShort\ urls id="https://varcache.lovd.nl/redirect/$$"\ visibility hide\ MaxCounts_Fwd Max counts of CAGE reads (fwd) bigWig Max counts of CAGE reads forward 2 1 255 0 0 255 127 127 0 0 0 regulation 0 bigDataUrl /gbdb/hg38/fantom5/ctssMaxCounts.fwd.bw\ color 255,0,0\ dataVersion FANTOM5 reprocessed7\ longLabel Max counts of CAGE reads forward\ parent Max_counts_multiwig\ shortLabel Max counts of CAGE reads (fwd)\ subGroups category=max strand=forward\ track MaxCounts_Fwd\ type bigWig\ hprc90way Multiple Alignment wigMaf 0.0 1.0 Multiple Alignment on 90 human genome assemblies 3 1 0 10 100 0 90 10 0 0 0

Description

\ This track shows multiple alignments of 90 human genomes generated by the Minigraph-Cactus\ pangenome pipeline, which creates pangenomes directly from whole-genome alignments. This method\ builds graphs containing all forms of genetic variation while allowing use of current mapping and\ genotyping tools.\

\ \

Display Conventions and Configuration

\ To view detailed information about the alignments at a specific\ position, zoom the display in to 30,000 or fewer bases, then click on\ the alignment.

\ \

Gap Annotation

Single line: No bases in the aligned species. Possibly due to a\ lineage-specific insertion between the aligned blocks in the human genome\ or a lineage-specific deletion between the aligned blocks in the aligning\ species.\
Double line: Aligning species has one or more unalignable bases in\ the gap region. Possibly due to excessive evolutionary distance between\ species or independent indels in the region between the aligned blocks in both\ species.\
Pale yellow coloring: Aligning species has Ns in the gap region.\ Reflects uncertainty in the relationship between the DNA of both species, due\ to lack of sequence in relevant portions of the aligning species.\

\ \

Genomic Breaks

\ Discontinuities in the genomic context (chromosome, scaffold or region) of the\ aligned DNA in the aligning species are shown as follows:\

\ Vertical blue bar: Represents a discontinuity that persists indefinitely\ on either side, e.g. a large region of DNA on either side of the bar\ comes from a different chromosome in the aligned species due to a large scale\ rearrangement.\
\ Green square brackets: Enclose shorter alignments consisting of DNA from\ one genomic context in the aligned species nested inside a larger chain of\ alignments from a different genomic context. The alignment within the\ brackets may represent a short misalignment, a lineage-specific insertion of a\ transposon in the human genome that aligns to a paralogous copy somewhere\ else in the aligned species, or other similar occurrence.\

\ \

Base Level

\ \

Methods

\ The MAF was obtained from the HPRC v1.0 minigraph-cactus HAL file (renamed\ to replace all "." characters in sample names with "#" using\ halRenameGenomes) using cactus v2.6.4 as follows.\

\
cactus-hal2maf ./js ./hprc-v1.0-mc-grch38.h\
al hprc-v1.0-mc-grch38.maf.gz --noAncestors --refGenome GRCh38\
--filterGapCausingDupes --chunkSize 100000 --batchCores 96 --batchCount 1\
0 --noAncestors --batchParallelTaf 32 --batchSystem slurm --logFile\
hprc-v1.0-mc-grch38.maf.gz.log\
\
zcat hprc-v1.0-mc-grch38.maf.gz | mafDuplicateFilter -m - -k | bgzip >\
hprc-v1.0-mc-grch38-single-copy.maf.gz

\ \

Credits

\ Thank you to Glenn Hickey for providing the HAL file from the HPRC project.\

\ \

References

\ Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ et\ al.\ \ A draft human pangenome reference.\ Nature. 2023 May;617(7960):312-324.\ DOI: 10.1038/s41586-023-05896-x; PMID: 37165242; PMC: PMC10172123\

\ \

\ Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium,\ Marschall T, Li H, Paten B.\ \ Pangenome graph construction from genome alignments with Minigraph-Cactus.\ Nat Biotechnol. 2023 May 10;.\ DOI: 10.1038/s41587-023-01793-w; PMID: 37165083; PMC: PMC10638906\

\ \

\ Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J\ et al.\ \ Progressive Cactus is a multiple-genome aligner for the thousand-genome era.\ Nature. 2020 Nov;587(7833):246-251.\ DOI: 10.1038/s41586-020-2871-y; PMID: 33177663; PMC: PMC7673649\

\ \

\ Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D.\ \ Cactus: Algorithms for genome multiple sequence alignment.\ Genome Res. 2011 Sep;21(9):1512-28.\ DOI: 10.1101/gr.123356.111;\ PMID: 21665927; PMC: PMC3166836\

\ hprc 1 altColor 0,90,10\ color 0, 10, 100\ irows on\ itemFirstCharCase noChange\ longLabel Multiple Alignment on 90 human genome assemblies\ mafDot on\ noInherit on\ parent consHprc90wayViewalign\ sGroup_Afr_Carib_Barabdos GCA_018466835.1 GCA_018466845.1 GCA_018466855.1 GCA_018466985.1 GCA_018467005.1 GCA_018467015.1 GCA_018467155.1 GCA_018467165.1 GCA_018505825.1 GCA_018505855.1 GCA_018505865.1 GCA_018506125.1 GCA_018852585.1 GCA_018852595.1\ sGroup_African_SW_USA GCA_018504625.1 GCA_018504635.1\ sGroup_Columbia_Medellin GCA_018469405.1 GCA_018469665.1 GCA_018469675.1 GCA_018469685.1 GCA_018469695.1 GCA_018469705.1 GCA_018469865.1 GCA_018469965.1\ sGroup_Esan_Nigeria GCA_018469415.1 GCA_018469425.1\ sGroup_Gambian GCA_018469875.1 GCA_018469925.1 GCA_018469935.1 GCA_018469945.1 GCA_018469955.1 GCA_018470425.1 GCA_018470435.1 GCA_018470445.1 GCA_018470455.1 GCA_018470465.1 GCA_018473295.1 GCA_018473315.1 GCA_018503575.1 GCA_018503585.1 GCA_018504065.1 GCA_018504075.1\ sGroup_HAPMAP GCA_018504655.1 GCA_018504665.1\ sGroup_Han_SoChina GCA_018471515.1 GCA_018472565.1 GCA_018472575.1 GCA_018472585.1 GCA_018472595.1 GCA_018472605.1\ sGroup_Mende_Sierra_Leone GCA_018472825.1 GCA_018472835.1 GCA_018472855.1 GCA_018473305.1 GCA_018503245.1 GCA_018503525.1 GCA_018506155.1 GCA_018506165.1\ sGroup_Peru_Lima GCA_018471525.1 GCA_018471535.1 GCA_018471545.1 GCA_018471555.1 GCA_018472695.1 GCA_018472705.1 GCA_018472845.1 GCA_018472865.1\ sGroup_Puerto_Rico GCA_018471065.1 GCA_018471075.1 GCA_018471085.1 GCA_018471095.1 GCA_018471105.1 GCA_018471345.1 GCA_018472685.1 GCA_018472715.1 GCA_018472725.1 GCA_018472765.1 GCA_018504045.1 GCA_018504365.1 GCA_018504375.1 GCA_018504645.1 GCA_018506955.1 GCA_018506975.1\ sGroup_Punjabo_Pakis GCA_018505835.1 GCA_018505845.1\ sGroup_T2T hs1\ sGroup_Vietnam_Kinh GCA_018504055.1 GCA_018504085.1\ sGroup_Yoruba_Nigeria GCA_018503255.1 GCA_018503285.1\ shortLabel Multiple Alignment\ speciesCodonDefault hg38\ speciesGroups T2T HAPMAP Yoruba_Nigeria Esan_Nigeria Gambian Mende_Sierra_Leone Afr_Carib_Barabdos African_SW_USA Puerto_Rico Peru_Lima Columbia_Medellin Han_SoChina Vietnam_Kinh Punjabo_Pakis\ speciesLabels GCA_018466835.1="HG02257.pat" GCA_018466845.1="HG02257.mat" GCA_018466855.1="HG02559.pat" GCA_018466985.1="HG02559.mat" GCA_018467005.1="HG02486.pat" GCA_018467015.1="HG02486.mat" GCA_018467155.1="HG01891.mat" GCA_018467165.1="HG01891.pat" GCA_018469405.1="HG01258.mat" GCA_018469415.1="HG03516.pat" GCA_018469425.1="HG03516.mat" GCA_018469665.1="HG01123.mat" GCA_018469675.1="HG01258.pat" GCA_018469685.1="HG01361.mat" GCA_018469695.1="HG01123.pat" GCA_018469705.1="HG01361.pat" GCA_018469865.1="HG01358.mat" GCA_018469875.1="HG02622.mat" GCA_018469925.1="HG02622.pat" GCA_018469935.1="HG02717.mat" GCA_018469945.1="HG02630.pat" GCA_018469955.1="HG02630.mat" GCA_018469965.1="HG01358.pat" GCA_018470425.1="HG02717.pat" GCA_018470435.1="HG02572.pat" GCA_018470445.1="HG02572.mat" GCA_018470455.1="HG02886.mat" GCA_018470465.1="HG02886.pat" GCA_018471065.1="HG01175.pat" GCA_018471075.1="HG01106.pat" GCA_018471085.1="HG01175.mat" GCA_018471095.1="HG00741.mat" GCA_018471105.1="HG00741.pat" GCA_018471345.1="HG01106.mat" GCA_018471515.1="HG00438.mat" GCA_018471525.1="HG02148.pat" GCA_018471535.1="HG02148.mat" GCA_018471545.1="HG01952.mat" GCA_018471555.1="HG01952.pat" GCA_018472565.1="HG00673.mat" GCA_018472575.1="HG00621.pat" GCA_018472585.1="HG00673.pat" GCA_018472595.1="HG00438.pat" GCA_018472605.1="HG00621.mat" GCA_018472685.1="HG01071.mat" GCA_018472695.1="HG01928.mat" GCA_018472705.1="HG01928.pat" GCA_018472715.1="HG00735.pat" GCA_018472725.1="HG01071.pat" GCA_018472765.1="HG00735.mat" GCA_018472825.1="HG03579.mat" GCA_018472835.1="HG03579.pat" GCA_018472845.1="HG01978.pat" GCA_018472855.1="HG03453.mat" GCA_018472865.1="HG01978.mat" GCA_018473295.1="HG03540.mat" GCA_018473305.1="HG03453.pat" GCA_018473315.1="HG03540.pat" GCA_018503245.1="HG03486.pat" GCA_018503255.1="NA18906.mat" GCA_018503285.1="NA18906.pat" GCA_018503525.1="HG03486.mat" GCA_018503575.1="HG02818.pat" GCA_018503585.1="HG02818.mat" GCA_018504045.1="HG01243.pat" GCA_018504055.1="HG02080.pat" GCA_018504065.1="HG02723.mat" GCA_018504075.1="HG02723.pat" GCA_018504085.1="HG02080.mat" GCA_018504365.1="HG01109.mat" GCA_018504375.1="HG01243.mat" GCA_018504625.1="NA20129.pat" GCA_018504635.1="NA20129.mat" GCA_018504645.1="HG01109.pat" GCA_018504655.1="NA21309.mat" GCA_018504665.1="NA21309.pat" GCA_018505825.1="HG02109.mat" GCA_018505835.1="HG03492.pat" GCA_018505845.1="HG03492.mat" GCA_018505855.1="HG02055.pat" GCA_018505865.1="HG02109.pat" GCA_018506125.1="HG02055.mat" GCA_018506155.1="HG03098.pat" GCA_018506165.1="HG03098.mat" GCA_018506955.1="HG00733.pat" GCA_018506975.1="HG00733.mat" GCA_018852585.1="HG02145.mat" GCA_018852595.1="HG02145.pat" hs1="T2T-CHM13v2.0"\ subGroups view=align\ summary hprc90waySummary\ track hprc90way\ treeImage phylo/hprc_90way.png\ type wigMaf 0.0 1.0\ viewUi on\ cons100wayViewalign Multiz Alignments bed 4 Vertebrate Multiz Alignment & Conservation (100 Species) 3 1 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Vertebrate Multiz Alignment & Conservation (100 Species)\ parent cons100way\ shortLabel Multiz Alignments\ track cons100wayViewalign\ view align\ viewUi on\ visibility pack\ cadd1_7_A Mutation: A bigWig CADD 1.7 Score: Mutation is A 1 1 100 130 160 177 192 207 0 0 0 phenDis 0 bigDataUrl /gbdb/hg38/cadd1.7/a.bw\ longLabel CADD 1.7 Score: Mutation is A\ maxHeightPixels 128:20:8\ parent cadd1_7 on\ shortLabel Mutation: A\ track cadd1_7_A\ type bigWig\ viewLimits 10:50\ viewLimitsMax 0:100\ visibility dense\ revelA Mutation: A bigWig REVEL: Mutation is A 1 1 150 80 200 202 167 227 0 0 0 phenDis 0 bigDataUrl /gbdb/hg38/revel/a.bw\ longLabel REVEL: Mutation is A\ maxHeightPixels 128:20:8\ maxWindowToDraw 10000000\ maxWindowToQuery 500000\ mouseOverFunction noAverage\ parent revel on\ shortLabel Mutation: A\ track revelA\ type bigWig\ viewLimits 0:1.0\ viewLimitsMax 0:1.0\ visibility dense\ caddA Mutation: A bigWig CADD 1.6 Score: Mutation is A 1 1 100 130 160 177 192 207 0 0 0 phenDis 0 bigDataUrl /gbdb/hg38/cadd/a.bw\ longLabel CADD 1.6 Score: Mutation is A\ maxHeightPixels 128:20:8\ parent cadd on\ shortLabel Mutation: A\ track caddA\ type bigWig\ viewLimits 10:50\ viewLimitsMax 0:100\ visibility dense\ omimContainer OMIM Online Mendelian Inheritance in Man 0 1 0 0 0 127 127 127 0 0 0

\ OMIM is a compendium of human genes and genetic phenotypes. The full-text, \ referenced overviews in OMIM contain information on all known Mendelian \ disorders and over 12,000 genes. OMIM is authored and edited at the McKusick-Nathans \ Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under \ the direction of Dr. Ada Hamosh. This database was initiated in the early 1960s \ by Dr. Victor A. McKusick as a catalog of Mendelian traits and disorders, \ entitled Mendelian Inheritance in Man (MIM).

\ \

\ The OMIM data are separated into three separate tracks:

\ \ OMIM Alellic Variant Phenotypes (OMIM Alleles) - Variants in the OMIM \ database that have associated dbSNP identifiers.

\ \ OMIM Gene Phenotypes (OMIM Genes) - The genomic positions of gene \ entries in the OMIM database. The coloring indicates the associated OMIM phenotype map key.

\ \ OMIM Cytogenetic Loci Phenotypes: Gene Unknown (OMIM Cyto Loci) - Regions \ known to be associated with a phenotype, but for which no specific gene is known \ to be causative. This track also includes known multi-gene syndromes.

\ \ Clicking into the individual tracks provides additional information including display conventions.\

\ phenDis 0 cartVersion 5\ group phenDis\ longLabel Online Mendelian Inheritance in Man\ priority 1\ shortLabel OMIM\ superTrack on show\ track omimContainer\ omimAvSnp OMIM Alleles bed 4 OMIM Allelic Variant Phenotypes 1 1 0 80 0 127 167 127 0 0 0 http://www.omim.org/entry/

Description

\ \

NOTE:
\ OMIM is intended for use primarily by physicians and other\ professionals concerned with genetic disorders, by genetics researchers, and\ by advanced students in science and medicine. While the OMIM database is\ open to the public, users seeking information about a personal medical or\ genetic condition are urged to consult with a qualified physician for\ diagnosis and for answers to personal questions. Further, please be\ sure to click through to omim.org for the very latest, as they are continually \ updating data.

\ \

NOTE ABOUT DOWNLOADS:
\ OMIM is the property \ of Johns Hopkins University and is not available for download or mirroring \ by any third party without their permission. Please see \ OMIM\ for downloads.

\ \ \

OMIM is a compendium of human genes and genetic phenotypes. The full-text,\ referenced overviews in OMIM contain information on all known Mendelian\ disorders and over 12,000 genes. OMIM is authored and edited at the\ McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University\ School of Medicine, under the direction of Dr. Ada Hamosh. This database\ was initiated in the early 1960s by Dr. Victor A. McKusick as a catalog\ of Mendelian traits and disorders, entitled Mendelian Inheritance\ in Man (MIM).\

\ \

\ The OMIM data are separated into three separate tracks:\

\ \

OMIM Alellic Variant Phenotypes (OMIM Alleles)\
Variants in the OMIM database that have associated \ dbSNP identifiers.\ \

OMIM Gene Phenotypes (OMIM Genes)\
The genomic positions of gene entries in the OMIM \ database. The coloring indicates the associated OMIM phenotype map key.\

\ \

OMIM Cytogenetic Loci Phenotypes - Gene Unknown (OMIM Cyto Loci)\
Regions known to be associated with a phenotype, \ but for which no specific gene is known to be causative. This track \ also includes known multi-gene syndromes.\

\ \

\ \ \

\ This track shows the allelic variants in the Online Mendelian Inheritance in Man\ (OMIM) database that have associated\ dbSNP identifiers.\

\ \

Display Conventions and Configuration

\ \

Genomic positions of OMIM allelic variants are marked by solid blocks, which appear\ as tick marks when zoomed out. \

The details page for each variant displays the allelic variant description, the amino\ acid replacement, and the associated\ dbSNP and/or\ ClinVar identifiers with links to the\ variant's details at those resources.\

The descriptions of OMIM entries are shown on the main browser display when Full display\ mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry.\

\ \

Methods

\ This track was constructed as follows: \

The OMIM allelic variant data file mimAV.txt was obtained from OMIM and\ loaded into the MySQL table omimAv.\
The genomic position for each allelic variant in omimAv with an associated\ dbSnp identifier was obtained from the snp151 table. The OMIM AV identifiers and\ their corresponding genomic positions from dbSNP were then loaded into the omimAvSnp\ table.\

\ \

Data Updates

\ This track is automatically updated once a week from OMIM data. The most recent update time is shown\ at the top of the track documentation page.\ \

Data Access

\ Because OMIM has only allowed Data queries within individual chromosomes, no download files are\ available from the Genome Browser. Full genome datasets can be downloaded directly from the\ OMIM Downloads page.\ All genome-wide downloads are freely available from OMIM after registration.

\ If you need the OMIM data in exactly the format of the UCSC Genome Browser,\ for example if you are running a UCSC Genome Browser local installation (a partial "mirror"),\ please create a user account on omim.org and contact OMIM via\ https://omim.org/contact. Send them your OMIM\ account name and request access to the UCSC Genome Browser 'entitlement'. They will\ then grant you access to a MySQL/MariaDB data dump that contains all UCSC\ Genome Browser OMIM tables.

\ UCSC offers queries within chromosomes from\ Table Browser that include a variety\ of filtering options and cross-referencing other datasets using our\ Data Integrator tool.\ UCSC also has an API\ that can be used to retrieve data in JSON format from a particular chromosome range.

\ Please refer to our searchable\ mailing list archives\ for more questions and example queries, or our\ Data Access FAQ\ for more information.

\ \

Credits

\ Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu,\ Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group.

\ \

References

\ Amberger J, Bocchini CA, Scott AF, Hamosh A.\ McKusick's Online Mendelian Inheritance in Man (OMIM).\ Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6.\ PMID: 18842627; PMC: PMC2686440\

\ \

\ Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA.\ \ Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic\ disorders.\ Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7.\ PMID: 15608251; PMC: PMC539987\

\ phenDis 1 color 0, 80, 0\ hgsid on\ longLabel OMIM Allelic Variant Phenotypes\ noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org\ parent omimContainer\ priority 1\ shortLabel OMIM Alleles\ tableBrowser noGenome omimAv omimAvRepl\ track omimAvSnp\ type bed 4\ url http://www.omim.org/entry/\ visibility dense\ panelAppCNVs PanelApp CNVs bigBed 9 + Genomics England PanelApp CNV Regions 3 1 0 0 0 127 127 127 0 0 0 phenDis 1 bigDataUrl /gbdb/hg38/panelApp/cnv.bb\ filterValues.confidenceLevel 3,2,1,0\ itemRgb on\ labelFields entityName\ longLabel Genomics England PanelApp CNV Regions\ parent panelApp on\ shortLabel PanelApp CNVs\ skipEmptyFields on\ skipFields chrom,chromStart,blockStarts,blockSizes\ track panelAppCNVs\ type bigBed 9 +\ urls omimGene="https://www.omim.org/entry/$$" panelID="https://panelapp.genomicsengland.co.uk/panels/$$/" entityName="https://panelapp.genomicsengland.co.uk/panels/entities/$$"\ visibility pack\ pHaplo pHaploinsufficiency bigBed 9 + 2 Probability of haploinsufficiency 3 1 0 0 0 127 127 127 0 0 0 https://www.deciphergenomics.org/search?q=$$ phenDis 1 bigDataUrl /gbdb/hg38/bbi/dosageSensitivityCollins2022/pHaploDosageSensitivity.bb\ filter.pHaplo 0\ filterByRange.pHaplo on\ filterLimits.pHaplo 0:1\ itemRgb on\ longLabel Probability of haploinsufficiency\ mouseOver $name, $ensGene, pHaplo:$pHaplo\ parent dosageSensitivity on\ shortLabel pHaploinsufficiency\ showCfg on\ track pHaplo\ type bigBed 9 + 2\ url https://www.deciphergenomics.org/search?q=$$\ urlLabel Link to DECIPHER\ visibility pack\ problematic Problematic Regions bigBed 3 + Problematic/special genomic regions for sequencing or very variable regions 3 1 0 0 0 127 127 127 0 0 0

Description

\ \

\ This container track helps call out sections of the genome that often cause problems or\ confusion when working with the genome. The hg19 genome has a track with the same name, but with\ many more subtracks, as the GeT-RM and Genome-in-a-Bottle artifact variants do not exist yet\ for hg38, to our knowledge. If you are missing a track here that you know from\ hg19 and have an idea how to add it hg38, do not hesitate to contact us.

\ \ \

Problematic Regions

\ The Problematic Regions track contains the following subtracks:\

\ The UCSC Unusual Regions subtrack contains annotations collected at UCSC, \ put together from other tracks, our experiences and support email list\ requests over the years. For example, it contains the most well-known gene\ clusters (IGH, IGL, PAR1/2, TCRA, TCRB, etc) and annotations for the GRC\ fixed sequences, alternate haplotypes, unplaced\ contigs, pseudo-autosomal regions, and mitochondria. These loci can yield alignments with\ low-quality mapping scores and discordant read pairs, especially for short-read sequencing data.\ This data set was manually curated, based on the Genome Browser's\ assembly description, the FAQs about assembly, and the\ NCBI RefSeq "other" annotations\ track data.\
\ The ENCODE Blacklist subtrack contains a comprehensive set of regions which are troublesome\ for high-throughput Next-Generation Sequencing (NGS) aligners. These regions tend to have a very\ high ratio of multi-mapping to unique mapping reads and high variance in mappability due to\ repetitive elements such as satellite, centromeric and telomeric repeats. \
\ The GRC Exclusions subtrack contains a set of regions that have been flagged by the GRC to\ contain false duplications or contamination sequences. The GRC has now removed these sequences from\ the files that it uses to generate the reference assembly, however, removing the sequences from the\ GRCh38/hg38 assembly would trigger the next major release of the human assembly. In order to\ help users recognize these regions and avoid them in their analyses, the GRC have produced a masking\ file to be used as a companion to GRCh38, and the BED file is available from the\ GenBank FTP site.\

\ \

Highly Reproducible Regions

\ The Highly Reproducible Regions track highlights regions and variants\ from eight samples that can be used to assess variant detection pipelines. The\ "Highly Reproducible Regions" subtrack comprises the intersection of the reproducible\ regions across all eight samples, while the "Variants" subtracks contain the reproducible\ variants from each assayed sample. Both tracks contain data from the following samples:\

a Chinese Quartet, samples CQ-5, CQ-6, CQ-7, CQ-8
a HapMap Trio, samples NA10385, NA12248, NA12249
a Genome in a Bottle sample, NA12878s

\ \ Please refer to the Pan et al reference for more information on how\ these regions were defined.\

\ \

GIAB Problematic Regions

The Genome in a Bottle (GIAB) Problematic Regions tracks provide stratifications of the\ genome to evaluate variant calls in complex regions. It is designed for use with Global Alliance\ for Genomic Health (GA4GH) benchmarking tools like\ hap.py\ and includes regions with low complexity, segmental duplications, functional regions,\ and difficult-to-sequence areas. Developed in collaboration with GA4GH, the\ Genome in a Bottle (GIAB) consortium, and the\ Telomere-to-Telomere Consortium (T2T), the dataset aims to standardize the\ analysis of genetic variation by offering pre-defined BED files for stratifying true and false\ positives in genomic studies, facilitating accurate assessments in complex areas of the genome.

\ \

\ The creation of the GIAB Problematic Regions tracks involves using a pipeline and configuration to\ generate stratification BED files that categorize genomic regions based on specific challenges,\ such as low complexity or difficult mapping, to facilitate accurate benchmarking of variant calls.\ For more information on the pipeline and configuration used, please visit the following webpage:\ \ https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/README.md.\ If you have questions or comments, please write to Justin Zook (jzook@nist.gov).

\ \ \ \

Display Conventions and Configuration

\ \

\ Each track contains a set of regions of varying length with no special configuration options. \ The UCSC Unusual Regions track has a mouse-over description, all other tracks have at most\ a name field, which can be shown in pack mode. The tracks are usually kept in dense mode.\

\ \

\ The Hide empty subtracks control hides subtracks with no data in the browser window.\ Changing the browser window by zooming or scrolling may result in the display of a different\ selection of tracks.\

\ \

Data access

\ The raw data can be explored interactively with the Table Browser\ or the Data Integrator.\ \

\ For automated download and analysis, the genome annotation is stored in bigBed files that\ can be downloaded from\ our download server.\ Individual\ regions or the whole genome annotation can be obtained using our tool bigBedToBed\ which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tool\ can also be used to obtain only features within a given range, e.g. \
\ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/problematic/comments.bb -chrom=chr21 -start=0 -end=100000000 stdout

\ \

Methods

\ \

\ Files were downloaded from the respective databases and converted to bigBed format.\ The procedure is documented in our\ hg38 makeDoc file.\

\ \

Credits

\ Thanks to Anna Benet-Pagès, Max Haeussler, Angie Hinrichs, Daniel Schmelter, and Jairo\ Navarro at the UCSC Genome Browser for planning, building, and testing these tracks. The\ underlying data comes from the\ ENCODE Blacklist and some parts were copied manually from the HGNC and NCBI\ RefSeq tracks.\

\ \

References

\ Amemiya HM, Kundaje A, Boyle AP.\ \ The ENCODE Blacklist: Identification of Problematic Regions of the Genome.\ Sci Rep. 2019 Jun 27;9(1):9354.\ PMID: 31249361; PMC: PMC6597582\

\ \

\ Dwarshuis N, Kalra D, McDaniel J, Sanio P, Alvarez Jerez P, Jadhav B, Huang WE, Mondal R, Busby B,\ Olson ND et al.\ \ The GIAB genomic stratifications resource for human reference genomes.\ Nat Commun. 2024 Oct 19;15(1):9029.\ PMID: 39424793; PMC: PMC11489684\

\ \

\ Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA,\ Tezak Z, Lababidi S et al.\ \ Best practices for benchmarking germline small-variant calls in human genomes.\ Nat Biotechnol. 2019 May;37(5):555-560.\ PMID: 30858580; PMC: PMC6699627\

\ \

\ Pan B, Ren L, Onuchic V, Guan M, Kusko R, Bruinsma S, Trigg L, Scherer A, Ning B, Zhang C et\ al.\ \ Assessing reproducibility of inherited variants detected with short-read whole genome\ sequencing.\ Genome Biol. 2022 Jan 3;23(1):2.\ PMID: 34980216; PMC: PMC8722114\

\ map 1 compositeTrack on\ hideEmptySubtracks off\ longLabel Problematic/special genomic regions for sequencing or very variable regions\ parent problematicSuper\ priority 1\ shortLabel Problematic Regions\ track problematic\ type bigBed 3 +\ visibility pack\ recombAvg Recomb. deCODE Avg bigWig Recombination rate: deCODE Genetics, average from paternal and maternal (mat for chrX) 2 1 0 130 0 127 192 127 0 0 0

Description

\ The recombination rate track represents calculated rates of recombination based\ on the genetic maps from deCODE (Halldorsson et al., 2019) and 1000 Genomes\ (2013 Phase 3 release, lifted from hg19). The deCODE map is more recent, has a higher \ resolution and was natively created on hg38 and therefore recommended. \ For the Recomb. deCODE average track, the recombination rates for chrX represent the female rate.\

\ \

This track also includes a subtrack with all the\ individual deCODE recombination events and another subtrack with several thousand\ de-novo mutations found in the deCODE sequencing data. These two tracks are hidden by\ default and have to be switched on explicitly on the configuration page.\

\ \

Display Conventions and Configuration

\ This is a super track that contains different subtracks, three with the deCODE\ recombination rates (paternal, maternal and average) and one with the 1000\ Genomes recombination rate (average). These tracks are in \ signal graph\ (wiggle) format. By default, to show most recombination hotspots, their maximum\ value is set to 100 cM, even though many regions have values higher than 100.\ The maximum value can be changed on the configuration pages of the tracks.\

\ \

\ There are two more tracks that show additional details provided by deCODE: one\ subtrack with the raw data of all cross-overs tagged with their proband ID and\ another one with around 8000 human de-novo mutation variants that are linked to\ cross-over changes.\

\ \

Methods

\ The deCODE genetic map was created at \ deCODE Genetics. It is based \ on microarrays assaying 626,828 SNP markers that allowed to identify 1,476,140 crossovers in\ 56,321 paternal meioses and 3,055,395 crossovers in 70,086 maternal meioses.\ In total, the data is based on 4,531,535 crossovers in 126,427 meioses. By\ using WGS data with 9,305,070 SNPs, the boundaries for 761,981 crossovers were\ refined: 247,942 crossovers in 9423 paternal meioses and 514,039 crossovers in\ 11,750 maternal meioses. The average resolution of the genetic map is 682 base\ pairs (bp): 655 and 708 bp for the paternal and maternal maps, respectively.\

\ \

The 1000 Genomes genetic map is based on the IMPUTE genetic map based on 1000 Genomes Phase 3, on hg19 coordinates. It\ was converted to hg38 by Po-Ru Loh at the Broad Institute. After a run of \ liftOver, he post-processed the data to deal with situations in which\ consecutive map locations became much closer/farther after lifting. The\ heuristic used is sufficient for statistical phasing but may not be optimal for\ other analyses. For this reason, and because of its higher resolution, the DeCODE\ map is therefore recommended for hg38.\

\ \

As with all other tracks, the data conversion commands and pointers to the\ original data files are documented in the \ makeDoc file of this track.

\ \

Data Access

\ \

\ For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed\ files that can be downloaded from\ our download server.\ Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig\ or bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\

\ bigWigToBedGraph -chrom=chr17 -start=45941345 -end=45942345 http://hgdownload.soe.ucsc.edu/gbdb/hg38/recombRate/recombAvg.bw stdout\
\

\ \

\ Please refer to our\ Data Access FAQ\ for more information.\

\ \

Credits

\ This track was produced at UCSC using data that are freely available for\ the deCODE\ and 1000 Genomes genetic maps. Thanks to Po-Ru Loh at the\ Broad Institute for providing the code to lift the hg19 1000 Genomes map data to hg38.\

\ \

References

\ 1000 Genomes Project Consortium., Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA,\ Hurles ME, McVean GA.\ \ A map of human genome variation from population-scale sequencing.\ Nature. 2010 Oct 28;467(7319):1061-73.\ PMID: 20981092; PMC: PMC3042601\

\ \

\ Halldorsson BV, Palsson G, Stefansson OA, Jonsson H, Hardarson MT, Eggertsson HP, Gunnarsson B,\ Oddsson A, Halldorsson GH, Zink F et al.\ \ Characterizing mutagenic effects of recombination through a sequence-level genetic map.\ Science. 2019 Jan 25;363(6425).\ PMID: 30679340\

\ map 0 bigDataUrl /gbdb/hg38/recombRate/recombAvg.bw\ html recombRate2.html\ longLabel Recombination rate: deCODE Genetics, average from paternal and maternal (mat for chrX)\ maxHeightPixels 128:60:8\ parent recombRate2\ priority 1\ shortLabel Recomb. deCODE Avg\ track recombAvg\ type bigWig\ viewLimits 0.0:100\ viewLimitsMax 0:150000\ visibility full\ ncbiRefSeq RefSeq All genePred NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) 1 1 12 12 120 133 133 187 0 0 0 genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ color 12,12,120\ idXref ncbiRefSeqLink mrnaAcc name\ longLabel NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*)\ parent refSeqComposite off\ priority 1\ shortLabel RefSeq All\ track ncbiRefSeq\ ReMapDensity ReMap density bigWig ReMap density 0 1 0 0 0 127 127 127 0 0 0

Description

\ This track represents the ReMap Atlas of regulatory regions, which consists of a\ large-scale integrative analysis of all Public ChIP-seq data for transcriptional\ regulators from GEO, ArrayExpress, and ENCODE. \

\ \

\ Below is a schematic diagram of the types of regulatory regions: \

ReMap 2022 Atlas (all peaks for each analyzed data set)
ReMap 2022 Non-redundant peaks (merged similar target)
ReMap 2022 Cis Regulatory Modules

\ \

Display Conventions and Configuration

\ Each transcription factor follows a specific RGB color.\
\ ChIP-seq peak summits are represented by vertical bars.\
\ Hsap: A data set is defined as a ChIP/Exo-seq experiment in a given\ GEO/ArrayExpress/ENCODE series (e.g. GSE41561), for a given TF (e.g. ESR1), in\ a particular biological condition (e.g. MCF-7).\
Data sets are labeled with the concatenation of these three pieces of\ information (e.g. GSE41561.ESR1.MCF-7).\
\ Atha: The data set is defined as a ChIP-seq experiment in a given series\ (e.g. GSE94486), for a given target (e.g. ARR1), in a particular biological\ condition (i.e. ecotype, tissue type, experimental conditions; e.g.\ Col-0_seedling_3d-6BA-4h).\
Data sets are labeled with the concatenation of these three pieces of\ information (e.g. GSE94486.ARR1.Col-0_seedling_3d-6BA-4h).\

\ \

Methods

\ This 4th release of ReMap (2022) presents the analysis of a total of 8,103 \ quality controlled ChIP-seq (n=7,895) and ChIP-exo (n=208) data sets from public\ sources (GEO, ArrayExpress, ENCODE). The ChIP-seq/exo data sets have been mapped\ to the GRCh38/hg38 human assembly. The data set is defined as a ChIP-seq \ experiment in a given series (e.g. GSE46237), for a given TF (e.g. NR2C2), in a\ particular biological condition (i.e. cell line, tissue type, disease state, or\ experimental conditions; e.g. HELA). Data sets were labeled by concatenating\ these three pieces of information, such as GSE46237.NR2C2.HELA. \ \

Those merged analyses cover a total of 1,211 DNA-binding proteins\ (transcriptional regulators) such as a variety of transcription factors (TFs),\ transcription co-activators (TCFs), and chromatin-remodeling factors (CRFs) for\ 182 million peaks. \

\ \

GEO & ArrayExpress

\ Public ChIP-seq data sets were extracted from Gene Expression Omnibus (GEO) and\ ArrayExpress (AE) databases. For GEO, the query\ \ '('chip seq' OR 'chipseq' OR\ 'chip sequencing') AND 'Genome binding/occupancy profiling by high throughput\ sequencing' AND 'homo sapiens'[organism] AND NOT 'ENCODE'[project]'\\ was used to return a list of all potential data sets to analyze, which were then manually \ assessed for further analyses. Data sets involving polymerases (i.e. Pol2 and\ Pol3), and some mutated or fused TFs (e.g. KAP1 N/C terminal mutation, GSE27929)\ were excluded.\

\ \

ENCODE

\ Available ENCODE ChIP-seq data sets for transcriptional regulators from the\ ENCODE portal were processed with the\ standardized ReMap pipeline. The list of ENCODE data was retrieved as FASTQ files from the\ ENCODE portal\ using the following filters:\

Assay: "ChIP-seq"
Organism: "Homo sapiens"
Target of assay: "transcription factor"
Available data: "fastq" on 2016 June 21st

\ Metadata information in JSON format and FASTQ files\ were retrieved using the Python requests module.\

\ \

ChIP-seq processing

\ Both Public and ENCODE data were processed similarly. Bowtie 2 (PMC3322381) (version 2.2.9) with options -end-to-end -sensitive was used to align all\ reads on the genome. Biological and technical\ replicates for each unique combination of GSE/TF/Cell type or Biological condition\ were used for peak calling. TFBS were identified using MACS2 peak-calling tool\ (PMC3120977) (version 2.1.1.2) in order to follow ENCODE ChIP-seq guidelines,\ with stringent thresholds (MACS2 default thresholds, p-value: 1e-5). An input data\ set was used when available.\

\ \ \

Quality assessment

\ To assess the quality of public data sets, a score was computed based on the\ cross-correlation and the FRiP (fraction of reads in peaks) metrics developed by\ the ENCODE Consortium (https://genome.ucsc.edu/ENCODE/qualityMetrics.html). Two\ thresholds were defined for each of the two cross-correlation ratios (NSC,\ normalized strand coefficient: 1.05 and 1.10; RSC, relative strand coefficient:\ 0.8 and 1.0). Detailed descriptions of the ENCODE quality coefficients can be\ found at https://genome.ucsc.edu/ENCODE/qualityMetrics.html. The\ phantompeak tools suite was used\ (https://code.google.com/p/phantompeakqualtools/) to compute\ RSC and NSC.\

\ Please refer to the ReMap 2022, 2020, and 2018 publications for more details\ (citation below).\

\ \ \ \

Data Access

\ ReMap Atlas of regulatory regions data can be explored interactively with the\ Table Browser and cross-referenced with the \ Data Integrator. For programmatic access,\ the track can be accessed using the Genome Browser's\ REST API.\ ReMap annotations can be downloaded from the\ Genome Browser's download server\ as a bigBed file. This compressed binary format can be remotely queried through\ command line utilities. Please note that some of the download files can be quite large.

\ \

\ Individual BED files for specific TFs, cells/biotypes, or data sets can be\ found and downloaded on the ReMap website.\

\ \

References

\ \

\ Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B.\ \ ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-\ seq experiments.\ Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275.\ PMID: 29126285; PMC: PMC5753247\

\ Chèneby J, Ménétrier Z, Mestdagh M, Rosnet T, Douida A, Rhalloussi W, Bergon A, Lopez\ F, Ballester B.\ \ ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis\ DNA-binding sequencing experiments.\ Nucleic Acids Res. 2020 Jan 8;48(D1):D180-D188.\ PMID: 31665499; PMC: PMC7145625\

\ Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B.\ \ Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory\ landscape.\ Nucleic Acids Res. 2015 Feb 27;43(4):e27.\ PMID: 25477382; PMC: PMC4344487\

\ Hammal F, de Langen P, Bergon A, Lopez F, Ballester B.\ \ ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an\ integrative analysis of DNA-binding sequencing experiments.\ Nucleic Acids Res. 2022 Jan 7;50(D1):D316-D325.\ PMID: 34751401; PMC: PMC8728178\

\ \ regulation 0 autoScale on\ bigDataUrl /gbdb/hg38/reMap/reMapDensity2022.bw\ html ../reMap\ longLabel ReMap density\ parent ReMap on\ priority 1\ shortLabel ReMap density\ track ReMapDensity\ type bigWig\ visibility hide\ rmsk RepeatMasker rmsk Repeating Elements by RepeatMasker 1 1 0 0 0 127 127 127 1 0 0

Description

\ \

\ This track was created by using Arian Smit's\ RepeatMasker\ program, which screens DNA sequences\ for interspersed repeats and low complexity DNA sequences. The program\ outputs a detailed annotation of the repeats that are present in the\ query sequence (represented by this track), as well as a modified version\ of the query sequence in which all the annotated repeats have been masked\ (generally available on the\ Downloads page). RepeatMasker uses the\ Repbase Update library of repeats from the\ Genetic \ Information Research Institute (GIRI).\ Repbase Update is described in Jurka (2000) in the References section below.

\ \

This track and the masking information in our \ hg38 genome download FASTA files was created in 2010 with the original RepBase library from 2010-03-02 and RepeatMasker 3.0.1.\ Since April 2019, RepBase is under a commercial license, we cannot distribute\ it or update the track using the RepBase library without a license. Therefore, and for\ compatibility with past results, given how central the masking is for many other\ annotations, we decided to not update the repeatmasking of hg38. However, you can show the\ small differences between the RepeatMasker 3/RepBase from 2010 and RepeatMasker 4/DFAM\ from 2020 using the track "RepeatMasker Viz" in the same track group. It\ contains two subtracks, one with the old and one with the new data. Also, these\ tracks have many more visusalisation options than the original RepeatMasker\ track.\

\ \

However, the last track update time of this track at UCSC is not 2010, because we had to add\ repeatmasking annotations to the rarely used _alt and _fix "patch" sequences of\ the hg38 genome. The repeatmasking annotations of the main chromosomes were unaffected\ and have not changed since 2010.\ For more information on genome patches, see our blog post.\

\ \

Display Conventions and Configuration

\ \

\ In full display mode, this track displays up to ten different classes of repeats:\

Short interspersed nuclear elements (SINE), which include ALUs
Long interspersed nuclear elements (LINE)
Long terminal repeat elements (LTR), which include retroposons
DNA repeat elements (DNA)
Simple repeats (micro-satellites)
Low complexity repeats
Satellite repeats
RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
Other repeats, which includes class RC (Rolling Circle)
Unknown

\ \

\ The level of color shading in the graphical display reflects the amount of\ base mismatch, base deletion, and base insertion associated with a repeat\ element. The higher the combined number of these, the lighter the shading.\

\ \

\ A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that\ the curator was unsure of the classification. At some point in the future,\ either the "?" will be removed or the classification will be changed.

\ \

Methods

\ \

\ Data are generated using the RepeatMasker -s flag. Additional flags\ may be used for certain organisms. Repeats are soft-masked. Alignments may\ extend through repeats, but are not permitted to initiate in them.\ See the FAQ for more information.\

\ \

Credits

\ \

\ Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and\ repeat libraries used to generate this track.\

\ \

References

\ \

\ Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0.\ \ http://www.repeatmasker.org. 1996-2010.\

\ \

\ Repbase Update is described in:\

\ \

\ Jurka J.\ \ Repbase Update: a database and an electronic journal of repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-420.\ PMID: 10973072\

\ \

\ For a discussion of repeats in mammalian genomes, see:\

\ \

\ Smit AF.\ \ Interspersed repeats and other mementos of transposable elements in mammalian genomes.\ Curr Opin Genet Dev. 1999 Dec;9(6):657-63.\ PMID: 10607616\

\ \

\ Smit AF.\ \ The origin of interspersed repeats in the human genome.\ Curr Opin Genet Dev. 1996 Dec;6(6):743-8.\ PMID: 8994846\

\ rep 0 canPack off\ group rep\ html rmsk\ longLabel Repeating Elements by RepeatMasker\ maxWindowToDraw 10000000\ priority 1\ shortLabel RepeatMasker\ spectrum on\ track rmsk\ type rmsk\ visibility dense\ miRnaAtlasSample1BarChart Sample 1 bigBarChart miRNA Tissue Atlas microRna Expression 2 1 0 0 0 127 127 127 0 0 0

Description

\ The Human miRNA Tissue Atlas is a\ catalog of tissue-specific microRNA (miRNA) expression across 62 tissues. This track contains\ quantile normalized miRNA expression data sampled from two individuals and mapped to\ miRBase v21 coordinates. The track contains two subtracks, one\ for each individual sampled.

\ \

\ The Tissue Specificity Index (TSI) is analogous to the "tau" value for mRNA expression,\ and is calculated as described in the\ \ associated publication. Values closer to 0 indicate miRNAs expressed in many or all tissues,\ while values closer to 1 indicate miRNAs expressed only in a specific tissue or tissues. To\ browse miRNAs by TSI value, please see the\ miRNA Tissue Atlas.

\ \

Display Conventions and Configuration

\ This track is formatted as a barChart track,\ similar to the GTEx or the\ TCGA Cancer Expression tracks, where the\ heights of each bar indicate the expression value for the miRNA in a specific tissue. The tissues\ sampled are described in the table below:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

Bar Color	Sample 1	Sample 2
	Adipocyte	Adipocyte
	Artery	Artery
	Colon	Colon
	Dura mater	Dura mater
	Kidney	Kidney
	Liver	Liver
	Lung	Lung
	Muscle	Muscle
	Myocardium	Myocardium
	Skin	Skin
	Spleen	Spleen
	Stomach	Stomach
	Testis	Testis
	Thyroid	Thyroid
	Small intestine
	Bone
	Gallbladder
	Fascia
	Bladder
	Epididymis
	Tunica albuginea
	Nervus intercostalis
	Arachnoid mater
	Brain
		Small intestine duodenum
		Small intestine jejunum
		Pancreas
		Kidney glandula suprarenalis
		Kidney cortex renalis
		Esophagus
		Prostate
		Bone marrow
		Vein
		Lymph node
		Nerve not specified
		Pleura
		Pituitary gland
		Spinal cord
		Thalamus
		Brain white matter
		Nucleus caudatus
		Kidney medulla renalis
		Brain gray_matter
		Cerebral cortex temporal
		Cerebral cortex frontal
		Cerebral cortex occipital
		Cerebellum

\ The 14 shared tissues sampled across both individuals are presented in the same order for easier comparison.\

\ \

Data Access

\ The underlying expression matrix and TSI values can be obtained from the\ miRNA tissue atlas website, in the\ data_matrix_quantile.txt and tsi_quantile.csv files.\

\ \

References

\ Ludwig N, Leidinger P, Becker K, Backes C, Fehlmann T, Pallasch C, Rheinheimer S, Meder B,\ Stähler C, Meese E et al.\ \ Distribution of miRNA expression across human tissues.\ Nucleic Acids Res. 2016 May 5;44(8):3865-77.\ PMID: 26921406; PMC: PMC4856985\

\ expression 1 barChartBars adipocyte artery colon dura_mater kidney liver lung muscle myocardium skin spleen stomach testis thyroid small_intestine bone gallbladder fascia bladder epididymis tunica_albuginea nerve_nervus_intercostalis arachnoid_mater brain\ barChartColors #F7A028 #F73528 #DEBE98 #86BF80 #CDB79E #CDB79E #9ACD32 #7A67AE #9745AC #1E90FF \\#CDB79E #FFD39B #A6A6A6 #008B45 #CDB79E #BD34D7 #CDA7FE #4C7CD7 #CBD79E #A6F6A1 \\#A6CEA4 #FFD700 #86BF10 #EEEE00\ barChartLabel Tissue\ barChartMatrixUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample1Matrix.txt\ barChartSampleUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample1.txt\ barChartUnit Quantile_Normalized_Expression\ bigDataUrl /gbdb/hg38/bbi/miRnaAtlasSample1.bb\ configurable on\ group expression\ html miRnaAtlas\ longLabel miRNA Tissue Atlas microRna Expression\ maxLimit 52000\ parent miRnaAtlasSample1\ searchIndex name\ shortLabel Sample 1\ subGroups view=a_A\ track miRnaAtlasSample1BarChart\ url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$\ url2Label miRBase v21 Precursor Accession:\ visibility full\ covidHgiGwasR4PvalA2 Severe COVID vars bigLolly 9 + Severe respiratory COVID risk variants from the COVID-19 HGI GWAS Analysis A2 (4336 cases, 12 studies, Rel 4: Oct 2020) 0 1 0 0 0 127 127 127 0 0 22 chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, phenDis 1 bigDataUrl /gbdb/hg38/covidHgiGwas/covidHgiGwasR4.A2.hg38.bb\ longLabel Severe respiratory COVID risk variants from the COVID-19 HGI GWAS Analysis A2 (4336 cases, 12 studies, Rel 4: Oct 2020)\ parent covidHgiGwasR4Pval on\ priority 1\ shortLabel Severe COVID vars\ track covidHgiGwasR4PvalA2\ snpediaAll SNPedia all bigBed 9 + SNPedia all SNPs (including empty pages) 0 1 50 0 100 152 127 177 0 0 0 https://www.snpedia.com/index.php/$$ phenDis 1 bigDataUrl /gbdb/hg38/bbi/snpediaAll.bb\ color 50,0,100\ exonNumbers off\ itemRgb on\ longLabel SNPedia all SNPs (including empty pages)\ mouseOverField note\ parent snpedia\ searchIndex name\ shortLabel SNPedia all\ track snpediaAll\ type bigBed 9 +\ url https://www.snpedia.com/index.php/$$\ urlLabel Link to SNPedia page:\ spliceAIsnvs SpliceAI SNVs bigBed 9 + SpliceAI SNVs (unmasked) 3 1 0 0 0 127 127 127 0 0 0

\ Important: The SpliceAI data on the UCSC Genome Browser is directly from \ Illumina (See Data Access below). However, since SpliceAI refers to the\ algorithm, and not the computed dataset, the data on the Broad server or other sources may have\ some differences between them.\

Description

\ SpliceAI is an open-source deep\ learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. \ Such variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms.\ SpliceAI was developed at Illumina; a \ lookup tool \ is provided by the Broad institute.\

Why are some variants not scored by SpliceAI?

\ SpliceAI only annotates variants within genes defined by the gene\ annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome\ ends (5kb on either side), deletions of length greater than twice the input parameter -D, or\ inconsistent with the reference fasta file.\

\ \

What are the differeneces between masked and unmasked tracks?

\ The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites\ and weakening unannotated splice sites, which are typically much less pathogenic than weakening\ annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing\ changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative\ splicing analysis and masked tracks for variant interpretation.\

\ \

Display Conventions and Interpretation

\ Variants are colored according to Walker et al. 2023 splicing imact:\

Predicted impact on splicing: Score >= 0.2
Not informative: Score < 0.2 and > 0.1
No impact on splicing: Score <= 0.1

\ Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor\ gain/loss), location of affected cryptic splice, and spliceAI score. Clicking on any item brings up\ a table with this information.\

\ The scores range from 0 to 1 and can be interpreted as the \ probability of the variant being splice-altering. In the paper, a detailed characterization is \ provided for 0.2 (high recall), 0.5 (recommended), and 0.8 (high precision) cutoffs.

\ \

Methods

\ The data were downloaded from Illumina. \ The spliceAI scores are represented in the VCF INFO field as \ SpliceAI=G|OR4F5|0.01|0.00|0.00|0.00|-32|49|-40|-31

\ Here, the pipe-separated fields contain \

ALT allele
Gene name
Acceptor gain score
Acceptor loss score
Donor gain score
Donor loss score
Relative location of affected cryptic acceptor
Relative location of affected acceptor
Relative location of affected cryptic donor
Relative location of affected donor

\ Since most of the values are 0 or almost 0, we selected only those variants \ with a score equal to or greater than 0.02.\

\ The complete processing of this track can be found in the \ makedoc.\

\ \ \

Data Access

\ These data are not available for download from the Genome Browser. \ The raw data can be found directly on\ Illumina. \ See below for a copy of the license restrictions pertaining to these data.\

\ \

License

\ FOR ACADEMIC AND NOT-FOR-PROFIT RESEARCH USE ONLY. The SpliceAI scores are \ made available by Illumina only for academic or not-for-profit research only. \ By accessing the SpliceAI data, you acknowledge and agree that you may only \ use this data for your own personal academic or not-for-profit research only, \ and not for any other purposes. You may not use this data for any for-profit, \ clinical, or other commercial purpose without obtaining a commercial license \ from Illumina, Inc.\

\ \

References

\ Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA,\ Arbelaez J, Cui W, Schwartz GB et al.\ \ Predicting Splicing from Primary Sequence with Deep Learning.\ Cell. 2019 Jan 24;176(3):535-548.e24.\ PMID: 30661751\

\ \

\ Walker LC, Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A,\ Tchourbanov A et al.\ \ Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on\ splicing: Recommendations from the ClinGen SVI Splicing Subgroup.\ Am J Hum Genet. 2023 Jul 6;110(7):1046-1067.\ PMID: 37352859; PMC: PMC10357475\

\ phenDis 1 bigDataUrl /gbdb/hg38/bbi/spliceAIsnvs.bb\ filter.AIscore 0.02\ filterLabel.spliceType Splice type\ filterLimits.AIscore 0.02:1\ filterValues.spliceType donor_gain|Donor gain,donor_loss|Donor loss,acceptor_gain|Acceptor gain,acceptor_loss|Acceptor loss\ html spliceAI\ itemRgb on\ longLabel SpliceAI SNVs (unmasked)\ mouseOver Change: $name
Gene: $gene
Type of change: $spliceType
Affected splice location: $relativePos
Score: $AIscore\ noScoreFilter on\ priority 1\ shortLabel SpliceAI SNVs\ superTrack spliceAI pack\ tableBrowser off\ track spliceAIsnvs\ type bigBed 9 +\ unipAliSwissprot SwissProt Aln. bigPsl UCSC alignment of SwissProt proteins to genome (dark blue: main isoform, light blue: alternative isoforms) 3 1 0 0 0 127 127 127 0 0 0 genes 1 baseColorDefault genomicCodons\ baseColorTickColor contrastingColor\ baseColorUseCds given\ bigDataUrl /gbdb/hg38/uniprot/unipAliSwissprot.bb\ indelDoubleInsert on\ indelQueryInsert on\ itemRgb on\ labelFields name,acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt\ longLabel UCSC alignment of SwissProt proteins to genome (dark blue: main isoform, light blue: alternative isoforms)\ mouseOverField protFullNames\ parent uniprot\ priority 1\ searchIndex name,acc\ shortLabel SwissProt Aln.\ showDiffBasesAllScales on\ skipFields isMain\ track unipAliSwissprot\ type bigPsl\ urls acc="https://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$" refSeqProt="https://www.ncbi.nlm.nih.gov/protein/$$" ncbiGene="https://www.ncbi.nlm.nih.gov/gene/$$" entrezGene="https://www.ncbi.nlm.nih.gov/gene/$$" ensGene="https://www.ensembl.org/Gene/Summary?g=$$"\ visibility pack\ TotalCounts_Fwd Total counts of CAGE reads (fwd) bigWig Total counts of CAGE reads forward 2 1 255 0 0 255 127 127 0 0 0 regulation 0 bigDataUrl /gbdb/hg38/fantom5/ctssTotalCounts.fwd.bw\ color 255,0,0\ dataVersion FANTOM5 reprocessed7\ longLabel Total counts of CAGE reads forward\ parent Total_counts_multiwig\ shortLabel Total counts of CAGE reads (fwd)\ subGroups category=total strand=forward\ track TotalCounts_Fwd\ type bigWig\ liftOverHg19 UCSC liftOver to hg19 chain hg19 UCSC liftOver alignments to hg19 0 1 0 0 0 127 127 127 0 0 0 map 1 chainLinearGap medium\ chainMinScore 3000\ longLabel UCSC liftOver alignments to hg19\ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb hg19\ parent liftHg19\ priority 1\ shortLabel UCSC liftOver to hg19\ track liftOverHg19\ type chain hg19\ comments UCSC Unusual Regions bigBed 9 + UCSC unusual regions on assembly structure (manually annotated) 1 1 0 0 0 127 127 127 0 0 0 map 1 bigDataUrl /gbdb/hg38/problematic/comments.bb\ longLabel UCSC unusual regions on assembly structure (manually annotated)\ mouseOverField note\ noScoreFilter on\ parent problematic\ priority 1\ searchIndex name\ searchTrix /gbdb/hg38/problematic/notes.ix\ shortLabel UCSC Unusual Regions\ track comments\ type bigBed 9 +\ visibility dense\ umap24 Umap S24 bigBed 6 Single-read mappability with 24-mers 4 1 80 20 240 167 137 247 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k24.Unique.Mappability.bb\ color 80,20,240\ longLabel Single-read mappability with 24-mers\ parent umapBigBed on\ priority 1\ shortLabel Umap S24\ subGroups view=SR\ track umap24\ lincRNAsAllCellTypeTopView lincRNA RNA-Seq bed 5 + lincRNA RNA-Seq reads expression abundances 1 1.1 0 0 0 127 127 127 0 0 0

Description

\ \

This track displays the Human Body Map lincRNAs (large intergenic non\ coding RNAs) and TUCPs (transcripts of uncertain coding potential), as well as their\ expression levels across 22 human tissues and cell lines. The Human Body Map catalog was generated\ by integrating previously existing annotation sources with transcripts that were de-novo assembled\ from RNA-Seq data. These transcripts were collected from ~4 billion RNA-Seq reads across 24 tissues \ and cell types.

\ \

Expression abundance was estimated by Cufflinks (Trapnell et al., 2010) based on RNA-Seq. \ Expression abundances were estimated on the gene locus level, rather than for each transcript \ separately and are given as raw FPKM. The prefixes tcons_ and tcons_l2_ are used to describe \ lincRNAs and TUCP transcripts, respectively. Specific details about the catalog generation and data \ sets used for this study can be found in Cabili et al (2011). Extended \ characterization of each transcript in the human body map catalog can be found at the Human lincRNA\ Catalog website.

\ \

Expression abundance scores range from 0 to 1000, and are displayed from light blue to dark blue\ respectively:

\ \ \

01000

\ \

Credits

\ \

The body map RNA-Seq data was kindly provided by the Gene Expression\ Applications research group at Illumina.

\ \

References

\ \

\ Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL.\ \ Integrative annotation of human large intergenic noncoding RNAs reveals global properties and\ specific subclasses.\ Genes Dev. 2011 Sep 15;25(18):1915-27.\ PMID: 21890647; PMC: PMC3185964\

\ \

\ Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter\ L.\ \ Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform\ switching during cell differentiation.\ Nat Biotechnol. 2010 May;28(5):511-5.\ PMID: 20436464; PMC: PMC3146043\

\ genes 1 compositeTrack on\ configurable on\ dimensions dimensionY=tissueType\ dragAndDrop subTracks\ html lincRNAs\ longLabel lincRNA RNA-Seq reads expression abundances\ noInherit on\ onlyVisibility dense\ origAssembly hg19\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ priority 1.1\ shortLabel lincRNA RNA-Seq\ sortOrder view=+ tissueType=+\ subGroup1 view Views lincRNAsRefseqExp=RefSeq_Expression_Ratio\ subGroup2 tissueType Tissue_Type adipose=Adipose adrenal=Adrenal brain=Brain brain_r=Brain_R breast=Breast colon=Colon foreskin_r=Foreskin_R heart=Heart hlf_r1=hLF_r1 hlf_r2=hLF_r2 kidney=Kidney liver=Liver lung=Lung lymphnode=LymphNode ovary=Ovary placenta_r=Placenta_R prostate=Prostate skeletalmuscle=SkeletalMuscle testes=Testes testes_r=Testes_R thyroid=Thyroid whitebloodcell=WhiteBloodCell\ superTrack nonCodingRNAs dense\ track lincRNAsAllCellTypeTopView\ type bed 5 +\ lincRNAsAllCellType lincRNAsCellType bed 5 + lincRNA RNA-Seq reads expression abundances 1 1.1 0 60 120 127 157 187 1 0 0 genes 1 color 0, 60, 120\ longLabel lincRNA RNA-Seq reads expression abundances\ origAssembly hg19\ parent lincRNAsAllCellTypeTopView\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel lincRNAsCellType\ track lincRNAsAllCellType\ useScore 1\ view lincRNAsRefseqExp\ visibility dense\ spliceAIindels SpliceAI indels bigBed 9 + SpliceAI Indels (unmasked) 1 1.1 0 0 0 127 127 127 0 0 0

\ Important: The SpliceAI data on the UCSC Genome Browser is directly from \ Illumina (See Data Access below). However, since SpliceAI refers to the\ algorithm, and not the computed dataset, the data on the Broad server or other sources may have\ some differences between them.\

Description

Why are some variants not scored by SpliceAI?

\ \

What are the differeneces between masked and unmasked tracks?

\ \

Display Conventions and Interpretation

\ Variants are colored according to Walker et al. 2023 splicing imact:\

Predicted impact on splicing: Score >= 0.2
Not informative: Score < 0.2 and > 0.1
No impact on splicing: Score <= 0.1

\ \

Methods

ALT allele
Gene name
Acceptor gain score
Acceptor loss score
Donor gain score
Donor loss score
Relative location of affected cryptic acceptor
Relative location of affected acceptor
Relative location of affected cryptic donor
Relative location of affected donor

\ Since most of the values are 0 or almost 0, we selected only those variants \ with a score equal to or greater than 0.02.\

\ The complete processing of this track can be found in the \ makedoc.\

\ \ \

Data Access

\ These data are not available for download from the Genome Browser. \ The raw data can be found directly on\ Illumina. \ See below for a copy of the license restrictions pertaining to these data.\

\ \

\ \

Display Conventions and Interpretation

\ Variants are colored according to Walker et al. 2023 splicing imact:\

Predicted impact on splicing: Score >= 0.2
Not informative: Score < 0.2 and > 0.1
No impact on splicing: Score <= 0.1

\ \

Methods

ALT allele
Gene name
Acceptor gain score
Acceptor loss score
Donor gain score
Donor loss score
Relative location of affected cryptic acceptor
Relative location of affected acceptor
Relative location of affected cryptic donor
Relative location of affected donor

\ Since most of the values are 0 or almost 0, we selected only those variants \ with a score equal to or greater than 0.02.\

\ The complete processing of this track can be found in the \ makedoc.\

\ \ \

Data Access

\ These data are not available for download from the Genome Browser. \ The raw data can be found directly on\ Illumina. \ See below for a copy of the license restrictions pertaining to these data.\

\ \

License

\ \

References

\ \

\ phenDis 1 bigDataUrl /gbdb/hg38/bbi/spliceAIsnvsMasked.bb\ filter.AIscore 0.02\ filterLabel.spliceType Splice type\ filterLimits.AIscore 0.02:1\ filterValues.spliceType donor_gain|Donor gain,donor_loss|Donor loss,acceptor_gain|Acceptor gain,acceptor_loss|Acceptor loss\ html spliceAI\ itemRgb on\ longLabel SpliceAI SNVs (masked)\ mouseOver Change: $name
Gene: $gene
Type of change: $spliceType
Affected splice location: $relativePos
Score: $AIscore\ noScoreFilter on\ priority 1.2\ shortLabel SpliceAI SNVs (masked)\ superTrack spliceAI hide\ tableBrowser off\ track spliceAIsnvsMasked\ type bigBed 9 +\ robustPeaks TSS peaks bigBed 8 + FANTOM5: DPI peak, robust set 1 1.2 0 0 0 127 127 127 0 0 0

Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells,\ cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the\ human body. 5′-end of the mapped CAGE reads are counted at a single base pair resolution\ (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the\ sample. Individual samples shown in "TSS activity" tracks are grouped as below.\

Primary cell
Tissue
Cell Line
Time course
Fractionation

TSS peaks

TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI\ (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of\ neighboring and related TSSs. The peaks are used as anchors to define promoters and units of\ promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read\ counts, depending on scopes of subsequent analyses, and the first subset (referred as a\ robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are\ named "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND"\ otherwise. The summary tracks consist of the TSS (CAGE) peaks and summary profiles of TSS\ activities (total and maximum values). The summary track consists of the following tracks.\

TSS (CAGE) peaks\
- the robust peaks
\
TSS summary profiles\
- Total counts and TPM (tags per million) in all the samples
- Maximum counts and TPM among the samples
\

\ \

TSS activity

\ 5′-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million).\

\ \

Categories of individual samples: - Cell Line hCAGE; - Cell Line LQhCAGE; - fractionation hCAGE; - Primary cell hCAGE; - Primary cell LQhCAGE; - Time course hCAGE; - Tissue hCAGE

\ \

Data Access

\ FANTOM5 data can be explored interactively with the\ Table Browser and cross-referenced with the \ Data Integrator. For programmatic access,\ the track can be accessed using the Genome Browser's\ REST API.\ ReMap annotations can be downloaded from the\ Genome Browser's download server\ as a bigBed file. This compressed binary format can be remotely queried through\ command line utilities. Please note that some of the download files can be quite large.

\ \

\ The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website.

\ \

Credits

\ \

\ Thanks to the FANTOM5 consortium,\ the Large Scale Data Managing Unit and Preventive Medicine and\ Applied Genomics Unit, the Center for Integrative Medical Sciences (IMS), and\ RIKEN for providing this data\ and its analysis.

\ \

References

\ FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de\ Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al.\ \ A promoter-level mammalian expression atlas.\ Nature. 2014 Mar 27;507(7493):462-70.\ PMID: 24670764; PMC: PMC4529748\

\ \

\ Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya\ N, Daub CO et al.\ \ Unamplified cap analysis of gene expression on a single-molecule sequencer.\ Genome Res. 2011 Jul;21(7):1150-9.\ PMID: 21596820; PMC: PMC3129257\

\ \

\ Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F,\ Ishikawa-Kato S et al.\ \ Gateways to the FANTOM5 promoter level mammalian expression atlas.\ Genome Biol. 2015 Jan 5;16(1):22.\ PMID: 25723102; PMC: PMC4310165\

\ \

Display Conventions and Interpretation

\ Variants are colored according to Walker et al. 2023 splicing imact:\

Predicted impact on splicing: Score >= 0.2
Not informative: Score < 0.2 and > 0.1
No impact on splicing: Score <= 0.1

\ \

Methods

ALT allele
Gene name
Acceptor gain score
Acceptor loss score
Donor gain score
Donor loss score
Relative location of affected cryptic acceptor
Relative location of affected acceptor
Relative location of affected cryptic donor
Relative location of affected donor

\ Since most of the values are 0 or almost 0, we selected only those variants \ with a score equal to or greater than 0.02.\

\ The complete processing of this track can be found in the \ makedoc.\

Methods

Protocol

hCAGE
LQhCAGE

Samples

Primary cell
Tissue
Cell Line
Time course
Fractionation

TSS peaks

TSS (CAGE) peaks\
- the robust peaks
\
TSS summary profiles\
- Total counts and TPM (tags per million) in all the samples
- Maximum counts and TPM among the samples
\

\ \

TSS activity

\ \

Categories of individual samples: - Cell Line hCAGE; - Cell Line LQhCAGE; - fractionation hCAGE; - Primary cell hCAGE; - Primary cell LQhCAGE; - Time course hCAGE; - Tissue hCAGE

\ \

Data Access

\ \

\ The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website.

\ \

Credits

\ \

References

\ \

\ regulation 0 aggregate transparentOverlay\ autoScale off\ configurable on\ container multiWig\ dataVersion FANTOM5 reprocessed7\ dragAndDrop subTracks\ html fantom5.html\ longLabel FANTOM5: Total counts of CAGE reads\ maxHeightPixels 64:64:11\ priority 1.3\ shortLabel Total counts of CAGE reads\ showSubtrackColorOnUi on\ subGroups group=counts\ superTrack fantom5 full\ track Total_counts_multiwig\ type bigWig 0 100\ viewLimits 0:100\ visibility full\ wgEncodeRegMarkH3k27ac Layered H3K27Ac bigWig 0 10000 H3K27Ac Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE 2 1.4 0 0 0 127 127 127 0 0 0

Description

\ Chemical modifications (e.g., methylation and acetylation) to the histone proteins\ present in chromatin influence gene expression by changing how\ accessible the chromatin is to transcription. A specific modification of\ a specific histone protein is called a histone mark.\ This track shows the levels of enrichment of the H3K27Ac histone mark across the genome as\ determined by a ChIP-seq assay. The H3K27Ac histone mark is the acetylation of lysine 27 of the H3\ histone protein, and it is thought to enhance transcription possibly by blocking the\ spread of the repressive histone mark H3K27Me3. Additional histone marks and other chromatin \ associated ChIP-seq data is available at the \ Broad Histone page.\

\ \

Display Conventions and Configuration

\ By default, this track uses a transparent overlay method of displaying data from a number of cell\ lines in the same vertical space. Each of the cell lines in this track\ is associated with a particular color, and these colors are relatively light and saturated so\ as to work best with the transparent overlay. The color of these tracks\ match their versions from their lifted source on the hg19 assembly. The colors are consistent with the \ other hg19 lifted tracks located in the ENCODE Regulation\ supertrack, with the exception being the DNase tracks, as they were not lifted from hg19 and are\ colored to reflect similarity of cell types. \

\ \

Credits

\ This track shows data from the Bernstein Lab at the Broad Institute, as part of\ the ENCODE Consortium.\

\ \

Data Release Policy

\ regulation 1 aggregate transparentOverlay\ allButtonPair on\ container multiWig\ dragAndDrop subtracks\ longLabel H3K27Ac Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE\ maxHeightPixels 100:30:11\ noInherit on\ origAssembly hg19\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ priority 1.4\ shortLabel Layered H3K27Ac\ showSubtrackColorOnUi on\ superTrack wgEncodeReg full\ track wgEncodeRegMarkH3k27ac\ type bigWig 0 10000\ viewLimits 0:100\ visibility full\ Max_counts_multiwig Max counts of CAGE reads bigWig 0 100 FANTOM5: Max counts of CAGE reads 2 1.4 0 0 0 127 127 127 0 0 0

Description

\ \

Display Conventions and Configuration

\ \

Items in this track are colored according to their strand orientation. Blue\ indicates alignment to the negative strand, and red indicates\ alignment to the positive strand.\

\ \

Methods

Protocol

hCAGE
LQhCAGE

Samples

Primary cell
Tissue
Cell Line
Time course
Fractionation

TSS peaks

TSS (CAGE) peaks\
- the robust peaks
\
TSS summary profiles\
- Total counts and TPM (tags per million) in all the samples
- Maximum counts and TPM among the samples
\

\ \

TSS activity

\ \

Categories of individual samples: - Cell Line hCAGE; - Cell Line LQhCAGE; - fractionation hCAGE; - Primary cell hCAGE; - Primary cell LQhCAGE; - Time course hCAGE; - Tissue hCAGE

\ \

Data Access

\ \

Methods

\ Raw sequence data files were processed by the UCSC ENCODE DNase analysis pipeline (July 2014\ specification), diagrammed here:\

\ \

\ Credit: Qian Alvin Qin, X. Liu lab\

\ \

\ Peaks of DNaseI hypersensitivity from the ENCODE DNase Analysis Pipeline at UCSC\ were assigned normalized scores (by UCSC regClusterMakeTableOfTables) in the range 0-1000 based\ on the \ narrowPeak\ signalValue and then clustered on score (by UCSC regCluster) to generate singly-linked clusters. \ Additional documentation on the methods used to identify hypersensitive sites are \ available from the\ DNaseI HS track.\

\ \

Credits

\ This track is based on sequence data from the University of Washington ENCODE group, \ with subsequent processing by UCSC.\ For additional credits and references, see the\ DNaseI HS track.\

\ regulation 1 controlledVocabulary cellType=wgEncodeCell treatment=wgEncodeTreatment\ group regulation\ html wgEncodeRegDnaseClustered\ inputTableFieldDisplay cellType treatment\ inputTrackTable wgEncodeRegDnaseClusteredInputs\ longLabel DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)\ priority 1.6\ scoreFilter 200\ scoreFilterLimits 1:1000\ shortLabel DNase Clusters\ sourceTable wgEncodeRegDnaseClusteredSources\ spectrum on\ superTrack wgEncodeReg hide\ track wgEncodeRegDnaseClustered\ type bed 5 .\ wgEncodeRegDnaseWig DNase Signal bigWig 0 10000 DNase I Hypersensitivity Signal Colored by Similarity from ENCODE 0 1.8 0 0 0 127 127 127 0 0 0

Description

\ This track provides an integrated display of DNase hypersensitivity in multiple\ cell types using overlapping colored graphs of signal density with graph colors\ assigned to cell types based on similarity of signal. The track is based on\ results of experiments performed by the John Stamatoyannapoulos lab at the\ University of Washington from September 2007 to January 2011 as part of the\ ENCODE project first production phase.

\ The signal graphs displayed here are also included in the comprehensive\ DNaseI HS track,\ which also provides peak and region calls and uses the same coloring based on\ similiarity of cell types (please note there is different coloring on the ENCODE hg38\ Transcription track,\ Layered H3K4Me1 track,\ Layered H3K4Me3 track, and\ Layered H3K27Ac track,\ which match the coloring used in their previous versions lifted from the hg19 assembly). \

\ \

Methods

\ Raw sequence data files were processed by the UCSC ENCODE DNase analysis pipeline\ described in the \ DNaseI HS\ track description.\ Signal graphs were normalized so the average value genome-wide is 1.\ Colors for the signal graphs were assigned by the UCSC BigWigCluster tool.\ \

\ The cell types were clustered into a binary tree, a rainbow was cast to the leaf nodes providing coloring based on similarity. \

\ Credit: Chris Eisenhart, J. Kent lab \

\ \

Credits

\ The processed data for this track were generated at UCSC.\ Credits for the primary data underlying this track are included in the\ DNaseI HS\ track description.\

\ \

References

\ Miga KH, Eisenhart C, Kent WJ.\ \ Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false\ positive alignments.\ Nucleic Acids Res. 2015 Nov 16;43(20):e133.\ PMID: 26163063\

\ Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang\ H, Vernot B et al.\ \ The accessible chromatin landscape of the human genome.\ Nature. 2012 Sep 6;489(7414):75-82.\ PMID: 22955617; PMC: PMC3721348\

\ \

\ See also the references in the\ DNaseI HS\ track.\

\ regulation 1 aggregate transparentOverlay\ configurable on\ container multiWig\ controlledVocabulary cellType=wgEncodeCell\ dimensions dimA=tissue dimB=cancer\ filterComposite dimA dimB\ group regulation\ html wgEncodeRegDnaseSignal\ longLabel DNase I Hypersensitivity Signal Colored by Similarity from ENCODE\ maxHeightPixels 128:64:11\ priority 1.8\ shortLabel DNase Signal\ showSubtrackColorOnUi on\ sortOrder subtrackColor=+ cellType=+ tissue=+\ subGroup1 cellType Cell_Type A549=A549 AG04449=AG04449 AG04450=AG04450 AG09309=AG09309 AG09319=AG09319 AG10803=AG10803 AoAF=AoAF bone_marrow_MSC=bone_marrow_MSC BE2_C=BE2_C BJ=BJ CD20_RO01778=CD20+_RO01778 Caco-2=Caco-2 GM04503=GM04503 GM04504=GM04504 GM06990=GM06990 GM12865=GM12865 GM12878=GM12878 H7-hESC=H7-hESC HA-h=HA-h HA-sp=HA-sp HAEpiC=HAEpiC HAc=HAc HBMEC=HBMEC HBVSMC=HBVSMC HCF=HCF HCFaa=HCFaa HCM=HCM HCPEpiC=HCPEpiC HCT-116=HCT-116 HConF=HConF HEEpiC=HEEpiC HFF-Myc=HFF-Myc HFF=HFF HGF=HGF HIPEpiC=HIPEpiC HL-60=HL-60 HMEC=HMEC HMF=HMF HMVEC-LBl=HMVEC-LBl HMVEC-LLy=HMVEC-LLy HMVEC-dAd=HMVEC-dAd HMVEC-dBl-Ad=HMVEC-dBl-Ad HMVEC-dBl-Neo=HMVEC-dBl-Neo HMVEC-dLy-Ad=HMVEC-dLy-Ad HMVEC-dLy-Neo=HMVEC-dLy-Neo HMVEC-dNeo=HMVEC-dNeo HNPCEpiC=HNPCEpiC HPAF=HPAF HPF=HPF HPdLF=HPdLF HRCEpiC=HRCEpiC HRE=HRE HRGEC=HRGEC HRPEpiC=HRPEpiC HSMM=HSMM HSMMtube=HSMMtube HUVEC=HUVEC HVMF=HVMF HeLa-S3=HeLa-S3 HepG2=HepG2 Jurkat=Jurkat K562=K562 LHCN-M2=LHCN-M2 LNCaP=LNCaP M059J=M059J MCF-7=MCF-7 Monocytes_CD14_RO01746=Monocytes-CD14+_RO01746 NB4=NB4 NH-A=NH-A NHBE_RA=NHBE_RA NHDF-Ad=NHDF-Ad NHDF-neo=NHDF-neo NHEK=NHEK NHLF=NHLF NT2-D1=NT2-D1 PANC-1=PANC-1 PrEC=PrEC RPMI-7951=RPMI-7951 RPTEC=RPTEC SAEC=SAEC SK-N-MC=SK-N-MC SK-N-SH_RA=SK-N-SH_RA SKMC=SKMC T-47D=T-47D Th1=Th1 Th1_Wb54553204=Th1_Wb54553204 Th2=Th2 WERI-Rb-1=WERI-Rb-1 WI-38=WI-38\ subGroup2 treatment Treatment diffProtA_5d=diffProtA_5d diffProtA_14d=diffProtA_14d DIFF_4d=DIFF_4d n_a=n/a 4OHTAM_20nM_72hr=4OHTAM_20nM_72hr Estradiol_ctrl_0hr=Estradiol_ctrl_0hr Estradiol_100nM_1hr=Estradiol_100nM_1hr\ subGroup3 tissue Tissue blood=blood blood_vessel=blood_vessel bone_marrow=bone_marrow brain=brain breast=breast cervix=cervix colon=colon embryo=embryo esophagus=esophagus eye=eye heart=heart kidney=kidney liver=liver lung=lung muscle=muscle pancreas=pancreas periodontium=periodontium periodontium=periodontium placenta=placenta prostate=prostate skin=skin spinal_cord=spinal_cord testis=testis\ subGroup4 cancer Cancer cancer=cancer normal=normal unknown=unknown\ subGroup5 subtrackColor Similarity\ superTrack wgEncodeReg hide\ track wgEncodeRegDnaseWig\ type bigWig 0 10000\ viewLimits 0:200\ visibility hide\ wgEncodeRegDnase DNase HS bed 3 + DNase I Hypersensitivity in 95 cell types from ENCODE 0 1.9 0 0 0 127 127 127 0 0 0

Description

\ These tracks contain the results of DNase I hypersensitivity experiments performed by the\ John Stamatoyannapoulos lab\ at the University of Washington from September 2007 to January 2011, as part of the\ ENCODE project first production phase.\ Colors were assigned to cell types based on similarity of signal.\

\ \

\ Other views of this data (along with additional documentation) are available from the hg19\ ENCODE UW DNaseI HS track.\

\ \

Display Conventions and Configuration

\ This track is a composite annotation track containing multiple subtracks, one for each cell type.\ The display mode and filtering of each subtrack can be individually controlled. \ For more information about track configuration, see\ Configuring Multi-View Tracks.\

\ \

Methods

\ Raw sequence data files were processed by the UCSC ENCODE DNase analysis pipeline (July 2014 specification), diagrammed here:\

\ Credit: Qian Alvin Qin, X. Liu lab\

\ Briefly, sequence files were aligned to the hg38 (GRCh38) genome assembly augmented with 'sponge'\ sequence (ref). Multi-mapped reads were removed, as were reads that aligned to 'sponge' or\ mitochondiral sequence. Results from all replicates were pooled, and further processed by\ the Hotspot program to call peaks as well as broader regions of activity ('hotspots'), and to\ create signal density graphs.\ Signal graphs were normalized so the average value genome-wide is 1.\

\ The cell types were clustered into a binary tree, a rainbow was cast to the leaf nodes providing coloring based on similarity.\

\ Credit: Chris Eisenhart, J. Kent lab \

\ (Please note there is different coloring on the ENCODE hg38\ Transcription track,\ Layered H3K4Me1 track,\ Layered H3K4Me3 track, and\ Layered H3K27Ac track,\ which match the coloring used in their previous versions lifted from the hg19 assembly).\

Credits

\ The processed data for this track were produced by UCSC. Credits for the primary data \ underlying this track are included in the\ ENCODE UW DNaseI HS track\ description.\

\ \

References

\ \

\ See also the references in the\ ENCODE UW DNaseI HS\ track.\

\ regulation 1 compositeTrack on\ controlledVocabulary cellType=wgEncodeCell\ dimensions dimA=cellType dimB=tissue dimC=cancer\ dragAndDrop subTracks\ filterComposite dimA dimB dimC\ group regulation\ html wgEncodeRegDnase\ longLabel DNase I Hypersensitivity in 95 cell types from ENCODE\ noInherit on\ priority 1.9\ shortLabel DNase HS\ showSubtrackColorOnUi on\ sortOrder view=+ subtrackColor=+ cellType=+ tissue=+\ subGroup1 view Views a_Peaks=Peaks b_Hot=Hotspots c_Signal=Signal\ subGroup2 cellType Cell_Type A549=A549 AG04449=AG04449 AG04450=AG04450 AG09309=AG09309 AG09319=AG09319 AG10803=AG10803 AoAF=AoAF bone_marrow_MSC=bone_marrow_MSC BE2_C=BE2_C BJ=BJ CD20_RO01778=CD20+_RO01778 Caco-2=Caco-2 GM04503=GM04503 GM04504=GM04504 GM06990=GM06990 GM12865=GM12865 GM12878=GM12878 H7-hESC=H7-hESC HA-h=HA-h HA-sp=HA-sp HAEpiC=HAEpiC HAc=HAc HBMEC=HBMEC HBVSMC=HBVSMC HCF=HCF HCFaa=HCFaa HCM=HCM HCPEpiC=HCPEpiC HCT-116=HCT-116 HConF=HConF HEEpiC=HEEpiC HFF-Myc=HFF-Myc HFF=HFF HGF=HGF HIPEpiC=HIPEpiC HL-60=HL-60 HMEC=HMEC HMF=HMF HMVEC-LBl=HMVEC-LBl HMVEC-LLy=HMVEC-LLy HMVEC-dAd=HMVEC-dAd HMVEC-dBl-Ad=HMVEC-dBl-Ad HMVEC-dBl-Neo=HMVEC-dBl-Neo HMVEC-dLy-Ad=HMVEC-dLy-Ad HMVEC-dLy-Neo=HMVEC-dLy-Neo HMVEC-dNeo=HMVEC-dNeo HNPCEpiC=HNPCEpiC HPAF=HPAF HPF=HPF HPdLF=HPdLF HRCEpiC=HRCEpiC HRE=HRE HRGEC=HRGEC HRPEpiC=HRPEpiC HSMM=HSMM HSMMtube=HSMMtube HUVEC=HUVEC HVMF=HVMF HeLa-S3=HeLa-S3 HepG2=HepG2 Jurkat=Jurkat K562=K562 LHCN-M2=LHCN-M2 LNCaP=LNCaP M059J=M059J MCF-7=MCF-7 Monocytes_CD14_RO01746=Monocytes-CD14+_RO01746 NB4=NB4 NH-A=NH-A NHBE_RA=NHBE_RA NHDF-Ad=NHDF-Ad NHDF-neo=NHDF-neo NHEK=NHEK NHLF=NHLF NT2-D1=NT2-D1 PANC-1=PANC-1 PrEC=PrEC RPMI-7951=RPMI-7951 RPTEC=RPTEC SAEC=SAEC SK-N-MC=SK-N-MC SK-N-SH_RA=SK-N-SH_RA SKMC=SKMC T-47D=T-47D Th1=Th1 Th1_Wb54553204=Th1_Wb54553204 Th2=Th2 WERI-Rb-1=WERI-Rb-1 WI-38=WI-38\ subGroup3 treatment Treatment diffProtA_5d=diffProtA_5d diffProtA_14d=diffProtA_14d DIFF_4d=DIFF_4d n_a=n/a OHTAM_20nM_72hr=4OHTAM_20nM_72hr Estradiol_ctrl_0hr=Estradiol_ctrl_0hr Estradiol_100nM_1hr=Estradiol_100nM_1hr\ subGroup4 tissue Tissue blood=blood blood_vessel=blood_vessel bone_marrow=bone_marrow brain=brain breast=breast cervix=cervix colon=colon embryo=embryo esophagus=esophagus eye=eye heart=heart kidney=kidney liver=liver lung=lung muscle=muscle pancreas=pancreas periodontium=periodontium periodontium=periodontium placenta=placenta prostate=prostate skin=skin spinal_cord=spinal_cord testis=testis\ subGroup5 cancer Cancer cancer=cancer normal=normal unknown=unknown\ subGroup6 subtrackColor Similarity\ superTrack wgEncodeReg hide\ track wgEncodeRegDnase\ type bed 3 +\ wgEncodeRegDnaseHotspot Hotspots bed 3 + Hotspot5 hotspot calls on BWA. Dupe, sponge and mitochondria filtered 0 1.9 0 0 0 127 127 127 1 0 0 regulation 1 longLabel Hotspot5 hotspot calls on BWA. Dupe, sponge and mitochondria filtered\ minGrayLevel 2\ parent wgEncodeRegDnase\ scoreFilter 0\ scoreFilterLimits 0:1000\ shortLabel Hotspots\ spectrum on\ track wgEncodeRegDnaseHotspot\ view b_Hot\ visibility hide\ wgEncodeRegDnasePeak Peaks narrowPeak HotSpot5 peak calls on BWA. Dupe, sponge and mitochondria filtered 1 1.9 0 0 0 127 127 127 1 0 0 regulation 1 longLabel HotSpot5 peak calls on BWA. Dupe, sponge and mitochondria filtered\ minGrayLevel 2\ parent wgEncodeRegDnase\ scoreFilter 0\ scoreFilterLimits 0:1000\ shortLabel Peaks\ spectrum on\ track wgEncodeRegDnasePeak\ type narrowPeak\ view a_Peaks\ visibility dense\ wgEncodeRegDnaseSignal Signal bed 3 + HotSpot5 signal on BWA. Dupe, sponge and mitochondria filtered 0 1.9 0 0 0 127 127 127 0 0 0

Description

\ \

Methods

\ The cell types were clustered into a binary tree, a rainbow was cast to the leaf nodes providing coloring based on similarity. \

\ Credit: Chris Eisenhart, J. Kent lab \

\ \

Credits

\ The processed data for this track were generated at UCSC.\ Credits for the primary data underlying this track are included in the\ DNaseI HS\ track description.\

\ \

\ regulation 1 dataVersion ENCODE 3 Nov 2018\ filterBy name:factor=AFF1,AGO1,AGO2,ARHGAP35,ARID1B,ARID2,ARID3A,ARNT,ASH1L,ASH2L,ATF2,ATF3,ATF4,ATF7,ATM,BACH1,BATF,BCL11A,BCL3,BCOR,BHLHE40,BMI1,BRCA1,BRD4,BRD9,C11orf30,CBFA2T2,CBFA2T3,CBFB,CBX1,CBX2,CBX3,CBX5,CBX8,CC2D1A,CCAR2,CDC5L,CEBPB,CHAMP1,CHD1,CHD4,CHD7,CLOCK,COPS2,CREB1,CREB3L1,CREBBP,CREM,CTBP1,CTCF,CUX1,DACH1,DEAF1,DNMT1,DPF2,E2F1,E2F4,E2F6,E2F7,E2F8,E4F1,EBF1,EED,EGR1,EHMT2,ELF1,ELF4,ELK1,EP300,EP400,ESR1,ESRRA,ETS1,ETV4,ETV6,EWSR1,EZH2,FIP1L1,FOS,FOSL1,FOSL2,FOXA1,FOXA2,FOXK2,FOXM1,FOXP1,FUS,GABPA,GABPB1,GATA1,GATA2,GATA3,GATA4,GATAD2A,GATAD2B,GMEB1,HCFC1,HDAC1,HDAC2,HDAC3,HDAC6,HES1,HMBOX1,HNF1A,HNF4A,HNF4G,HNRNPH1,HNRNPK,HNRNPL,HNRNPLL,HNRNPUL1,HSF1,IKZF1,IKZF2,IRF1,IRF2,IRF3,IRF4,IRF5,JUN,JUNB,JUND,KAT2A,KAT2B,KAT8,KDM1A,KDM4A,KDM4B,KDM5A,KDM5B,KLF16,KLF5,L3MBTL2,LCORL,LEF1,MAFF,MAFK,MAX,MBD2,MCM2,MCM3,MCM5,MCM7,MEF2A,MEF2B,MEF2C,MEIS2,MGA,MIER1,MITF,MLLT1,MNT,MTA1,MTA2,MTA3,MXI1,MYB,MYBL2,MYC,MYNN,NANOG,NBN,NCOA1,NCOA2,NCOA3,NCOA4,NCOA6,NCOR1,NEUROD1,NFATC1,NFATC3,NFE2,NFE2L2,NFIB,NFIC,NFRKB,NFXL1,NFYA,NFYB,NR0B1,NR2C1,NR2C2,NR2F1,NR2F2,NR2F6,NR3C1,NRF1,NUFIP1,PAX5,PAX8,PBX3,PCBP1,PCBP2,PHB2,PHF20,PHF21A,PHF8,PKNOX1,PLRG1,PML,POLR2A,POLR2G,POU2F2,PRDM10,PRPF4,PTBP1,PYGO2,RAD21,RAD51,RB1,RBBP5,RBFOX2,RBM14,RBM15,RBM17,RBM22,RBM25,RBM34,RBM39,RCOR1,RELB,REST,RFX1,RFX5,RLF,RNF2,RUNX1,RUNX3,RXRA,SAFB,SAFB2,SAP30,SETDB1,SIN3A,SIN3B,SIRT6,SIX4,SIX5,SKI,SKIL,SMAD1,SMAD2,SMAD5,SMARCA4,SMARCA5,SMARCB1,SMARCC2,SMARCE1,SMC3,SNRNP70,SOX13,SOX6,SP1,SPI1,SREBF1,SREBF2,SRF,SRSF4,SRSF7,SRSF9,STAT1,STAT2,STAT3,STAT5A,SUPT20H,SUZ12,TAF1,TAF15,TAF7,TAF9B,TAL1,TBL1XR1,TBP,TBX21,TBX3,TCF12,TCF7,TCF7L2,TEAD4,TFAP4,THAP1,THRA,TRIM22,TRIM24,TRIM28,TRIP13,U2AF1,U2AF2,UBTF,USF1,USF2,WHSC1,WRNIP1,XRCC3,XRCC5,YY1,ZBED1,ZBTB1,ZBTB11,ZBTB2,ZBTB33,ZBTB40,ZBTB5,ZBTB7A,ZBTB7B,ZBTB8A,ZEB1,ZEB2,ZFP91,ZFX,ZHX1,ZHX2,ZKSCAN1,ZMIZ1,ZMYM3,ZNF143,ZNF184,ZNF207,ZNF217,ZNF24,ZNF263,ZNF274,ZNF280A,ZNF282,ZNF316,ZNF318,ZNF384,ZNF407,ZNF444,ZNF507,ZNF512B,ZNF574,ZNF579,ZNF592,ZNF639,ZNF687,ZNF8,ZNF830,ZSCAN29,ZZZ3\ idInUrlSql select value from factorbookGeneAlias where name='%s'\ inputTableFieldDisplay cellType factor experiment lab\ inputTableFieldUrls experiment="https://www.encodeproject.org/experiments/$$"\ inputTrackTable encRegTfbsClusteredInputs\ longLabel Transcription Factor ChIP-seq Clusters (340 factors, 129 cell types) from ENCODE 3\ maxWindowToDraw 10000000\ parent wgEncodeReg\ priority 1.90\ shortLabel TF Clusters\ sourceTable encRegTfbsClusteredSources\ track encRegTfbsClustered\ type factorSource\ url http://www.factorbook.org/mediawiki/index.php/$$\ urlLabel Factorbook Link:\ useScore 1\ visibility hide\ encTfChipPk TF ChIP narrowPeak Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3 0 1.91 0 0 0 127 127 127 0 0 0

Description

\ This track represents a comprehensive set of human transcription factor binding sites based on \ ChIP-seq experiments generated by production groups in the ENCODE Consortium between \ February 2011 and November 2018.

\ Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE \ production laboratory(s) that generated the datasets used, as described in\ Citing ENCODE.

\ \ regulation 1 compositeTrack on\ darkerLabels on\ dataVersion ENCODE 3 Nov 2018\ dimensions dimX=cellType dimY=factor\ dragAndDrop subTracks\ group regulation\ longLabel Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3\ parent wgEncodeReg\ priority 1.91\ scoreFilter 0\ scoreFilterLimits 0:1000\ shortLabel TF ChIP\ sortOrder cellType=+ factor=+\ subGroup1 cellType Cell_Type X22Rv1=22Rv1 A549=A549 A673=A673 AG04449=AG04449 AG04450=AG04450 AG09309=AG09309 AG09319=AG09319 AG10803=AG10803 BE2C=BE2C BJ=BJ B_cell=B_cell C4-2B=C4-2B CD14-positive_monocyte=CD14-positive_monocyte Caco-2=Caco-2 DOHH2=DOHH2 GM06990=GM06990 GM08714=GM08714 GM10266=GM10266 GM12864=GM12864 GM12865=GM12865 GM12873=GM12873 GM12874=GM12874 GM12878=GM12878 GM12891=GM12891 GM12892=GM12892 GM13977=GM13977 GM20000=GM20000 GM23248=GM23248 GM23338=GM23338 H1-hESC=H1-hESC H54=H54 HCT116=HCT116 HEK293=HEK293 HEK293T=HEK293T HFF-Myc=HFF-Myc HL-60=HL-60 HeLa-S3=HeLa-S3 HepG2=HepG2 IMR-90=IMR-90 Ishikawa=Ishikawa K562=K562 KMS-11=KMS-11 LNCAP=LNCAP LNCaP_clone_FGC=LNCaP_clone_FGC Loucy=Loucy MCF-7=MCF-7 MCF_10A=MCF_10A MM_1S=MM.1S NB4=NB4 NCI-H929=NCI-H929 NT2_D1=NT2/D1 OCI-LY1=OCI-LY1 OCI-LY3=OCI-LY3 OCI-LY7=OCI-LY7 PC-3=PC-3 PC-9=PC-9 PFSK-1=PFSK-1 Panc1=Panc1 Parathyroid_adenoma=Parathyroid_adenoma Peyers_patch=Peyer's_patch RWPE1=RWPE1 RWPE2=RWPE2 Raji=Raji SH-SY5Y=SH-SY5Y SK-N-MC=SK-N-MC SK-N-SH=SK-N-SH SU-DHL-6=SU-DHL-6 T47D=T47D VCaP=VCaP WERI-Rb-1=WERI-Rb-1 WI38=WI38 adrenal_gland=adrenal_gland ascending_aorta=ascending_aorta astrocyte=astrocyte astrocyte_of_the_cerebellum=astrocyte_of_the_cerebellum astrocyte_of_the_spinal_cord=astrocyte_of_the_spinal_cord bipolar_neuron=bipolar_neuron body_of_pancreas=body_of_pancreas brain_microvascular_endothelial_cell=brain_microvascular_endothelial_cell breast_epithelium=breast_epithelium cardiac_fibroblast=cardiac_fibroblast cardiac_muscle_cell=cardiac_muscle_cell choroid_plexus_epithelial_cell=choroid_plexus_epithelial_cell endothelial_cell_of_umbilical_vein=endothelial_cell_of_umbilical_vein epithelial_cell_of_esophagus=epithelial_cell_of_esophagus epithelial_cell_of_prostate=epithelial_cell_of_prostate erythroblast=erythroblast esophagus_muscularis_mucosa=esophagus_muscularis_mucosa esophagus_squamous_epithelium=esophagus_squamous_epithelium fibroblast_of_lung=fibroblast_of_lung fibroblast_of_mammary_gland=fibroblast_of_mammary_gland fibroblast_of_pulmonary_artery=fibroblast_of_pulmonary_artery fibroblast_of_the_aortic_adventitia=fibroblast_of_the_aortic_adventitia fibroblast_of_villous_mesenchyme=fibroblast_of_villous_mesenchyme foreskin_fibroblast=foreskin_fibroblast foreskin_keratinocyte=foreskin_keratinocyte gastrocnemius_medialis=gastrocnemius_medialis gastroesophageal_sphincter=gastroesophageal_sphincter heart_left_ventricle=heart_left_ventricle hepatocyte=hepatocyte keratinocyte=keratinocyte kidney_epithelial_cell=kidney_epithelial_cell liver=liver lower_leg_skin=lower_leg_skin mammary_epithelial_cell=mammary_epithelial_cell medulloblastoma=medulloblastoma myotube=myotube neural_cell=neural_cell neural_progenitor_cell=neural_progenitor_cell neutrophil=neutrophil omental_fat_pad=omental_fat_pad ovary=ovary prostate_gland=prostate_gland retinal_pigment_epithelial_cell=retinal_pigment_epithelial_cell right_lobe_of_liver=right_lobe_of_liver sigmoid_colon=sigmoid_colon smooth_muscle_cell=smooth_muscle_cell spleen=spleen stomach=stomach subcutaneous_adipose_tissue=subcutaneous_adipose_tissue suprapubic_skin=suprapubic_skin testis=testis thyroid_gland=thyroid_gland tibial_artery=tibial_artery tibial_nerve=tibial_nerve transverse_colon=transverse_colon upper_lobe_of_left_lung=upper_lobe_of_left_lung uterus=uterus vagina=vagina\ subGroup2 factor Factor AFF1=AFF1 AGO1=AGO1 AGO2=AGO2 ARHGAP35=ARHGAP35 ARID1B=ARID1B ARID2=ARID2 ARID3A=ARID3A ARNT=ARNT ASH1L=ASH1L ASH2L=ASH2L ATF2=ATF2 ATF3=ATF3 ATF4=ATF4 ATF7=ATF7 ATM=ATM BACH1=BACH1 BATF=BATF BCL11A=BCL11A BCL3=BCL3 BCOR=BCOR BHLHE40=BHLHE40 BMI1=BMI1 BRCA1=BRCA1 BRD4=BRD4 BRD9=BRD9 C11orf30=C11orf30 CBFA2T2=CBFA2T2 CBFA2T3=CBFA2T3 CBFB=CBFB CBX1=CBX1 CBX2=CBX2 CBX3=CBX3 CBX5=CBX5 CBX8=CBX8 CC2D1A=CC2D1A CCAR2=CCAR2 CDC5L=CDC5L CEBPB=CEBPB CHAMP1=CHAMP1 CHD1=CHD1 CHD4=CHD4 CHD7=CHD7 CLOCK=CLOCK COPS2=COPS2 CREB1=CREB1 CREB3L1=CREB3L1 CREBBP=CREBBP CREM=CREM CTBP1=CTBP1 CTCF=CTCF CUX1=CUX1 DACH1=DACH1 DEAF1=DEAF1 DNMT1=DNMT1 DPF2=DPF2 E2F1=E2F1 E2F4=E2F4 E2F6=E2F6 E2F7=E2F7 E2F8=E2F8 E4F1=E4F1 EBF1=EBF1 EED=EED EGR1=EGR1 EHMT2=EHMT2 ELF1=ELF1 ELF4=ELF4 ELK1=ELK1 EP300=EP300 EP400=EP400 ESR1=ESR1 ESRRA=ESRRA ETS1=ETS1 ETV4=ETV4 ETV6=ETV6 EWSR1=EWSR1 EZH2=EZH2 FIP1L1=FIP1L1 FOS=FOS FOSL1=FOSL1 FOSL2=FOSL2 FOXA1=FOXA1 FOXA2=FOXA2 FOXK2=FOXK2 FOXM1=FOXM1 FOXP1=FOXP1 FUS=FUS GABPA=GABPA GABPB1=GABPB1 GATA1=GATA1 GATA2=GATA2 GATA3=GATA3 GATA4=GATA4 GATAD2A=GATAD2A GATAD2B=GATAD2B GMEB1=GMEB1 HCFC1=HCFC1 HDAC1=HDAC1 HDAC2=HDAC2 HDAC3=HDAC3 HDAC6=HDAC6 HES1=HES1 HMBOX1=HMBOX1 HNF1A=HNF1A HNF4A=HNF4A HNF4G=HNF4G HNRNPH1=HNRNPH1 HNRNPK=HNRNPK HNRNPL=HNRNPL HNRNPLL=HNRNPLL HNRNPUL1=HNRNPUL1 HSF1=HSF1 IKZF1=IKZF1 IKZF2=IKZF2 IRF1=IRF1 IRF2=IRF2 IRF3=IRF3 IRF4=IRF4 IRF5=IRF5 JUN=JUN JUNB=JUNB JUND=JUND KAT2A=KAT2A KAT2B=KAT2B KAT8=KAT8 KDM1A=KDM1A KDM4A=KDM4A KDM4B=KDM4B KDM5A=KDM5A KDM5B=KDM5B KLF16=KLF16 KLF5=KLF5 L3MBTL2=L3MBTL2 LCORL=LCORL LEF1=LEF1 MAFF=MAFF MAFK=MAFK MAX=MAX MBD2=MBD2 MCM2=MCM2 MCM3=MCM3 MCM5=MCM5 MCM7=MCM7 MEF2A=MEF2A MEF2B=MEF2B MEF2C=MEF2C MEIS2=MEIS2 MGA=MGA MIER1=MIER1 MITF=MITF MLLT1=MLLT1 MNT=MNT MTA1=MTA1 MTA2=MTA2 MTA3=MTA3 MXI1=MXI1 MYB=MYB MYBL2=MYBL2 MYC=MYC MYNN=MYNN NANOG=NANOG NBN=NBN NCOA1=NCOA1 NCOA2=NCOA2 NCOA3=NCOA3 NCOA4=NCOA4 NCOA6=NCOA6 NCOR1=NCOR1 NEUROD1=NEUROD1 NFATC1=NFATC1 NFATC3=NFATC3 NFE2=NFE2 NFE2L2=NFE2L2 NFIB=NFIB NFIC=NFIC NFRKB=NFRKB NFXL1=NFXL1 NFYA=NFYA NFYB=NFYB NR0B1=NR0B1 NR2C1=NR2C1 NR2C2=NR2C2 NR2F1=NR2F1 NR2F2=NR2F2 NR2F6=NR2F6 NR3C1=NR3C1 NRF1=NRF1 NUFIP1=NUFIP1 PAX5=PAX5 PAX8=PAX8 PBX3=PBX3 PCBP1=PCBP1 PCBP2=PCBP2 PHB2=PHB2 PHF20=PHF20 PHF21A=PHF21A PHF8=PHF8 PKNOX1=PKNOX1 PLRG1=PLRG1 PML=PML POLR2A=POLR2A POLR2G=POLR2G POU2F2=POU2F2 PRDM10=PRDM10 PRPF4=PRPF4 PTBP1=PTBP1 PYGO2=PYGO2 RAD21=RAD21 RAD51=RAD51 RB1=RB1 RBBP5=RBBP5 RBFOX2=RBFOX2 RBM14=RBM14 RBM15=RBM15 RBM17=RBM17 RBM22=RBM22 RBM25=RBM25 RBM34=RBM34 RBM39=RBM39 RCOR1=RCOR1 RELB=RELB REST=REST RFX1=RFX1 RFX5=RFX5 RLF=RLF RNF2=RNF2 RUNX1=RUNX1 RUNX3=RUNX3 RXRA=RXRA SAFB=SAFB SAFB2=SAFB2 SAP30=SAP30 SETDB1=SETDB1 SIN3A=SIN3A SIN3B=SIN3B SIRT6=SIRT6 SIX4=SIX4 SIX5=SIX5 SKI=SKI SKIL=SKIL SMAD1=SMAD1 SMAD2=SMAD2 SMAD5=SMAD5 SMARCA4=SMARCA4 SMARCA5=SMARCA5 SMARCB1=SMARCB1 SMARCC2=SMARCC2 SMARCE1=SMARCE1 SMC3=SMC3 SNRNP70=SNRNP70 SOX13=SOX13 SOX6=SOX6 SP1=SP1 SPI1=SPI1 SREBF1=SREBF1 SREBF2=SREBF2 SRF=SRF SRSF4=SRSF4 SRSF7=SRSF7 SRSF9=SRSF9 STAT1=STAT1 STAT2=STAT2 STAT3=STAT3 STAT5A=STAT5A SUPT20H=SUPT20H SUZ12=SUZ12 TAF1=TAF1 TAF15=TAF15 TAF7=TAF7 TAF9B=TAF9B TAL1=TAL1 TBL1XR1=TBL1XR1 TBP=TBP TBX21=TBX21 TBX3=TBX3 TCF12=TCF12 TCF7=TCF7 TCF7L2=TCF7L2 TEAD4=TEAD4 TFAP4=TFAP4 THAP1=THAP1 THRA=THRA TRIM22=TRIM22 TRIM24=TRIM24 TRIM28=TRIM28 TRIP13=TRIP13 U2AF1=U2AF1 U2AF2=U2AF2 UBTF=UBTF USF1=USF1 USF2=USF2 WHSC1=WHSC1 WRNIP1=WRNIP1 XRCC3=XRCC3 XRCC5=XRCC5 YY1=YY1 ZBED1=ZBED1 ZBTB1=ZBTB1 ZBTB11=ZBTB11 ZBTB2=ZBTB2 ZBTB33=ZBTB33 ZBTB40=ZBTB40 ZBTB5=ZBTB5 ZBTB7A=ZBTB7A ZBTB7B=ZBTB7B ZBTB8A=ZBTB8A ZEB1=ZEB1 ZEB2=ZEB2 ZFP91=ZFP91 ZFX=ZFX ZHX1=ZHX1 ZHX2=ZHX2 ZKSCAN1=ZKSCAN1 ZMIZ1=ZMIZ1 ZMYM3=ZMYM3 ZNF143=ZNF143 ZNF184=ZNF184 ZNF207=ZNF207 ZNF217=ZNF217 ZNF24=ZNF24 ZNF263=ZNF263 ZNF274=ZNF274 ZNF280A=ZNF280A ZNF282=ZNF282 ZNF316=ZNF316 ZNF318=ZNF318 ZNF384=ZNF384 ZNF407=ZNF407 ZNF444=ZNF444 ZNF507=ZNF507 ZNF512B=ZNF512B ZNF574=ZNF574 ZNF579=ZNF579 ZNF592=ZNF592 ZNF639=ZNF639 ZNF687=ZNF687 ZNF8=ZNF8 ZNF830=ZNF830 ZSCAN29=ZSCAN29 ZZZ3=ZZZ3\ track encTfChipPk\ type narrowPeak\ visibility hide\ netMonDom5 Opossum Net netAlign monDom5 chainMonDom5 Opossum (Oct. 2006 (Broad/monDom5)) Alignment Net 1 2 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Opossum (Oct. 2006 (Broad/monDom5)) Alignment Net\ otherDb monDom5\ parent vertebrateChainNetViewnet on\ shortLabel Opossum Net\ subGroups view=net species=s003 clade=c00\ track netMonDom5\ type netAlign monDom5 chainMonDom5\ netPanTro6 Chimp Net netAlign panTro6 chainPanTro6 Chimp (Jan. 2018 (Clint_PTRv2/panTro6)) Alignment Net 1 2 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Chimp (Jan. 2018 (Clint_PTRv2/panTro6)) Alignment Net\ otherDb panTro6\ parent primateChainNetViewnet off\ shortLabel Chimp Net\ subGroups view=net species=s0025 clade=c00\ track netPanTro6\ type netAlign panTro6 chainPanTro6\ netCriGriChoV2 Chinese hamster Net netAlign criGriChoV2 chainCriGriChoV2 Chinese hamster (Jun. 2017 (CHOK1S_HZDv1/criGriChoV2)) Alignment Net 1 2 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Chinese hamster (Jun. 2017 (CHOK1S_HZDv1/criGriChoV2)) Alignment Net\ otherDb criGriChoV2\ parent placentalChainNetViewnet off\ shortLabel Chinese hamster Net\ subGroups view=net species=s004b clade=c00\ track netCriGriChoV2\ type netAlign criGriChoV2 chainCriGriChoV2\ encTfChipPkENCFF093ZAB A549 BCL3 narrowPeak Transcription Factor ChIP-seq Peaks of BCL3 in A549 from ENCODE 3 (ENCFF093ZAB) 0 2 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of BCL3 in A549 from ENCODE 3 (ENCFF093ZAB)\ parent encTfChipPk off\ shortLabel A549 BCL3\ subGroups cellType=A549 factor=BCL3\ track encTfChipPkENCFF093ZAB\ wgEncodeRegDnaseUwA549Peak A549 Pk narrowPeak A549 lung adenocarcinoma cell line DNaseI Peaks from ENCODE 1 2 254 93 85 254 174 170 1 0 0 regulation 1 color 254,93,85\ longLabel A549 lung adenocarcinoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel A549 Pk\ subGroups view=a_Peaks cellType=A549 treatment=n_a tissue=lung cancer=cancer\ track wgEncodeRegDnaseUwA549Peak\ wgEncodeRegDnaseUwA549Wig A549 Sg bigWig 0 30091.1 A549 lung adenocarcinoma cell line DNaseI Signal from ENCODE 0 2 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel A549 lung adenocarcinoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.00887\ shortLabel A549 Sg\ subGroups cellType=A549 treatment=n_a tissue=lung cancer=cancer\ table wgEncodeRegDnaseUwA549Signal\ track wgEncodeRegDnaseUwA549Wig\ type bigWig 0 30091.1\ cloneEndABC11 ABC11 bed 12 Agencourt fosmid library 11 0 2 0 0 0 127 127 127 0 0 0 map 1 colorByStrand 0,0,128 0,128,0\ longLabel Agencourt fosmid library 11\ parent cloneEndSuper off\ priority 2\ shortLabel ABC11\ subGroups source=agencourt\ track cloneEndABC11\ type bed 12\ visibility hide\ ACC ACC bigLolly 12 + Adrenocortical carcinoma 0 2 0 0 0 127 127 127 0 0 0 phenDis 1 autoScale on\ bigDataUrl /gbdb/hg38/gdcCancer/ACC.bb\ configurable off\ group phenDis\ lollyField 13\ longLabel Adrenocortical carcinoma\ parent gdcCancer off\ priority 2\ shortLabel ACC\ track ACC\ type bigLolly 12 +\ urls case_id=https://portal.gdc.cancer.gov/cases/193294\ gtexCovAdiposeVisceralOmentum Adip Visc Om bigWig Adipose Visceral Omentum - GTEX-14BMU-0626-SM-73KZ6 0 2 238 154 0 246 204 127 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-14BMU-0626-SM-73KZ6.Adipose_Visceral_Omentum.RNAseq.bw\ color 238,154,0\ longLabel Adipose Visceral Omentum - GTEX-14BMU-0626-SM-73KZ6\ parent gtexCov\ shortLabel Adip Visc Om\ track gtexCovAdiposeVisceralOmentum\ lincRNAsCTAdrenal Adrenal bed 5 + lincRNAs from adrenal 1 2 0 60 120 127 157 187 1 0 0 genes 1 longLabel lincRNAs from adrenal\ origAssembly hg19\ parent lincRNAsAllCellType on\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel Adrenal\ subGroups view=lincRNAsRefseqExp tissueType=adrenal\ track lincRNAsCTAdrenal\ genetiSureCytoCgh4x180 Agilent GenetiSure Cyto CGH 4x180K bigBed 4 Agilent GenetiSure Cyto CGH 4x180K 085589 20200302 3 2 0 0 0 127 127 127 0 0 0 varRep 1 bigDataUrl /gbdb/hg38/snpCnvArrays/agilent/hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bb\ longLabel Agilent GenetiSure Cyto CGH 4x180K 085589 20200302\ parent genotypeArrays on\ priority 2\ shortLabel Agilent GenetiSure Cyto CGH 4x180K\ track genetiSureCytoCgh4x180\ type bigBed 4\ visibility pack\ AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_tpm_rev AorticSmsToFgf2_00hr00minBr1- bigWig Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_reverse 1 2 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12642-134G5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr00min%2c%20biol_rep1%20%28LK1%29.CNhs13339.12642-134G5.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12642-134G5 sequence_tech=hCAGE\ parent TSS_activity_TPM on\ shortLabel AorticSmsToFgf2_00hr00minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12642-134G5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_ctss_rev AorticSmsToFgf2_00hr00minBr1- bigWig Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_reverse 0 2 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12642-134G5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr00min%2c%20biol_rep1%20%28LK1%29.CNhs13339.12642-134G5.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12642-134G5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_00hr00minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12642-134G5\ urlLabel FANTOM5 Details:\ cons241wayViewphyloP Basewise Conservation (phyloP) bed 4 Cactus Alignment & Conservation of Zoonomia Placental Mammals (241 Species) 2 2 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Cactus Alignment & Conservation of Zoonomia Placental Mammals (241 Species)\ parent cons241way\ shortLabel Basewise Conservation (phyloP)\ track cons241wayViewphyloP\ view phyloP\ viewLimits -20.0:9.869\ viewLimitsMax -20:0.869\ visibility full\ iscaBenign Benign gvf ClinGen CNVs: Benign 3 2 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/?term=$$ phenDis 1 longLabel ClinGen CNVs: Benign\ parent iscaViewDetail off\ shortLabel Benign\ subGroups view=cnv class=ben level=sub\ track iscaBenign\ bismap36Pos Bismap S36 + bigBed 6 Single-read mappability with 36-mers after bisulfite conversion (forward strand) 0 2 240 70 80 247 162 167 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k36.C2T-Converted.bb\ color 240,70,80\ longLabel Single-read mappability with 36-mers after bisulfite conversion (forward strand)\ parent bismapBigBed off\ priority 2\ shortLabel Bismap S36 +\ subGroups view=SR\ track bismap36Pos\ visibility hide\ cons241way Cactus 241-way bed 4 Cactus Alignment & Conservation of Zoonomia Placental Mammals (241 Species) 0 2 0 0 0 127 127 127 0 0 0

\ Downloads for data in this track are available:\

\ Cactus alignments (MAF format), and phylogenetic trees, and PhyloP conservation (WIG and bigWig format)\

\ \

Description

\ \

Warning: Unlike other alignment tracks on the genome browser, this one does not show\ insertions in the query genomes. Also, all other alignment tracks show one query\ genome sequence for target target genome sequence, but in this track, each\ target genome sequence can be aligned to multiple query genome sequences.\ Only the first sequence is shown on the genome browser itself, the others are shown on the details page,\ when one clicks on the alignment. If you are interested in this track and want\ these shortcomings to be fixed, please contact us.\

\ \

\ This track shows multiple alignments of 241 vertebrate\ species and measurements of evolutionary conservation\ from the Zoonomia Project.\

\ \

\ The multiple alignments were generated using the\ Cactus comparative genomics alignment system.\ Cactus produces reference-free, whole-genome multiple alignments.\

\ \ \

\ The base-wise conservation scores are computed using phyloP from the\ PHAST package, for all species.\ This version was prepared by Michael Dong (Uppsala U) with an improved neutral\ model incorporating better versions of ancestral repeats.\

\ \

\ For genome assemblies not available in the genome browser, there are\ alternative assembly hub genome browsers. Missing sequence in any assembly is\ highlighted in the track display by regions of yellow when zoomed out and by\ Ns when displayed at base level (see Gap Annotation, below).

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
count common
name CLADE group scientific
name sequencing
source NCBI
assembly species
status
1 Cape golden mole AFROSORICIDA Chrysochloridae Chrysochloris asiatica 1. Zoonomia GCA_004027935.1 LC
2 Small madagascar hedgehog AFROSORICIDA Tenrecidae Echinops telfairi 2. Existing assembly GCF_000313985.1 LC
3 Talazac's shrew tenrec AFROSORICIDA Tenrecidae Microgale talazaci 1. Zoonomia GCA_004026705.1 LC
4 Cheetah CARNIVORA Felidae Acinonyx jubatus 2. Existing assembly GCF_001443585.1 CR
5 Giant panda CARNIVORA Ursidae Ailuropoda melanoleuca 2. Existing assembly GCA_002007445.1 VU
6 Lesser panda CARNIVORA Ailuridae Ailurus fulgens 2. Existing assembly GCA_002007465.1 EN
7 Domestic dog CARNIVORA Canidae Canis lupus familiaris 2. Existing assembly GCF_000002285.3 LC
8 Domestic dog (village dog) CARNIVORA Canidae Canis lupus familiaris 1. Zoonomia GCA_004027395.1 LC
9 Fossa CARNIVORA Eupleridae Cryptoprocta ferox 1. Zoonomia GCA_004023885.1 VU
10 Sea otter CARNIVORA Mustelidae Enhydra lutris 2. Existing assembly GCF_002288905.1 EN
11 Domestic cat CARNIVORA Felidae Felis catus 2. Existing assembly GCF_000181335.2 LC
12 Black-footed cat CARNIVORA Felidae Felis nigripes 1. Zoonomia GCA_004023925.1 VU
13 Dwarf mongoose CARNIVORA Herpestidae Helogale parvula 1. Zoonomia GCA_004023845.1 LC
14 Striped hyena CARNIVORA Hyaenidae Hyaena hyaena 1. Zoonomia GCA_004023945.1 NT
15 Weddell seal CARNIVORA Phocidae Leptonychotes weddellii 2. Existing assembly GCF_000349705.1 LC
16 African hunting dog CARNIVORA Canidae Lycaon pictus 2. Existing assembly GCA_001887905.1 EN
17 Honey badger CARNIVORA Mustelidae Mellivora capensis 1. Zoonomia GCA_004024625.1 LC
18 Northern elephant seal CARNIVORA Phocidae Mirounga angustirostris 1. Zoonomia GCA_004023865.1 LC
19 South African banded mongoose CARNIVORA Herpestidae Mungos mungo 1. Zoonomia GCA_004023785.1 LC
20 Domestic ferret CARNIVORA Mustelidae Mustela putorius 2. Existing assembly GCF_000239315.1 LC
21 Hawaiian monk seal CARNIVORA Phocidae Neomonachus schauinslandi 2. Existing assembly GCA_002201575.1 EN
22 Pacific walrus CARNIVORA Odobenidae Odobenus rosmarus 2. Existing assembly GCF_000321225.1 DD
23 Jaguar CARNIVORA Felidae Panthera onca 1. Zoonomia GCA_004023805.1 NT
24 Leopard CARNIVORA Felidae Panthera pardus 2. Existing assembly GCA_001857705.1 VU
25 Amur tiger CARNIVORA Felidae Panthera tigris 2. Existing assembly GCF_000464555.1 EN
26 Asian palm civet CARNIVORA Viverridae Paradoxurus hermaphroditus 1. Zoonomia GCA_004024585.1 LC
27 Giant otter CARNIVORA Mustelidae Pteronura brasiliensis 1. Zoonomia GCA_004024605.1 EN
28 Puma CARNIVORA Felidae Puma concolor 2. Existing assembly GCF_003327715.1 LC
29 Western spotted skunk CARNIVORA Mephitidae Spilogale gracilis 1. Zoonomia GCA_004023965.1 LC
30 Meerkat CARNIVORA Herpestidae Suricata suricatta 1. Zoonomia GCA_004023905.1 LC
31 Polar bear CARNIVORA Ursidae Ursus maritimus 2. Existing assembly GCF_000687225.1 VU
32 Arctic fox CARNIVORA Canidae Vulpes lagopus 1. Zoonomia GCA_004023825.1 LC
33 California sea lion CARNIVORA Otariidae Zalophus californianus 1. Zoonomia GCA_004024565.1 LC
34 Aoudad CETARTIODACTYLA Bovidae Ammotragus lervia 2. Existing assembly GCA_002201775.1 VU
35 Pronghorn CETARTIODACTYLA Antilocapridae Antilocapra americana 1. Zoonomia GCA_004027515.1 LC
36 Minke whale CETARTIODACTYLA Balaenopteridae Balaenoptera acutorostrata 2. Existing assembly GCF_000493695.1 LC
37 Antarctic minke whale CETARTIODACTYLA Balaenopteridae Balaenoptera bonaerensis 2. Existing assembly GCA_000978805.1 DD
38 Hirola CETARTIODACTYLA Bovidae Beatragus hunteri 1. Zoonomia GCA_004027495.1 CR
39 American bison CETARTIODACTYLA Bovidae Bison bison 2. Existing assembly GCF_000754665.1 NT
40 Zebu cattle CETARTIODACTYLA Bovidae Bos indicus 2. Existing assembly GCA_000247795.2 LC
41 Wild yak CETARTIODACTYLA Bovidae Bos mutus 2. Existing assembly GCF_000298355.1 VU
42 Cattle CETARTIODACTYLA Bovidae Bos taurus 2. Existing assembly GCF_000003205.7 LC
43 Water buffalo CETARTIODACTYLA Bovidae Bubalus bubalis 2. Existing assembly GCF_000471725.1 LC
44 Bactrian camel CETARTIODACTYLA Camelidae Camelus bactrianus 2. Existing assembly GCF_000767855.1 LC
45 Arabian camel CETARTIODACTYLA Camelidae Camelus dromedarius 2. Existing assembly GCF_000767585.1 LC
46 Wild bactrian camel CETARTIODACTYLA Camelidae Camelus ferus 2. Existing assembly GCF_000311805.1 CR
47 Wild goat CETARTIODACTYLA Bovidae Capra aegagrus 2. Existing assembly GCA_000978405.1 VU
48 Goat CETARTIODACTYLA Bovidae Capra hircus 2. Existing assembly GCF_001704415.1 LC
49 Chacoan peccary CETARTIODACTYLA Tayassuidae Catagonus wagneri 1. Zoonomia GCA_004024745.1 EN
50 Beluga whale CETARTIODACTYLA Monodontidae Delphinapterus leucas 2. Existing assembly GCF_002288925.1 LC
51 Pere david's deer CETARTIODACTYLA Cervidae Elaphurus davidianus 2. Existing assembly GCA_002443075.1 CR
52 Grey whale CETARTIODACTYLA Eschrichtiidae Eschrichtius robustus 1. Zoonomia GCA_004363415.1 LC
53 North Pacific right whale CETARTIODACTYLA Balaenidae Eubalaena japonica 1. Zoonomia GCA_004363455.1 EN
54 Giraffe CETARTIODACTYLA Giraffidae Giraffa tippelskirchi 2. Existing assembly GCA_001651235.1 VU
55 Nilgiri tahr CETARTIODACTYLA Bovidae Hemitragus hylocrius 1. Zoonomia GCA_004026825.1 EN
56 Hippopotamus CETARTIODACTYLA Hippopotamidae Hippopotamus amphibius 1. Zoonomia GCA_004027065.1 VU
57 Amazon river dolphin CETARTIODACTYLA Iniidae Inia geoffrensis 1. Zoonomia GCA_004363515.1 DD
58 Pygmy sperm whale CETARTIODACTYLA Physeteridae Kogia breviceps 1. Zoonomia GCA_004363705.1 DD
59 Yangtze river dolphin CETARTIODACTYLA Iniidae Lipotes vexillifer 2. Existing assembly GCF_000442215.1 CR
60 Sowerby's beaked whale CETARTIODACTYLA Ziphiidae Mesoplodon bidens 1. Zoonomia GCA_004027085.1 DD
61 Narwhal CETARTIODACTYLA Monodontidae Monodon monoceros 1. Zoonomia GCA_004026685.1 LC
62 Siberian musk deer CETARTIODACTYLA Moschidae Moschus moschiferus 1. Zoonomia GCA_004024705.1 VU
63 Yangtze finless porpoise CETARTIODACTYLA Phocoenidae Neophocaena asiaeorientalis 2. Existing assembly GCA_003031525.1 EN
64 White-tailed deer CETARTIODACTYLA Cervidae Odocoileus virginianus 2. Existing assembly GCA_002102435.1 LC
65 Okapi CETARTIODACTYLA Giraffidae Okapia johnstoni 2. Existing assembly GCA_001660835.1 EN
66 Killer whale CETARTIODACTYLA Delphinidae Orcinus orca 2. Existing assembly GCF_000331955.2 DD
67 Sheep CETARTIODACTYLA Bovidae Ovis aries 2. Existing assembly GCF_000298735.2 LC
68 Peninsular bighorn sheep CETARTIODACTYLA Bovidae Ovis canadensis cremnobates 1. Zoonomia GCA_004026945.1 EN
69 Chiru CETARTIODACTYLA Bovidae Pantholops hodgsonii 2. Existing assembly GCF_000400835.1 NT
70 Harbor porpoise CETARTIODACTYLA Phocoenidae Phocoena phocoena 1. Zoonomia GCA_004363495.1 LC
71 Indus river dolphin CETARTIODACTYLA Platanistidae Platanista gangetica minor 1. Zoonomia GCA_004363435.1 EN
72 Siberian reindeer CETARTIODACTYLA Cervidae Rangifer tarandus 1. Zoonomia GCA_004026565.1 VU
73 Russian saiga CETARTIODACTYLA Bovidae Saiga tatarica tatarica 1. Zoonomia GCA_004024985.1 CR
74 Pig CETARTIODACTYLA Suidae Sus scrofa 2. Existing assembly GCF_000003025.5 LC
75 Java lesser chevrotain CETARTIODACTYLA Tragulidae Tragulus javanicus 1. Zoonomia GCA_004024965.1 DD
76 Bottlenose dolphin CETARTIODACTYLA Delphinidae Tursiops truncatus 2. Existing assembly GCA_001922835.1 LC
77 Alpaca CETARTIODACTYLA Camelidae Vicugna pacos 2. Existing assembly GCA_000767525.1 LC
78 Cuvier's beaked whale CETARTIODACTYLA Ziphiidae Ziphius cavirostris 1. Zoonomia GCA_004364475.1 LC
79 Tailed tailless bat CHIROPTERA Phyllostomidae Anoura caudifer 1. Zoonomia GCA_004027475.1 LC
80 Jamacian fruit-eating bat CHIROPTERA Phyllostomidae Artibeus jamaicensis 1. Zoonomia GCA_004027435.1 LC
81 Seba's short-tailed bat CHIROPTERA Phyllostomidae Carollia perspicillata 1. Zoonomia GCA_004027735.1 LC
82 Bumblebee bat CHIROPTERA Craseonycteridae Craseonycteris thonglongyai 1. Zoonomia GCA_004027555.1 VU
83 Common vampire bat CHIROPTERA Phyllostomidae Desmodus rotundus 2. Existing assembly GCA_002940915.2 LC
84 Straw-colored fruit bat CHIROPTERA Pteropodidae Eidolon helvum 2. Existing assembly GCA_000465285.1 NT
85 Big brown bat CHIROPTERA Vespertilionidae Eptesicus fuscus 2. Existing assembly GCF_000308155.1 LC
86 Great roundleaf bat CHIROPTERA Hipposideridae Hipposideros armiger 2. Existing assembly GCA_001890085.1 LC
87 Cantor's leaf-nosed bat CHIROPTERA Hipposideridae Hipposideros galeritus 1. Zoonomia GCA_004027415.1 LC
88 Eastern red bat CHIROPTERA Vespertilionidae Lasiurus borealis 1. Zoonomia GCA_004026805.1 LC
89 Long-tongued fruit bat CHIROPTERA Pteropodidae Macroglossus sobrinus 1. Zoonomia GCA_004027375.1 LC
90 Greater false vampire bat CHIROPTERA Megadermatidae Megaderma lyra 1. Zoonomia GCA_004026885.1 LC
91 Hairy big-eared bat CHIROPTERA Phyllostomidae Micronycteris hirsuta 1. Zoonomia GCA_004026765.1 LC
92 Natal long-fingered bat CHIROPTERA Vespertilionidae Miniopterus natalensis 2. Existing assembly GCF_001595765.1 LC
93 Common bent-wing bat CHIROPTERA Vespertilionidae Miniopterus schreibersii 1. Zoonomia GCA_004026525.1 NT
94 Ghost-faced bat CHIROPTERA Mormoopidae Mormoops blainvillei 1. Zoonomia GCA_004026545.1 LC
95 Ashy-gray tube-nosed bat CHIROPTERA Vespertilionidae Murina feae 1. Zoonomia GCA_004026665.1 LC
96 Brandt's bat CHIROPTERA Vespertilionidae Myotis brandtii 2. Existing assembly GCF_000412655.1 LC
97 David's myotis bat CHIROPTERA Vespertilionidae Myotis davidii 2. Existing assembly GCF_000327345.1 LC
98 Little brown bat CHIROPTERA Vespertilionidae Myotis lucifugus 2. Existing assembly GCF_000147115.1 LC
99 Greater mouse-eared bat CHIROPTERA Vespertilionidae Myotis myotis 1. Zoonomia GCA_004026985.1 LC
100 Greater bulldog bat CHIROPTERA Noctilionidae Noctilio leporinus 1. Zoonomia GCA_004026585.1 LC
101 Common pipistrelle CHIROPTERA Vespertilionidae Pipistrellus pipistrellus 1. Zoonomia GCA_004026625.1 LC
102 Parnell's mustached bat CHIROPTERA Mormoopidae Pteronotus parnellii 2. Existing assembly GCA_000465405.1 LC
103 Black flying fox CHIROPTERA Pteropodidae Pteropus alecto 2. Existing assembly GCF_000325575.1 LC
104 Large flying fox CHIROPTERA Pteropodidae Pteropus vampyrus 2. Existing assembly GCF_000151845.1 NT
105 Chinese rufous horseshoe bat CHIROPTERA Rhinolophidae Rhinolophus sinicus 2. Existing assembly GCA_001888835.1 LC
106 Egyptian fruit bat CHIROPTERA Pteropodidae Rousettus aegyptiacus 1. Zoonomia GCA_004024865.1 LC
107 Mexican free-tailed bat CHIROPTERA Molossidae Tadarida brasiliensis 1. Zoonomia GCA_004025005.1 LC
108 Stripe-headed round-eared bat CHIROPTERA Phyllostomidae Tonatia saurophila 1. Zoonomia GCA_004024845.1 LC
109 Screaming hairy armadillo CINGULATA Dasypodidae Chaetophractus vellerosus 1. Zoonomia GCA_004027955.1 LC
110 Nine-banded armadillo CINGULATA Dasypodidae Dasypus novemcinctus 2. Existing assembly GCF_000208655.1 LC
111 Southern three-banded armadillo CINGULATA Dasypodidae Tolypeutes matacus 1. Zoonomia GCA_004025125.1 NT
112 Sunda flying lemur DERMOPTERA Cynocephalidae Galeopterus variegatus 1. Zoonomia GCA_004027255.1 LC
113 Star-nosed mole EULIPOTYPHLA Talpidae Condylura cristata 2. Existing assembly GCF_000260355.1 LC
114 Indochinese shrew EULIPOTYPHLA Soricidae Crocidura indochinensis 1. Zoonomia GCA_004027635.1 LC
115 Western european hedgehog EULIPOTYPHLA Erinaceidae Erinaceus europaeus 2. Existing assembly GCF_000296755.1 LC
116 Eastern mole EULIPOTYPHLA Talpidae Scalopus aquaticus 1. Zoonomia GCA_004024925.1 LC
117 Hispaniolan solenodon EULIPOTYPHLA Solenodontidae Solenodon paradoxus 1. Zoonomia GCA_004363575.1 EN
118 European shrew EULIPOTYPHLA Soricidae Sorex araneus 2. Existing assembly GCF_000181275.1 LC
119 Gracile shrew-like mole EULIPOTYPHLA Talpidae Uropsilus gracilis 1. Zoonomia GCA_004024945.1 LC
120 African yellow-spotted rock hyrax HYRACOIDEA Procaviidae Heterohyrax brucei 1. Zoonomia GCA_004026845.1 LC
121 South African rock hyrax HYRACOIDEA Procaviidae Procavia capensis 1. Zoonomia GCA_004026925.1 LC
122 Snowshoe hare LAGOMORPHA Leporidae Lepus americanus 1. Zoonomia GCA_004026855.1 LC
123 American pika LAGOMORPHA Ochotonidae Ochotona princeps 2. Existing assembly GCF_000292845.1 LC
124 Rabbit LAGOMORPHA Leporidae Oryctolagus cuniculus 2. Existing assembly GCF_000003625.3 NT
125 Cape elephant shrew MACROSCELIDEA Macroscelididae Elephantulus edwardii 1. Zoonomia GCA_004027355.1 LC
126 Southern white rhinoceros PERISSODACTYLA Rhinocerotidae Ceratotherium simum 2. Existing assembly GCF_000283155.1 NT
127 Northern white rhino PERISSODACTYLA Rhinocerotidae Ceratotherium simum cottoni 1. Zoonomia GCA_004027795.1 CR
128 Sumatran rhinoceros PERISSODACTYLA Rhinocerotidae Dicerorhinus sumatrensis 2. Existing assembly GCA_002844835.1 CR
129 Black rhinocerous PERISSODACTYLA Rhinocerotidae Diceros bicornis 1. Zoonomia GCA_004027315.1 CR
130 Ass PERISSODACTYLA Equidae Equus asinus 2. Existing assembly GCF_001305755.1 LC
131 Horse PERISSODACTYLA Equidae Equus caballus 2. Existing assembly GCF_000002305.2 LC
132 Przewalski's horse PERISSODACTYLA Equidae Equus przewalskii 2. Existing assembly GCF_000696695.1 EN
133 Malayan tapir PERISSODACTYLA Tapiridae Tapirus indicus 1. Zoonomia GCA_004024905.1 EN
134 South American tapir PERISSODACTYLA Tapiridae Tapirus terrestris 1. Zoonomia GCA_004025025.1 VU
135 Malayan pangolin PHOLIDOTA Manidae Manis javanica 2. Existing assembly GCF_001685135.1 CR
136 Chinese pangolin PHOLIDOTA Manidae Manis pentadactyla 2. Existing assembly GCA_000738955.1 CR
137 Linnaeus's two toed sloth PILOSA Megalonychidae Choloepus didactylus 1. Zoonomia GCA_004027855.1 LC
138 Hoffmann's two-fingered sloth PILOSA Megalonychidae Choloepus hoffmanni 2. Existing assembly GCA_000164785.2 LC
139 Giant anteater PILOSA Myrmecophagidae Myrmecophaga tridactyla 1. Zoonomia GCA_004026745.1 VU
140 Southern tamandua PILOSA Myrmecophagidae Tamandua tetradactyla 1. Zoonomia GCA_004025105.1 LC
141 Mexican howler monkey PRIMATES Atelidae Alouatta palliata mexicana 1. Zoonomia GCA_004027835.1 CR
142 Ma's night monkey PRIMATES Aotidae Aotus nancymaae 2. Existing assembly GCA_000952055.2 VU
143 Geoffroy's spider monkey PRIMATES Atelidae Ateles geoffroyi 1. Zoonomia GCA_004024785.1 EN
144 White-eared titi PRIMATES Pitheciidae Callicebus donacophilus 1. Zoonomia GCA_004027715.1 LC
145 White-tufted-ear marmoset PRIMATES Cebidae Callithrix jacchus 2. Existing assembly GCA_002754865.1 LC
146 White-fronted capuchin PRIMATES Cebidae Cebus albifrons 1. Zoonomia GCA_004027755.1 LC
147 White-faced sapajou PRIMATES Cebidae Cebus capucinus 2. Existing assembly GCF_001604975.1 LC
148 Sooty mangabey PRIMATES Cercopithecidae Cercocebus atys 2. Existing assembly GCF_000955945.1 NT
149 De brazza's monkey PRIMATES Cercopithecidae Cercopithecus neglectus 1. Zoonomia GCA_004027615.1 LC
150 Fat-tailed dwarf lemur PRIMATES Cheirogaleidae Cheirogaleus medius 1. Zoonomia GCA_004024725.1 LC
151 Green monkey PRIMATES Cercopithecidae Chlorocebus sabaeus 2. Existing assembly GCF_000409795.2 LC
152 Angolan colobus PRIMATES Cercopithecidae Colobus angolensis 2. Existing assembly GCF_000951035.1 VU
153 Aye-aye PRIMATES Daubentoniidae Daubentonia madagascariensis 1. Zoonomia GCA_004027145.1 EN
154 Patas monkey PRIMATES Cercopithecidae Erythrocebus patas 1. Zoonomia GCA_004027335.1 LC
155 Sclater's lemur PRIMATES Lemuridae Eulemur flavifrons 2. Existing assembly GCA_001262665.1 CR
156 Common brown lemur PRIMATES Lemuridae Eulemur fulvus 1. Zoonomia GCA_004027275.1 NT
157 Western lowland gorilla PRIMATES Hominidae Gorilla gorilla 2. Existing assembly GCA_900006655.3 CR
158 Human PRIMATES Hominidae Homo sapiens 2. Existing assembly GCA_000001405.27 LC
159 Indri PRIMATES Indridae Indri indri 1. Zoonomia GCA_004363605.1 CR
160 Ring tailed lemur PRIMATES Lemuridae Lemur catta 1. Zoonomia GCA_004024665.1 EN
161 Crab-eating macaque PRIMATES Cercopithecidae Macaca fascicularis 2. Existing assembly GCF_000364345.1 DD
162 Rhesus monkey PRIMATES Cercopithecidae Macaca mulatta 2. Existing assembly GCF_000772875.2 LC
163 Pig-tailed macaque PRIMATES Cercopithecidae Macaca nemestrina 2. Existing assembly GCF_000956065.1 VU
164 Drill PRIMATES Cercopithecidae Mandrillus leucophaeus 2. Existing assembly GCF_000951045.1 EN
165 Gray mouse lemur PRIMATES Cheirogaleidae Microcebus murinus 2. Existing assembly GCA_000165445.3 LC
166 Coquerel's giant mouse lemur PRIMATES Cheirogaleidae Mirza coquereli 1. Zoonomia GCA_004024645.1 EN
167 Proboscis monkey PRIMATES Cercopithecidae Nasalis larvatus 1. Zoonomia GCA_004027105.1 EN
168 Northern white-cheeked gibbon PRIMATES Hylobatidae Nomascus leucogenys 2. Existing assembly GCF_000146795.2 CR
169 Sunda slow loris PRIMATES Lorisidae Nycticebus coucang 1. Zoonomia GCA_004027815.1 VU
170 Small-eared galago PRIMATES Galagidae Otolemur garnettii 2. Existing assembly GCF_000181295.1 LC
171 Pygmy chimpanzee PRIMATES Hominidae Pan paniscus 2. Existing assembly GCF_000258655.2 EN
172 Chimpanzee PRIMATES Hominidae Pan troglodytes 2. Existing assembly GCA_002880755.3 EN
173 Olive baboon PRIMATES Cercopithecidae Papio anubis 2. Existing assembly GCA_000264685.2 LC
174 Ugandan red colobus PRIMATES Cercopithecidae Piliocolobus tephrosceles 2. Existing assembly GCA_002776525.1 EN
175 White-faced saki PRIMATES Pitheciidae Pithecia pithecia 1. Zoonomia GCA_004026645.1 LC
176 Sumatran orangutan PRIMATES Hominidae Pongo abelii 2. Existing assembly GCA_002880775.3 CR
177 Coquerel's sifaka PRIMATES Indridae Propithecus coquereli 2. Existing assembly GCF_000956105.1 EN
178 Red-shanked douc PRIMATES Cercopithecidae Pygathrix nemaeus 1. Zoonomia GCA_004024825.1 EN
179 Black snub-nosed monkey PRIMATES Cercopithecidae Rhinopithecus bieti 2. Existing assembly GCF_001698545.1 EN
180 Golden snub-nosed monkey PRIMATES Cercopithecidae Rhinopithecus roxellana 2. Existing assembly GCF_000769185.1 EN
181 Emperor tamarin PRIMATES Cebidae Saguinus imperator 1. Zoonomia GCA_004024885.1 LC
182 Bolivian squirrel monkey PRIMATES Cebidae Saimiri boliviensis 2. Existing assembly GCF_000235385.1 LC
183 Northern Plains gray langur PRIMATES Cercopithecidae Semnopithecus entellus 1. Zoonomia GCA_004025065.1 LC
184 African savanna elephant PROBOSCIDEA Elephantidae Loxodonta Africana 2. Existing assembly GCF_000001905.1 VU
185 Cairo spiny mouse RODENTIA Muridae Acomys cahirinus 1. Zoonomia GCA_004027535.1 LC
186 Gobi jerboa RODENTIA Dipodidae Allactaga bullata 1. Zoonomia GCA_004027895.1 LC
187 Mountain beaver RODENTIA Aplodontiidae Aplodontia rufa 1. Zoonomia GCA_004027875.1 LC
188 Desmarest's hutia RODENTIA Capromyidae Capromys pilorides 1. Zoonomia GCA_004027915.1 LC
189 North American beaver RODENTIA Castoridae Castor canadensis 1. Zoonomia GCA_004027675.1 LC
190 Brazilian guinea pig RODENTIA Caviidae Cavia aperea 2. Existing assembly GCA_000688575.1 LC
191 Domestic guinea pig RODENTIA Caviidae Cavia porcellus 2. Existing assembly GCF_000151735.1 LC
192 Montane guinea pig RODENTIA Caviidae Cavia tschudii 1. Zoonomia GCA_004027695.1 LC
193 Long-tailed chinchilla RODENTIA Chinchillidae Chinchilla lanigera 2. Existing assembly GCF_000276665.1 EN
194 Gambian pouched rat RODENTIA Nesomyidae Cricetomys gambianus 1. Zoonomia GCA_004027575.1 LC
195 Chinese hamster RODENTIA Nesomyidae Cricetulus griseus 2. Existing assembly GCA_900186095.1 LC
196 Common gundi RODENTIA Ctenodactylidae Ctenodactylus gundi 1. Zoonomia GCA_004027205.1 LC
197 Social tuco-tuco RODENTIA Ctenomyidae Ctenomys sociabilis 1. Zoonomia GCA_004027165.1 CR
198 Lowland paca RODENTIA Cuniculidae Cuniculus paca 1. Zoonomia GCA_004365215.1 LC
199 Central American agouti RODENTIA Dasyproctidae Dasyprocta punctata 1. Zoonomia GCA_004363535.1 LC
200 Pacarana RODENTIA Dinomyidae Dinomys branickii 1. Zoonomia GCA_004027595.1 LC
201 Ord's kangaroo rat RODENTIA Heteromyidae Dipodomys ordii 2. Existing assembly GCF_000151885.1 LC
202 Stephen's kangaroo rat RODENTIA Heteromyidae Dipodomys stephensi 1. Zoonomia GCA_004024685.1 VU
203 Patagonian mara RODENTIA Caviidae Dolichotis patagonum 1. Zoonomia GCA_004027295.1 NT
204 Transcaucasian mole vole RODENTIA Cricetidae Ellobius lutescens 2. Existing assembly GCA_001685075.1 LC
205 Northern mole vole RODENTIA Cricetidae Ellobius talpinus 2. Existing assembly GCA_001685095.1 LC
206 Damara mole-rat RODENTIA Bathyergidae Fukomys damarensis 2. Existing assembly GCF_000743615.1 LC
207 Edible dormouse RODENTIA Gliridae Glis glis 1. Zoonomia GCA_004027185.1 LC
208 Woodland doormouse RODENTIA Gliridae Graphiurus murinus 1. Zoonomia GCA_004027655.1 LC
209 Naked mole-rat RODENTIA Bathyergidae Heterocephalus glaber 2. Existing assembly GCF_000247695.1 LC
210 Capybara RODENTIA Caviidae Hydrochoerus hydrochaeris 1. Zoonomia GCA_004027455.1 LC
211 Northern crested porcupine RODENTIA Hystricidae Hystrix cristata 1. Zoonomia GCA_004026905.1 LC
212 Thirteen-lined ground squirrel RODENTIA Sciuridae Ictidomys tridecemlineatus 2. Existing assembly GCF_000236235.1 LC
213 Lesser egyptian jerboa RODENTIA Dipodidae Jaculus jaculus 2. Existing assembly GCF_000280705.1 LC
214 Alpine marmot RODENTIA Sciuridae Marmota marmota 2. Existing assembly GCF_001458135.1 LC
215 Mongolian jird RODENTIA Muridae Meriones unguiculatus 1. Zoonomia GCA_004026785.1 LC
216 Golden hamster RODENTIA Cricetidae Mesocricetus auratus 2. Existing assembly GCF_000349665.1 VU
217 Prairie vole RODENTIA Cricetidae Microtus ochrogaster 2. Existing assembly GCF_000317375.1 LC
218 Ryukyu mouse RODENTIA Muridae Mus caroli 2. Existing assembly GCA_900094665.2 LC
219 House mouse RODENTIA Muridae Mus musculus 2. Existing assembly GCF_000001635.26 LC
220 Shrew mouse RODENTIA Muridae Mus pahari 2. Existing assembly GCA_900095145.2 LC
221 Western wild mouse RODENTIA Muridae Mus spretus 2. Existing assembly GCA_001624865.1 LC
222 Hazel dormouse RODENTIA Gliridae Muscardinus avellanarius 1. Zoonomia GCA_004027005.1 LC
223 Coypu RODENTIA Myocastoridae Myocastor coypus 1. Zoonomia GCA_004027025.1 LC
224 Upper galilee mountains blind mole rat RODENTIA Spalacidae Nannospalax galili 2. Existing assembly GCF_000622305.1 DD
225 Degu RODENTIA Octodontidae Octodon degus 2. Existing assembly GCF_000260255.1 LC
226 Muskrat RODENTIA Cricetidae Ondatra zibethicus 1. Zoonomia GCA_004026605.1 LC
227 Scorpion mouse RODENTIA Cricetidae Onychomys torridus 1. Zoonomia GCA_004026725.1 LC
228 Pacific pocket mouse RODENTIA Heteromyidae Perognathus longimembris pacificus 1. Zoonomia GCA_004363475.1 LC
229 Prairie deer mouse RODENTIA Cricetidae Peromyscus maniculatus 2. Existing assembly GCF_000500345.1 LC
230 Dassie rat RODENTIA Petromuridae Petromus typicus 1. Zoonomia GCA_004026965.1 LC
231 Fat sand rat RODENTIA Muridae Psammomys obesus 2. Existing assembly GCA_002215935.1 LC
232 Norway rat RODENTIA Muridae Rattus norvegicus 2. Existing assembly GCF_000001895.5 LC
233 Hispid cotton rat RODENTIA Cricetidae Sigmodon hispidus 1. Zoonomia GCA_004025045.1 LC
234 Daurian ground squirrel RODENTIA Sciuridae Spermophilus dauricus 2. Existing assembly GCA_002406435.1 LC
235 Greater cane rat RODENTIA Thryonomyidae Thryonomys swinderianus 1. Zoonomia GCA_004025085.1 LC
236 Cape ground squirrel RODENTIA Sciuridae Xerus inauris 1. Zoonomia GCA_004024805.1 LC
237 Meadow jumping mouse RODENTIA Dipodidae Zapus hudsonius 1. Zoonomia GCA_004024765.1 LC
238 Northern tree shrew SCANDENTIA Tupaiidae Tupaia belangeri chinensis 2. Existing assembly GCF_000334495.1 LC
239 Large treeshrew SCANDENTIA Tupaiidae Tupaia tana 1. Zoonomia GCA_004365275.1 LC
240 Florida manatee SIRENIA Trichechidae Trichechus manatus 2. Existing assembly GCF_000243295.1 EN
241 Aardvark TUBULIDENTATA Orycteropodidae Orycteropus afer 1. Zoonomia GCA_004365145.1 LC

\ Table 1. Genome assemblies included in the 241-way Conservation track.
\ Species status:LC = Least Concern; NT = Near threatened; VU = Vulnerable; EN = Endangered; CR = Critically endangered
\

count	common name	CLADE	group	scientific name	sequencing source	NCBI assembly	species status
1	Cape golden mole	AFROSORICIDA	Chrysochloridae	Chrysochloris asiatica	1. Zoonomia	GCA_004027935.1	LC
2	Small madagascar hedgehog	AFROSORICIDA	Tenrecidae	Echinops telfairi	2. Existing assembly	GCF_000313985.1	LC
3	Talazac's shrew tenrec	AFROSORICIDA	Tenrecidae	Microgale talazaci	1. Zoonomia	GCA_004026705.1	LC
4	Cheetah	CARNIVORA	Felidae	Acinonyx jubatus	2. Existing assembly	GCF_001443585.1	CR
5	Giant panda	CARNIVORA	Ursidae	Ailuropoda melanoleuca	2. Existing assembly	GCA_002007445.1	VU
6	Lesser panda	CARNIVORA	Ailuridae	Ailurus fulgens	2. Existing assembly	GCA_002007465.1	EN
7	Domestic dog	CARNIVORA	Canidae	Canis lupus familiaris	2. Existing assembly	GCF_000002285.3	LC
8	Domestic dog (village dog)	CARNIVORA	Canidae	Canis lupus familiaris	1. Zoonomia	GCA_004027395.1	LC
9	Fossa	CARNIVORA	Eupleridae	Cryptoprocta ferox	1. Zoonomia	GCA_004023885.1	VU
10	Sea otter	CARNIVORA	Mustelidae	Enhydra lutris	2. Existing assembly	GCF_002288905.1	EN
11	Domestic cat	CARNIVORA	Felidae	Felis catus	2. Existing assembly	GCF_000181335.2	LC
12	Black-footed cat	CARNIVORA	Felidae	Felis nigripes	1. Zoonomia	GCA_004023925.1	VU
13	Dwarf mongoose	CARNIVORA	Herpestidae	Helogale parvula	1. Zoonomia	GCA_004023845.1	LC
14	Striped hyena	CARNIVORA	Hyaenidae	Hyaena hyaena	1. Zoonomia	GCA_004023945.1	NT
15	Weddell seal	CARNIVORA	Phocidae	Leptonychotes weddellii	2. Existing assembly	GCF_000349705.1	LC
16	African hunting dog	CARNIVORA	Canidae	Lycaon pictus	2. Existing assembly	GCA_001887905.1	EN
17	Honey badger	CARNIVORA	Mustelidae	Mellivora capensis	1. Zoonomia	GCA_004024625.1	LC
18	Northern elephant seal	CARNIVORA	Phocidae	Mirounga angustirostris	1. Zoonomia	GCA_004023865.1	LC
19	South African banded mongoose	CARNIVORA	Herpestidae	Mungos mungo	1. Zoonomia	GCA_004023785.1	LC
20	Domestic ferret	CARNIVORA	Mustelidae	Mustela putorius	2. Existing assembly	GCF_000239315.1	LC
21	Hawaiian monk seal	CARNIVORA	Phocidae	Neomonachus schauinslandi	2. Existing assembly	GCA_002201575.1	EN
22	Pacific walrus	CARNIVORA	Odobenidae	Odobenus rosmarus	2. Existing assembly	GCF_000321225.1	DD
23	Jaguar	CARNIVORA	Felidae	Panthera onca	1. Zoonomia	GCA_004023805.1	NT
24	Leopard	CARNIVORA	Felidae	Panthera pardus	2. Existing assembly	GCA_001857705.1	VU
25	Amur tiger	CARNIVORA	Felidae	Panthera tigris	2. Existing assembly	GCF_000464555.1	EN
26	Asian palm civet	CARNIVORA	Viverridae	Paradoxurus hermaphroditus	1. Zoonomia	GCA_004024585.1	LC
27	Giant otter	CARNIVORA	Mustelidae	Pteronura brasiliensis	1. Zoonomia	GCA_004024605.1	EN
28	Puma	CARNIVORA	Felidae	Puma concolor	2. Existing assembly	GCF_003327715.1	LC
29	Western spotted skunk	CARNIVORA	Mephitidae	Spilogale gracilis	1. Zoonomia	GCA_004023965.1	LC
30	Meerkat	CARNIVORA	Herpestidae	Suricata suricatta	1. Zoonomia	GCA_004023905.1	LC
31	Polar bear	CARNIVORA	Ursidae	Ursus maritimus	2. Existing assembly	GCF_000687225.1	VU
32	Arctic fox	CARNIVORA	Canidae	Vulpes lagopus	1. Zoonomia	GCA_004023825.1	LC
33	California sea lion	CARNIVORA	Otariidae	Zalophus californianus	1. Zoonomia	GCA_004024565.1	LC
34	Aoudad	CETARTIODACTYLA	Bovidae	Ammotragus lervia	2. Existing assembly	GCA_002201775.1	VU
35	Pronghorn	CETARTIODACTYLA	Antilocapridae	Antilocapra americana	1. Zoonomia	GCA_004027515.1	LC
36	Minke whale	CETARTIODACTYLA	Balaenopteridae	Balaenoptera acutorostrata	2. Existing assembly	GCF_000493695.1	LC
37	Antarctic minke whale	CETARTIODACTYLA	Balaenopteridae	Balaenoptera bonaerensis	2. Existing assembly	GCA_000978805.1	DD
38	Hirola	CETARTIODACTYLA	Bovidae	Beatragus hunteri	1. Zoonomia	GCA_004027495.1	CR
39	American bison	CETARTIODACTYLA	Bovidae	Bison bison	2. Existing assembly	GCF_000754665.1	NT
40	Zebu cattle	CETARTIODACTYLA	Bovidae	Bos indicus	2. Existing assembly	GCA_000247795.2	LC
41	Wild yak	CETARTIODACTYLA	Bovidae	Bos mutus	2. Existing assembly	GCF_000298355.1	VU
42	Cattle	CETARTIODACTYLA	Bovidae	Bos taurus	2. Existing assembly	GCF_000003205.7	LC
43	Water buffalo	CETARTIODACTYLA	Bovidae	Bubalus bubalis	2. Existing assembly	GCF_000471725.1	LC
44	Bactrian camel	CETARTIODACTYLA	Camelidae	Camelus bactrianus	2. Existing assembly	GCF_000767855.1	LC
45	Arabian camel	CETARTIODACTYLA	Camelidae	Camelus dromedarius	2. Existing assembly	GCF_000767585.1	LC
46	Wild bactrian camel	CETARTIODACTYLA	Camelidae	Camelus ferus	2. Existing assembly	GCF_000311805.1	CR
47	Wild goat	CETARTIODACTYLA	Bovidae	Capra aegagrus	2. Existing assembly	GCA_000978405.1	VU
48	Goat	CETARTIODACTYLA	Bovidae	Capra hircus	2. Existing assembly	GCF_001704415.1	LC
49	Chacoan peccary	CETARTIODACTYLA	Tayassuidae	Catagonus wagneri	1. Zoonomia	GCA_004024745.1	EN
50	Beluga whale	CETARTIODACTYLA	Monodontidae	Delphinapterus leucas	2. Existing assembly	GCF_002288925.1	LC
51	Pere david's deer	CETARTIODACTYLA	Cervidae	Elaphurus davidianus	2. Existing assembly	GCA_002443075.1	CR
52	Grey whale	CETARTIODACTYLA	Eschrichtiidae	Eschrichtius robustus	1. Zoonomia	GCA_004363415.1	LC
53	North Pacific right whale	CETARTIODACTYLA	Balaenidae	Eubalaena japonica	1. Zoonomia	GCA_004363455.1	EN
54	Giraffe	CETARTIODACTYLA	Giraffidae	Giraffa tippelskirchi	2. Existing assembly	GCA_001651235.1	VU
55	Nilgiri tahr	CETARTIODACTYLA	Bovidae	Hemitragus hylocrius	1. Zoonomia	GCA_004026825.1	EN
56	Hippopotamus	CETARTIODACTYLA	Hippopotamidae	Hippopotamus amphibius	1. Zoonomia	GCA_004027065.1	VU
57	Amazon river dolphin	CETARTIODACTYLA	Iniidae	Inia geoffrensis	1. Zoonomia	GCA_004363515.1	DD
58	Pygmy sperm whale	CETARTIODACTYLA	Physeteridae	Kogia breviceps	1. Zoonomia	GCA_004363705.1	DD
59	Yangtze river dolphin	CETARTIODACTYLA	Iniidae	Lipotes vexillifer	2. Existing assembly	GCF_000442215.1	CR
60	Sowerby's beaked whale	CETARTIODACTYLA	Ziphiidae	Mesoplodon bidens	1. Zoonomia	GCA_004027085.1	DD
61	Narwhal	CETARTIODACTYLA	Monodontidae	Monodon monoceros	1. Zoonomia	GCA_004026685.1	LC
62	Siberian musk deer	CETARTIODACTYLA	Moschidae	Moschus moschiferus	1. Zoonomia	GCA_004024705.1	VU
63	Yangtze finless porpoise	CETARTIODACTYLA	Phocoenidae	Neophocaena asiaeorientalis	2. Existing assembly	GCA_003031525.1	EN
64	White-tailed deer	CETARTIODACTYLA	Cervidae	Odocoileus virginianus	2. Existing assembly	GCA_002102435.1	LC
65	Okapi	CETARTIODACTYLA	Giraffidae	Okapia johnstoni	2. Existing assembly	GCA_001660835.1	EN
66	Killer whale	CETARTIODACTYLA	Delphinidae	Orcinus orca	2. Existing assembly	GCF_000331955.2	DD
67	Sheep	CETARTIODACTYLA	Bovidae	Ovis aries	2. Existing assembly	GCF_000298735.2	LC
68	Peninsular bighorn sheep	CETARTIODACTYLA	Bovidae	Ovis canadensis cremnobates	1. Zoonomia	GCA_004026945.1	EN
69	Chiru	CETARTIODACTYLA	Bovidae	Pantholops hodgsonii	2. Existing assembly	GCF_000400835.1	NT
70	Harbor porpoise	CETARTIODACTYLA	Phocoenidae	Phocoena phocoena	1. Zoonomia	GCA_004363495.1	LC
71	Indus river dolphin	CETARTIODACTYLA	Platanistidae	Platanista gangetica minor	1. Zoonomia	GCA_004363435.1	EN
72	Siberian reindeer	CETARTIODACTYLA	Cervidae	Rangifer tarandus	1. Zoonomia	GCA_004026565.1	VU
73	Russian saiga	CETARTIODACTYLA	Bovidae	Saiga tatarica tatarica	1. Zoonomia	GCA_004024985.1	CR
74	Pig	CETARTIODACTYLA	Suidae	Sus scrofa	2. Existing assembly	GCF_000003025.5	LC
75	Java lesser chevrotain	CETARTIODACTYLA	Tragulidae	Tragulus javanicus	1. Zoonomia	GCA_004024965.1	DD
76	Bottlenose dolphin	CETARTIODACTYLA	Delphinidae	Tursiops truncatus	2. Existing assembly	GCA_001922835.1	LC
77	Alpaca	CETARTIODACTYLA	Camelidae	Vicugna pacos	2. Existing assembly	GCA_000767525.1	LC
78	Cuvier's beaked whale	CETARTIODACTYLA	Ziphiidae	Ziphius cavirostris	1. Zoonomia	GCA_004364475.1	LC
79	Tailed tailless bat	CHIROPTERA	Phyllostomidae	Anoura caudifer	1. Zoonomia	GCA_004027475.1	LC
80	Jamacian fruit-eating bat	CHIROPTERA	Phyllostomidae	Artibeus jamaicensis	1. Zoonomia	GCA_004027435.1	LC
81	Seba's short-tailed bat	CHIROPTERA	Phyllostomidae	Carollia perspicillata	1. Zoonomia	GCA_004027735.1	LC
82	Bumblebee bat	CHIROPTERA	Craseonycteridae	Craseonycteris thonglongyai	1. Zoonomia	GCA_004027555.1	VU
83	Common vampire bat	CHIROPTERA	Phyllostomidae	Desmodus rotundus	2. Existing assembly	GCA_002940915.2	LC
84	Straw-colored fruit bat	CHIROPTERA	Pteropodidae	Eidolon helvum	2. Existing assembly	GCA_000465285.1	NT
85	Big brown bat	CHIROPTERA	Vespertilionidae	Eptesicus fuscus	2. Existing assembly	GCF_000308155.1	LC
86	Great roundleaf bat	CHIROPTERA	Hipposideridae	Hipposideros armiger	2. Existing assembly	GCA_001890085.1	LC
87	Cantor's leaf-nosed bat	CHIROPTERA	Hipposideridae	Hipposideros galeritus	1. Zoonomia	GCA_004027415.1	LC
88	Eastern red bat	CHIROPTERA	Vespertilionidae	Lasiurus borealis	1. Zoonomia	GCA_004026805.1	LC
89	Long-tongued fruit bat	CHIROPTERA	Pteropodidae	Macroglossus sobrinus	1. Zoonomia	GCA_004027375.1	LC
90	Greater false vampire bat	CHIROPTERA	Megadermatidae	Megaderma lyra	1. Zoonomia	GCA_004026885.1	LC
91	Hairy big-eared bat	CHIROPTERA	Phyllostomidae	Micronycteris hirsuta	1. Zoonomia	GCA_004026765.1	LC
92	Natal long-fingered bat	CHIROPTERA	Vespertilionidae	Miniopterus natalensis	2. Existing assembly	GCF_001595765.1	LC
93	Common bent-wing bat	CHIROPTERA	Vespertilionidae	Miniopterus schreibersii	1. Zoonomia	GCA_004026525.1	NT
94	Ghost-faced bat	CHIROPTERA	Mormoopidae	Mormoops blainvillei	1. Zoonomia	GCA_004026545.1	LC
95	Ashy-gray tube-nosed bat	CHIROPTERA	Vespertilionidae	Murina feae	1. Zoonomia	GCA_004026665.1	LC
96	Brandt's bat	CHIROPTERA	Vespertilionidae	Myotis brandtii	2. Existing assembly	GCF_000412655.1	LC
97	David's myotis bat	CHIROPTERA	Vespertilionidae	Myotis davidii	2. Existing assembly	GCF_000327345.1	LC
98	Little brown bat	CHIROPTERA	Vespertilionidae	Myotis lucifugus	2. Existing assembly	GCF_000147115.1	LC
99	Greater mouse-eared bat	CHIROPTERA	Vespertilionidae	Myotis myotis	1. Zoonomia	GCA_004026985.1	LC
100	Greater bulldog bat	CHIROPTERA	Noctilionidae	Noctilio leporinus	1. Zoonomia	GCA_004026585.1	LC
101	Common pipistrelle	CHIROPTERA	Vespertilionidae	Pipistrellus pipistrellus	1. Zoonomia	GCA_004026625.1	LC
102	Parnell's mustached bat	CHIROPTERA	Mormoopidae	Pteronotus parnellii	2. Existing assembly	GCA_000465405.1	LC
103	Black flying fox	CHIROPTERA	Pteropodidae	Pteropus alecto	2. Existing assembly	GCF_000325575.1	LC
104	Large flying fox	CHIROPTERA	Pteropodidae	Pteropus vampyrus	2. Existing assembly	GCF_000151845.1	NT
105	Chinese rufous horseshoe bat	CHIROPTERA	Rhinolophidae	Rhinolophus sinicus	2. Existing assembly	GCA_001888835.1	LC
106	Egyptian fruit bat	CHIROPTERA	Pteropodidae	Rousettus aegyptiacus	1. Zoonomia	GCA_004024865.1	LC
107	Mexican free-tailed bat	CHIROPTERA	Molossidae	Tadarida brasiliensis	1. Zoonomia	GCA_004025005.1	LC
108	Stripe-headed round-eared bat	CHIROPTERA	Phyllostomidae	Tonatia saurophila	1. Zoonomia	GCA_004024845.1	LC
109	Screaming hairy armadillo	CINGULATA	Dasypodidae	Chaetophractus vellerosus	1. Zoonomia	GCA_004027955.1	LC
110	Nine-banded armadillo	CINGULATA	Dasypodidae	Dasypus novemcinctus	2. Existing assembly	GCF_000208655.1	LC
111	Southern three-banded armadillo	CINGULATA	Dasypodidae	Tolypeutes matacus	1. Zoonomia	GCA_004025125.1	NT
112	Sunda flying lemur	DERMOPTERA	Cynocephalidae	Galeopterus variegatus	1. Zoonomia	GCA_004027255.1	LC
113	Star-nosed mole	EULIPOTYPHLA	Talpidae	Condylura cristata	2. Existing assembly	GCF_000260355.1	LC
114	Indochinese shrew	EULIPOTYPHLA	Soricidae	Crocidura indochinensis	1. Zoonomia	GCA_004027635.1	LC
115	Western european hedgehog	EULIPOTYPHLA	Erinaceidae	Erinaceus europaeus	2. Existing assembly	GCF_000296755.1	LC
116	Eastern mole	EULIPOTYPHLA	Talpidae	Scalopus aquaticus	1. Zoonomia	GCA_004024925.1	LC
117	Hispaniolan solenodon	EULIPOTYPHLA	Solenodontidae	Solenodon paradoxus	1. Zoonomia	GCA_004363575.1	EN
118	European shrew	EULIPOTYPHLA	Soricidae	Sorex araneus	2. Existing assembly	GCF_000181275.1	LC
119	Gracile shrew-like mole	EULIPOTYPHLA	Talpidae	Uropsilus gracilis	1. Zoonomia	GCA_004024945.1	LC
120	African yellow-spotted rock hyrax	HYRACOIDEA	Procaviidae	Heterohyrax brucei	1. Zoonomia	GCA_004026845.1	LC
121	South African rock hyrax	HYRACOIDEA	Procaviidae	Procavia capensis	1. Zoonomia	GCA_004026925.1	LC
122	Snowshoe hare	LAGOMORPHA	Leporidae	Lepus americanus	1. Zoonomia	GCA_004026855.1	LC
123	American pika	LAGOMORPHA	Ochotonidae	Ochotona princeps	2. Existing assembly	GCF_000292845.1	LC
124	Rabbit	LAGOMORPHA	Leporidae	Oryctolagus cuniculus	2. Existing assembly	GCF_000003625.3	NT
125	Cape elephant shrew	MACROSCELIDEA	Macroscelididae	Elephantulus edwardii	1. Zoonomia	GCA_004027355.1	LC
126	Southern white rhinoceros	PERISSODACTYLA	Rhinocerotidae	Ceratotherium simum	2. Existing assembly	GCF_000283155.1	NT
127	Northern white rhino	PERISSODACTYLA	Rhinocerotidae	Ceratotherium simum cottoni	1. Zoonomia	GCA_004027795.1	CR
128	Sumatran rhinoceros	PERISSODACTYLA	Rhinocerotidae	Dicerorhinus sumatrensis	2. Existing assembly	GCA_002844835.1	CR
129	Black rhinocerous	PERISSODACTYLA	Rhinocerotidae	Diceros bicornis	1. Zoonomia	GCA_004027315.1	CR
130	Ass	PERISSODACTYLA	Equidae	Equus asinus	2. Existing assembly	GCF_001305755.1	LC
131	Horse	PERISSODACTYLA	Equidae	Equus caballus	2. Existing assembly	GCF_000002305.2	LC
132	Przewalski's horse	PERISSODACTYLA	Equidae	Equus przewalskii	2. Existing assembly	GCF_000696695.1	EN
133	Malayan tapir	PERISSODACTYLA	Tapiridae	Tapirus indicus	1. Zoonomia	GCA_004024905.1	EN
134	South American tapir	PERISSODACTYLA	Tapiridae	Tapirus terrestris	1. Zoonomia	GCA_004025025.1	VU
135	Malayan pangolin	PHOLIDOTA	Manidae	Manis javanica	2. Existing assembly	GCF_001685135.1	CR
136	Chinese pangolin	PHOLIDOTA	Manidae	Manis pentadactyla	2. Existing assembly	GCA_000738955.1	CR
137	Linnaeus's two toed sloth	PILOSA	Megalonychidae	Choloepus didactylus	1. Zoonomia	GCA_004027855.1	LC
138	Hoffmann's two-fingered sloth	PILOSA	Megalonychidae	Choloepus hoffmanni	2. Existing assembly	GCA_000164785.2	LC
139	Giant anteater	PILOSA	Myrmecophagidae	Myrmecophaga tridactyla	1. Zoonomia	GCA_004026745.1	VU
140	Southern tamandua	PILOSA	Myrmecophagidae	Tamandua tetradactyla	1. Zoonomia	GCA_004025105.1	LC
141	Mexican howler monkey	PRIMATES	Atelidae	Alouatta palliata mexicana	1. Zoonomia	GCA_004027835.1	CR
142	Ma's night monkey	PRIMATES	Aotidae	Aotus nancymaae	2. Existing assembly	GCA_000952055.2	VU
143	Geoffroy's spider monkey	PRIMATES	Atelidae	Ateles geoffroyi	1. Zoonomia	GCA_004024785.1	EN
144	White-eared titi	PRIMATES	Pitheciidae	Callicebus donacophilus	1. Zoonomia	GCA_004027715.1	LC
145	White-tufted-ear marmoset	PRIMATES	Cebidae	Callithrix jacchus	2. Existing assembly	GCA_002754865.1	LC
146	White-fronted capuchin	PRIMATES	Cebidae	Cebus albifrons	1. Zoonomia	GCA_004027755.1	LC
147	White-faced sapajou	PRIMATES	Cebidae	Cebus capucinus	2. Existing assembly	GCF_001604975.1	LC
148	Sooty mangabey	PRIMATES	Cercopithecidae	Cercocebus atys	2. Existing assembly	GCF_000955945.1	NT
149	De brazza's monkey	PRIMATES	Cercopithecidae	Cercopithecus neglectus	1. Zoonomia	GCA_004027615.1	LC
150	Fat-tailed dwarf lemur	PRIMATES	Cheirogaleidae	Cheirogaleus medius	1. Zoonomia	GCA_004024725.1	LC
151	Green monkey	PRIMATES	Cercopithecidae	Chlorocebus sabaeus	2. Existing assembly	GCF_000409795.2	LC
152	Angolan colobus	PRIMATES	Cercopithecidae	Colobus angolensis	2. Existing assembly	GCF_000951035.1	VU
153	Aye-aye	PRIMATES	Daubentoniidae	Daubentonia madagascariensis	1. Zoonomia	GCA_004027145.1	EN
154	Patas monkey	PRIMATES	Cercopithecidae	Erythrocebus patas	1. Zoonomia	GCA_004027335.1	LC
155	Sclater's lemur	PRIMATES	Lemuridae	Eulemur flavifrons	2. Existing assembly	GCA_001262665.1	CR
156	Common brown lemur	PRIMATES	Lemuridae	Eulemur fulvus	1. Zoonomia	GCA_004027275.1	NT
157	Western lowland gorilla	PRIMATES	Hominidae	Gorilla gorilla	2. Existing assembly	GCA_900006655.3	CR
158	Human	PRIMATES	Hominidae	Homo sapiens	2. Existing assembly	GCA_000001405.27	LC
159	Indri	PRIMATES	Indridae	Indri indri	1. Zoonomia	GCA_004363605.1	CR
160	Ring tailed lemur	PRIMATES	Lemuridae	Lemur catta	1. Zoonomia	GCA_004024665.1	EN
161	Crab-eating macaque	PRIMATES	Cercopithecidae	Macaca fascicularis	2. Existing assembly	GCF_000364345.1	DD
162	Rhesus monkey	PRIMATES	Cercopithecidae	Macaca mulatta	2. Existing assembly	GCF_000772875.2	LC
163	Pig-tailed macaque	PRIMATES	Cercopithecidae	Macaca nemestrina	2. Existing assembly	GCF_000956065.1	VU
164	Drill	PRIMATES	Cercopithecidae	Mandrillus leucophaeus	2. Existing assembly	GCF_000951045.1	EN
165	Gray mouse lemur	PRIMATES	Cheirogaleidae	Microcebus murinus	2. Existing assembly	GCA_000165445.3	LC
166	Coquerel's giant mouse lemur	PRIMATES	Cheirogaleidae	Mirza coquereli	1. Zoonomia	GCA_004024645.1	EN
167	Proboscis monkey	PRIMATES	Cercopithecidae	Nasalis larvatus	1. Zoonomia	GCA_004027105.1	EN
168	Northern white-cheeked gibbon	PRIMATES	Hylobatidae	Nomascus leucogenys	2. Existing assembly	GCF_000146795.2	CR
169	Sunda slow loris	PRIMATES	Lorisidae	Nycticebus coucang	1. Zoonomia	GCA_004027815.1	VU
170	Small-eared galago	PRIMATES	Galagidae	Otolemur garnettii	2. Existing assembly	GCF_000181295.1	LC
171	Pygmy chimpanzee	PRIMATES	Hominidae	Pan paniscus	2. Existing assembly	GCF_000258655.2	EN
172	Chimpanzee	PRIMATES	Hominidae	Pan troglodytes	2. Existing assembly	GCA_002880755.3	EN
173	Olive baboon	PRIMATES	Cercopithecidae	Papio anubis	2. Existing assembly	GCA_000264685.2	LC
174	Ugandan red colobus	PRIMATES	Cercopithecidae	Piliocolobus tephrosceles	2. Existing assembly	GCA_002776525.1	EN
175	White-faced saki	PRIMATES	Pitheciidae	Pithecia pithecia	1. Zoonomia	GCA_004026645.1	LC
176	Sumatran orangutan	PRIMATES	Hominidae	Pongo abelii	2. Existing assembly	GCA_002880775.3	CR
177	Coquerel's sifaka	PRIMATES	Indridae	Propithecus coquereli	2. Existing assembly	GCF_000956105.1	EN
178	Red-shanked douc	PRIMATES	Cercopithecidae	Pygathrix nemaeus	1. Zoonomia	GCA_004024825.1	EN
179	Black snub-nosed monkey	PRIMATES	Cercopithecidae	Rhinopithecus bieti	2. Existing assembly	GCF_001698545.1	EN
180	Golden snub-nosed monkey	PRIMATES	Cercopithecidae	Rhinopithecus roxellana	2. Existing assembly	GCF_000769185.1	EN
181	Emperor tamarin	PRIMATES	Cebidae	Saguinus imperator	1. Zoonomia	GCA_004024885.1	LC
182	Bolivian squirrel monkey	PRIMATES	Cebidae	Saimiri boliviensis	2. Existing assembly	GCF_000235385.1	LC
183	Northern Plains gray langur	PRIMATES	Cercopithecidae	Semnopithecus entellus	1. Zoonomia	GCA_004025065.1	LC
184	African savanna elephant	PROBOSCIDEA	Elephantidae	Loxodonta Africana	2. Existing assembly	GCF_000001905.1	VU
185	Cairo spiny mouse	RODENTIA	Muridae	Acomys cahirinus	1. Zoonomia	GCA_004027535.1	LC
186	Gobi jerboa	RODENTIA	Dipodidae	Allactaga bullata	1. Zoonomia	GCA_004027895.1	LC
187	Mountain beaver	RODENTIA	Aplodontiidae	Aplodontia rufa	1. Zoonomia	GCA_004027875.1	LC
188	Desmarest's hutia	RODENTIA	Capromyidae	Capromys pilorides	1. Zoonomia	GCA_004027915.1	LC
189	North American beaver	RODENTIA	Castoridae	Castor canadensis	1. Zoonomia	GCA_004027675.1	LC
190	Brazilian guinea pig	RODENTIA	Caviidae	Cavia aperea	2. Existing assembly	GCA_000688575.1	LC
191	Domestic guinea pig	RODENTIA	Caviidae	Cavia porcellus	2. Existing assembly	GCF_000151735.1	LC
192	Montane guinea pig	RODENTIA	Caviidae	Cavia tschudii	1. Zoonomia	GCA_004027695.1	LC
193	Long-tailed chinchilla	RODENTIA	Chinchillidae	Chinchilla lanigera	2. Existing assembly	GCF_000276665.1	EN
194	Gambian pouched rat	RODENTIA	Nesomyidae	Cricetomys gambianus	1. Zoonomia	GCA_004027575.1	LC
195	Chinese hamster	RODENTIA	Nesomyidae	Cricetulus griseus	2. Existing assembly	GCA_900186095.1	LC
196	Common gundi	RODENTIA	Ctenodactylidae	Ctenodactylus gundi	1. Zoonomia	GCA_004027205.1	LC
197	Social tuco-tuco	RODENTIA	Ctenomyidae	Ctenomys sociabilis	1. Zoonomia	GCA_004027165.1	CR
198	Lowland paca	RODENTIA	Cuniculidae	Cuniculus paca	1. Zoonomia	GCA_004365215.1	LC
199	Central American agouti	RODENTIA	Dasyproctidae	Dasyprocta punctata	1. Zoonomia	GCA_004363535.1	LC
200	Pacarana	RODENTIA	Dinomyidae	Dinomys branickii	1. Zoonomia	GCA_004027595.1	LC
201	Ord's kangaroo rat	RODENTIA	Heteromyidae	Dipodomys ordii	2. Existing assembly	GCF_000151885.1	LC
202	Stephen's kangaroo rat	RODENTIA	Heteromyidae	Dipodomys stephensi	1. Zoonomia	GCA_004024685.1	VU
203	Patagonian mara	RODENTIA	Caviidae	Dolichotis patagonum	1. Zoonomia	GCA_004027295.1	NT
204	Transcaucasian mole vole	RODENTIA	Cricetidae	Ellobius lutescens	2. Existing assembly	GCA_001685075.1	LC
205	Northern mole vole	RODENTIA	Cricetidae	Ellobius talpinus	2. Existing assembly	GCA_001685095.1	LC
206	Damara mole-rat	RODENTIA	Bathyergidae	Fukomys damarensis	2. Existing assembly	GCF_000743615.1	LC
207	Edible dormouse	RODENTIA	Gliridae	Glis glis	1. Zoonomia	GCA_004027185.1	LC
208	Woodland doormouse	RODENTIA	Gliridae	Graphiurus murinus	1. Zoonomia	GCA_004027655.1	LC
209	Naked mole-rat	RODENTIA	Bathyergidae	Heterocephalus glaber	2. Existing assembly	GCF_000247695.1	LC
210	Capybara	RODENTIA	Caviidae	Hydrochoerus hydrochaeris	1. Zoonomia	GCA_004027455.1	LC
211	Northern crested porcupine	RODENTIA	Hystricidae	Hystrix cristata	1. Zoonomia	GCA_004026905.1	LC
212	Thirteen-lined ground squirrel	RODENTIA	Sciuridae	Ictidomys tridecemlineatus	2. Existing assembly	GCF_000236235.1	LC
213	Lesser egyptian jerboa	RODENTIA	Dipodidae	Jaculus jaculus	2. Existing assembly	GCF_000280705.1	LC
214	Alpine marmot	RODENTIA	Sciuridae	Marmota marmota	2. Existing assembly	GCF_001458135.1	LC
215	Mongolian jird	RODENTIA	Muridae	Meriones unguiculatus	1. Zoonomia	GCA_004026785.1	LC
216	Golden hamster	RODENTIA	Cricetidae	Mesocricetus auratus	2. Existing assembly	GCF_000349665.1	VU
217	Prairie vole	RODENTIA	Cricetidae	Microtus ochrogaster	2. Existing assembly	GCF_000317375.1	LC
218	Ryukyu mouse	RODENTIA	Muridae	Mus caroli	2. Existing assembly	GCA_900094665.2	LC
219	House mouse	RODENTIA	Muridae	Mus musculus	2. Existing assembly	GCF_000001635.26	LC
220	Shrew mouse	RODENTIA	Muridae	Mus pahari	2. Existing assembly	GCA_900095145.2	LC
221	Western wild mouse	RODENTIA	Muridae	Mus spretus	2. Existing assembly	GCA_001624865.1	LC
222	Hazel dormouse	RODENTIA	Gliridae	Muscardinus avellanarius	1. Zoonomia	GCA_004027005.1	LC
223	Coypu	RODENTIA	Myocastoridae	Myocastor coypus	1. Zoonomia	GCA_004027025.1	LC
224	Upper galilee mountains blind mole rat	RODENTIA	Spalacidae	Nannospalax galili	2. Existing assembly	GCF_000622305.1	DD
225	Degu	RODENTIA	Octodontidae	Octodon degus	2. Existing assembly	GCF_000260255.1	LC
226	Muskrat	RODENTIA	Cricetidae	Ondatra zibethicus	1. Zoonomia	GCA_004026605.1	LC
227	Scorpion mouse	RODENTIA	Cricetidae	Onychomys torridus	1. Zoonomia	GCA_004026725.1	LC
228	Pacific pocket mouse	RODENTIA	Heteromyidae	Perognathus longimembris pacificus	1. Zoonomia	GCA_004363475.1	LC
229	Prairie deer mouse	RODENTIA	Cricetidae	Peromyscus maniculatus	2. Existing assembly	GCF_000500345.1	LC
230	Dassie rat	RODENTIA	Petromuridae	Petromus typicus	1. Zoonomia	GCA_004026965.1	LC
231	Fat sand rat	RODENTIA	Muridae	Psammomys obesus	2. Existing assembly	GCA_002215935.1	LC
232	Norway rat	RODENTIA	Muridae	Rattus norvegicus	2. Existing assembly	GCF_000001895.5	LC
233	Hispid cotton rat	RODENTIA	Cricetidae	Sigmodon hispidus	1. Zoonomia	GCA_004025045.1	LC
234	Daurian ground squirrel	RODENTIA	Sciuridae	Spermophilus dauricus	2. Existing assembly	GCA_002406435.1	LC
235	Greater cane rat	RODENTIA	Thryonomyidae	Thryonomys swinderianus	1. Zoonomia	GCA_004025085.1	LC
236	Cape ground squirrel	RODENTIA	Sciuridae	Xerus inauris	1. Zoonomia	GCA_004024805.1	LC
237	Meadow jumping mouse	RODENTIA	Dipodidae	Zapus hudsonius	1. Zoonomia	GCA_004024765.1	LC
238	Northern tree shrew	SCANDENTIA	Tupaiidae	Tupaia belangeri chinensis	2. Existing assembly	GCF_000334495.1	LC
239	Large treeshrew	SCANDENTIA	Tupaiidae	Tupaia tana	1. Zoonomia	GCA_004365275.1	LC
240	Florida manatee	SIRENIA	Trichechidae	Trichechus manatus	2. Existing assembly	GCF_000243295.1	EN
241	Aardvark	TUBULIDENTATA	Orycteropodidae	Orycteropus afer	1. Zoonomia	GCA_004365145.1	LC

\ \

Display Conventions and Configuration

\ To view detailed information about the alignments at a specific\ position, zoom the display in to 30,000 or fewer bases, then click on\ the alignment.

\ \

Gap Annotation

Single line: No bases in the aligned species. Possibly due to a\ lineage-specific insertion between the aligned blocks in the human genome\ or a lineage-specific deletion between the aligned blocks in the aligning\ species.\
Double line: Aligning species has one or more unalignable bases in\ the gap region. Possibly due to excessive evolutionary distance between\ species or independent indels in the region between the aligned blocks in both\ species.\
Pale yellow coloring: Aligning species has Ns in the gap region.\ Reflects uncertainty in the relationship between the DNA of both species, due\ to lack of sequence in relevant portions of the aligning species.\

\ \

Genomic Breaks

\ Discontinuities in the genomic context (chromosome, scaffold or region) of the\ aligned DNA in the aligning species are shown as follows:\

\ Vertical blue bar: Represents a discontinuity that persists indefinitely\ on either side, e.g. a large region of DNA on either side of the bar\ comes from a different chromosome in the aligned species due to a large scale\ rearrangement.\
\ Green square brackets: Enclose shorter alignments consisting of DNA from\ one genomic context in the aligned species nested inside a larger chain of\ alignments from a different genomic context. The alignment within the\ brackets may represent a short misalignment, a lineage-specific insertion of a\ transposon in the human genome that aligns to a paralogous copy somewhere\ else in the aligned species, or other similar occurrence.\

\ \

Base Level

\ No codon translation: The gene annotation is not used; the bases are\ displayed without translation.\
\ Use default species reading frames for translation: The annotations from\ the genome displayed in the Default species to establish reading frame\ pull-down menu are used to translate all the aligned species present in the\ alignment.\
\ Use reading frames for species if available, otherwise no translation:\ Codon translation is performed only for those species where the region is\ annotated as protein coding.\
Use reading frames for species if available, otherwise use default species:\ Codon translation is done on those species that are annotated as being protein\ coding over the aligned region using species-specific annotation; the remaining\ species are translated using the default species annotation.\

\ Codon translation uses the following gene tracks as the basis for translation:\

\ \ \ \ \ \
Gene Track Species
UCSC Genes Human
Ensembl Genes v104 Brazilian guinea pig, gibbon
RefSeq Genes Angolan colobus, Balaenoptera acutorostrata, Bison bison, Black flying-fox, Brandt's myotis (bat), Bushbaby, Camelus bactrianus, Camelus ferus, Canis lupus familiaris, Cape elephant shrew, Capra hircus, Cavia porcellus, Ceratotherium simum, Cercocebus atys, Chinchilla, Chinese tree shrew, Chlorocebus sabaeus, Condylura cristata, Damara mole rat, Dasypus novemcinctus, David's myotis (bat), Delphinapterus leucas, Echinops telfairi, Enhydra lutris, Eptesicus fuscus, Equus asinus, Equus przewalskii, Erinaceus europaeus, Felis catus, Heterocephalus glaber, Jaculus jaculus, Kangaroo rat, Killer whale, Leptonychotes weddellii, Lipotes vexillifer, Little brown bat, Loxodonta africana, Macaca fascicularis, Macaca nemestrina, Mandrillus leucophaeus, Manis javanica, Marmota marmota, Mesocricetus auratus, Miniopterus natalensis, Mus musculus, Nannospalax galili, Ochotona princeps, Octodon degus, Oryctolagus cuniculus, Pacific walrus, Pan paniscus, Panthera tigris, Peromyscus maniculatus, Prairie vole, Propithecus coquereli, Pteropus vampyrus, Puma concolor, Rattus norvegicus, Rhinopithecus bieti, Shrew, Squirrel monkey, Squirrel, Sus scrofa, Trichechus manatus, Ursus maritimus, White-faced sapajou, Wild yak
no annotation Acinonyx jubatus, Acomys cahirinus, Ailuropoda melanoleuca, Ailurus fulgens, Allactaga bullata, Alouatta palliata, Ammotragus lervia, Anoura caudifer, Antilocapra americana, Aotus nancymaae, Aplodontia rufa, Artibeus jamaicensis, Ateles geoffroyi, Balaenoptera bonaerensis, Beatragus hunteri, Bos indicus, Bos taurus, Bubalus bubalis, Callicebus donacophilus, Callithrix jacchus, Camelus dromedarius, Canis lupus, Capra aegagrus, Capromys pilorides, Carollia perspicillata, Castor canadensis, Catagonus wagneri, Cavia tschudii, Cebus albifrons, Ceratotherium simum cottoni, Cercopithecus neglectus, Chaetophractus vellerosus, Cheirogaleus medius, Choloepus didactylus, Choloepus hoffmanni, Chrysochloris asiatica, Craseonycteris thonglongyai, Cricetomys gambianus, Cricetulus griseus, Crocidura indochinensis, Cryptoprocta ferox, Ctenodactylus gundi, Ctenomys sociabilis, Cuniculus paca, Dasyprocta punctata, Daubentonia madagascariensis, Desmodus rotundus, Dicerorhinus sumatrensis, Diceros bicornis, Dinomys branickii, Dipodomys stephensi, Dolichotis patagonum, Elaphurus davidianus, Ellobius lutescens, Ellobius talpinus, Equus caballus, Erythrocebus patas, Eschrichtius robustus, Eubalaena japonica, Eulemur flavifrons, Eulemur fulvus, Felis nigripes, Galeopterus variegatus, Giraffa tippelskirchi, Glis glis, Gorilla gorilla, Graphiurus murinus, Helogale parvula, Hemitragus hylocrius, Heterohyrax brucei, Hippopotamus amphibius, Hipposideros armiger, Hipposideros galeritus, Hyaena hyaena, Hydrochoerus hydrochaeris, Hystrix cristata, Indri indri, Inia geoffrensis, Kogia breviceps, Lasiurus borealis, Lemur catta, Lepus americanus, Lycaon pictus, Macaca mulatta, Macroglossus sobrinus, Manis pentadactyla, Megaderma lyra, Mellivora capensis, Meriones unguiculatus, Mesoplodon bidens, Microcebus murinus, Microgale talazaci, Micronycteris hirsuta, Miniopterus schreibersii, Mirounga angustirostris, Mirza coquereli, Monodon monoceros, Mormoops blainvillei, Moschus moschiferus, Mungos mungo, Murina feae, Mus caroli, Mus pahari, Mus spretus, Muscardinus avellanarius, Mustela putorius, Myocastor coypus, Myotis myotis, Myrmecophaga tridactyla, Nasalis larvatus, Neomonachus schauinslandi, Neophocaena asiaeorientalis, Noctilio leporinus, Nycticebus coucang, Odocoileus virginianus, Okapia johnstoni, Ondatra zibethicus, Onychomys torridus, Orycteropus afer, Ovis aries, Ovis canadensis, Pan troglodytes, Panthera onca, Panthera pardus, Pantholops hodgsonii, Papio anubis, Paradoxurus hermaphroditus
\ Table 2. Gene tracks used for codon translation.\

\ \

Methods

\ The Zoonomia alignment was composed of two sets of mammalian genomes: newly\ assembled DISCOVAR assemblies and GenBank assemblies. The DISCOVAR genomes\ were masked with RepeatMasker (commit 2d947604), using Repbase version\ 20170127 as the repeat library and CrossMatch as the alignment engine. The\ pipeline used is available at\ repeatMaskerPipeline\ (commit a6ad966). The\ guide-tree topology was taken from the TimeTree database (using release\ current in October 2018), and the branch lengths were estimated using the\ least-squares-fit mode of PHYLIP, version\ 3.695. The distance matrix used was largely based on distances from the 4d\ site trees from the UCSC browser. To add those species not present in the\ UCSC tree, approximate distances estimated by Mash (commit 541971b)\ to the closest UCSC species\ were added to the distance between the two closest UCSC species. We used the\ HAL package (commit 68db41d)\ produce the HAL file.\

\ \

Phylogenetic Tree Model

\ The phyloP are phylogenetic methods that rely\ on a tree model containing the tree topology, branch lengths representing\ evolutionary distance at neutrally evolving sites, the background distribution\ of nucleotides, and a substitution rate matrix.\ The\ all-species tree model for this track was\ generated using the phyloFit program from the PHAST package\ (REV model, EM algorithm, medium precision) using multiple alignments of\ 4-fold degenerate sites extracted from the 241-way alignment\ (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene\ set, filtered to select single-coverage long transcripts.\

\ This same tree model was used in the phyloP calculations; however, the\ background frequencies were modified to maintain reversibility.\ The resulting tree model:\ all species.\

PhyloP Conservation

\ \

\ Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.\ \ Detection of nonneutral substitution rates on mammalian phylogenies.\ Genome Res. 2010 Jan;20(1):110-21.\ PMID: 19858363;\ PMC: PMC2798823\

\ \

\ Siepel A, Haussler D.\ Phylogenetic Hidden Markov Models.\ In: Nielsen R, editor. Statistical Methods in Molecular Evolution.\ New York: Springer; 2005. pp. 325-351.\ DOI: 10.1007/0-387-27733-1_12\

\ \

\ Siepel A, Pollard KS, and Haussler D. New methods for detecting\ lineage-specific selection. In Proceedings of the 10th International\ Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205.\ DOI: 10.1007/11732990_17\

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wgEncodeGencode\ type genePred\ wgEncodeGencodeCompV47 Comprehensive genePred Comprehensive Gene Annotation Set from GENCODE Version 47 (Ensembl 113) 3 2 0 0 0 127 127 127 0 0 0 genes 1 longLabel Comprehensive Gene Annotation Set from GENCODE Version 47 (Ensembl 113)\ parent wgEncodeGencodeV47ViewGenes off\ priority 2\ shortLabel Comprehensive\ subGroups view=aGenes name=Comprehensive\ track wgEncodeGencodeCompV47\ trackHandler wgEncodeGencode\ type genePred\ cnvDevDelayControl Control gvf Copy Number Variation Morbidity Map of Developmental Delay - Control 3 2 0 0 0 127 127 127 0 0 0 phenDis 1 longLabel Copy Number Variation Morbidity Map of Developmental Delay - Control\ parent cnvDevDelay on\ priority 2\ shortLabel Control\ track cnvDevDelayControl\ type gvf\ visibility pack\ covidHgiGwasR4Pval COVID GWAS v4 bigLolly 9 + COVID risk variants from GWAS meta-analyses by the COVID-19 Host Genetics Initiative (Rel 4, Oct 2020) 3 2 0 0 0 127 127 127 0 0 22 chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,

Description

\ This track set shows the results of the\ GWAS Data Release 4 (October 2020) \ from the \ \ COVID-19 Host Genetics Initiative (HGI): \ a collaborative effort to facilitate \ the generation of meta-analysis across multiple studies contributed by\ partners world-wide\ to identify the genetic determinants of SARS-CoV-2 infection susceptibility, disease severity \ and outcomes. The COVID-19 HGI also aims to provide a platform for study partners to \ share analytical results in the form of summary statistics and/or individual level data of COVID-19\ host genetics research. At the time of this release, a total of 137 studies were registered with \ this effort.\

\ \

\ The specific phenotypes studied by the COVID-19 HGI are those that benefit from maximal sample \ size: primary analysis on disease severity. For the Data Release 4 the number of cases have\ increased by nearly ten-fold (more than 30,000 COVID-19 cases and 1.47 million controls) by combining\ data from 34 studies across 16 countries. \

\ \

\ The four tracks here are based on data from HGI meta-analyses A2, B2, C1, and C2, described here:\

\ \

Severe COVID vars (A2): Cases with very severe respiratory failure confirmed\ for COVID-19 vs. population (i.e. everybody that is not a case).\ The increased sample size resulted in strong evidence of \ seven genomic regions associated with severe COVID-19 and one additional signal associated with \ COVID-19 partial-susceptibility. Many of these regions were identified by the \ Genetics of Mortality in Critical Care (GenOMICC)\ study and are shown below (table adapted from \ Pairo-Castineira et. al.).\

SNP	Human GRCh37/hg19 Assembly	Human GRCh38/hg38 Assembly	Risk Allele	Alternative	Gene nearest to SNP
rs73064425	chr3:45901089-45901089	chr3:45859597-45859597	T	C	LZTFL1
rs9380142	chr6:29798794-29798794	chr6:29831017-29831017	A	G	HLA-G
rs143334143	chr6:31121426-31121426	chr6:31153649-31153649	A	G	CCHCR1
rs10735079	chr12:113380008-113380008	chr12:112942203-112942203	A	G	OAS3
rs74956615	chr19:10427721-10427721	chr19:10317045-10317045	A	T	ICAM5/TYK2
rs2109069	chr19:4719443-4719443	chr19:4719431-4719431	A	G	DPP9
rs2236757	chr21:34624917-34624917	chr21:33252612-33252612	A	G	IFNAR2

Hosp COVID vars (B2): Cases hospitalized and confirmed for COVID-19 vs. \ population (i.e. everybody that is not a case)

Tested COVID vars (C1): Cases with laboratory confirmed SARS-CoV-2 infection, or \ health record/physician-confirmed COVID-19, or self-reported COVID-19 via questionare vs. laboratory\ /self-reported negative cases

All COVID vars (C2): Cases with laboratory confirmed SARS-CoV-2 infection, or \ health record/physician-confirmed COVID-19, or self-reported COVID-19 vs. population (i.e. everybody\ that is not a case)

\ \ Due to privacy concerns, these browser tracks exclude data provided by 23andMe contributed\ studies in the full analysis results. The actual study and case \ and control counts for the individual browser tracks are listed in the track labels. Details on \ all studies can be found here.\ \

Display Conventions

\ Displayed items are colored by GWAS effect: red for positive (harmful) effect, \ blue for negative (protective) effect.\ The height ('lollipop stem') of the item is based on statistical significance (p-value). \ For better visualization of the data, only SNPs with p-values smaller than 1e-3 are \ displayed by default.

\ The color saturation indicates effect size (beta coefficient): values over the median of effect \ size are brightly colored (bright red\ \ , bright blue\ \ ),\ those below the median are paler (light red\ \ , light blue\ \ ). \

\ Each track has separate display controls and data can be filtered according to the\ number of studies, minimum -log10 p-value, and the\ effect size (beta coefficient), using the track Configure options.

\ Mouseover on items shows the rs ID (or chrom:pos if none assigned), both the non-effect \ and effect alleles, the effect size (beta coefficient), the p-value, and the number of \ studies.\ Additional information on each variant can be found on the details page by clicking on \ the item.

\ \

Methods

\ COVID-19 Host Genetics Initiative (HGI) GWAS meta-analysis round 4 (October 2020) results were \ used in this study. \ Each participating study partner submitted GWAS summary statistics for up to four \ of the COVID-19 phenotype definitions.

\ Data were generated from genome-wide SNP array and whole exome and genome\ sequencing, leveraging the impact of both common and rare variants. The statistical analysis\ performed takes into account differences between sex, ancestry, and date of sample collection. \ Alleles were harmonized across studies and reported allele frequencies are based on gnomAD \ version 3.0 reference data. Most study partners used the SAIGE GWAS pipeline in order \ to generate summary statistics used for the COVID-19 HGI meta-analysis. The summary statistics \ of individual studies were manually examined for inflation, \ deflation, and excessive number of false positives. \ Qualifying summary statistics were filtered for \ INFO > 0.6 and MAF > 0.0001 prior to meta-analyzing the entirety of the data. \

Display Conventions and Configuration

\ Tissue-cell type combinations in the Full and Combined tracks are\ colored by which cell type they belong to in the below table:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Color Cell Type
Endothelial
Epithelial
Glia
Immune
Neuron
Stromal
Other
\

Color	Cell Type
	Endothelial
	Epithelial
	Glia
	Immune
	Neuron
	Stromal
	Other

\ \

Color	Cell Type
	Inflammatory Macrophage
	Lung Macrophage
	Monocyte/Macrophage FCGR3A High
	Monocyte/Macrophage FCGR3A Low
	Macrophage HLAII High
	Macrophage LYVE1 High
	Proliferating Macrophage
	Dendritic Cell 1
	Dendritic Cell 2
	Mature Dendritic Cell
	Langerhans
	CD14+ Monocyte
	CD16+ Monocyte
	LAM-like
	Other

Methods

Coloring for the gene annotations is mostly based on the annotation type:

MANE: MANE Select Plus Clinical transcripts.\ For non-MANE transcripts, the following conventions apply.\
coding: protein coding transcripts, including polymorphic\ pseudogenes\
non-coding: non-protein coding transcripts\
pseudogene: pseudogene transcript annotations\
problem: problem transcripts (Biotypes of\ retained_intron, TEC, or disrupted_domain)

\ \

\ \ \

Squishy-pack Display

\ Protein_coding genes\

MANE or Ensembl canonical\
- 1st: MANE Select / Ensembl canonical
- 2nd: MANE Plus Clinical
\
Coding biotypes\
- 1st: protein_coding and protein_coding_LoF
- 2nd: NMDs and NSDs
- 3rd: retained intron and protein_coding_CDS_not_defined
\
Completeness\
- 1st: full length
- 2nd: CDS start/end not found
\
CARS score (only for coding transcripts)
Transcript genomic span and length (only for non-coding transcripts)

\ Non-coding genes\

Transcript biotype\
- 1st: transcript biotype identical to gene biotype
\
Ensembl canonical
GENCODE basic
Transcript genomic span
Transcript length

\ \ \

Methods

\ The GENCODE v46 track was built from the GENCODE downloads file \ gencode.v46.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources\ were correlated with the GENCODE data to build association tables.

\ \

Related Data

\ The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a\ downloadable\ file.\ \

Description

\ \

\ gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the\ GRCh38/hg38 lift-over provided by gnomAD on their downloads site.\

\ \

\ For questions on the gnomAD data, also see the gnomAD FAQ.

\ More details on the Variant type(s) can be found on the Sequence Ontology page.

\ \

Display Conventions and Configuration

gnomAD v4.1

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

\ \

gnomAD v3.1.1

\ The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,\ except as noted below.

\ \

There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).\
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one\ variant, with additional information available on the details page, which has roughly halved the\ number of items in the bigBed.\
The bigBed has been split into two files, one with the information necessary for the track\ display, and one with the information necessary for the details page. For more information on\ this data format, please see the Data Access section below.\
The VEP annotation is shown as a table instead of spread across multiple fields.\
Intergenic variants have not been pre-filtered.\

\ \

gnomAD v3.1

\ By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters\ described below), before the track switches to dense display mode.\

\ \

\ Mouse hover on an item will display many details about each variant, including the affected gene(s),\ the variant type, and annotation (missense, synonymous, etc).\

\ \

\ Clicking on an item will display additional details on the variant, including a population frequency\ table showing allele count in each sub-population.\

\ \

\ Following the conventions on the gnomAD browser, items are shaded according to their Annotation\ type:\ \ \ \ \ \
pLoF
Missense
Synonymous
Other
\

\ Four filters are available for these tracks, the same as the underlying VCF:\

AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))\
InbreedingCoeff: Inbreeding Coefficient < -0.3\
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)\
Pass: Variant passes all 3 filters\

\ \

\ There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.\

\ \ \

UCSC Methods

\ The gnomAD v3.1.1 and v4.1 data is unfiltered.

\ For the v3.1 update only, in order to cut \ down on the amount of displayed data, the following variant\ types have been filtered out, but are still viewable in the gnomAD browser:\

Regulatory Region Variants\
Downstream/Upstream Gene Variants\
Transcription Factor Binding Site Variants\

\ \

\ For the full steps used to create the gnomAD tracks at UCSC, please see the\ hg38 gnomad makedoc.\

\ \ \

Data Access

\ \

\
# find item of interest:\
bigBedToBed genomes.bb stdout | head -4 | tail -1\
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted for brevity..]    chr1-12417-G-A    67293    902\
\
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:\
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz\
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant",  [..omitted for brevity..]\

\ \

\ The data can also be found directly from the gnomAD downloads page. Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.\

\ \

\ Please note that some annotations within the provided files may have restrictions on usage. See here for more information. \

\ \

References

\ \

\ varRep 1 bigDataUrl /gbdb/hg38/gnomAD/v4.1/exomes/exomes.bb\ dataVersion Release v4.1 (April 19, 2024)\ defaultLabelFields _displayName\ detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies\ detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1/exomes/gnomad.v4.1.exomes.details.tab.gz\ filter.AF 0.0\ filterLabel.AF Minor Allele Frequency Filter\ filterType.FILTER multipleListAnd\ filterType.variation_type multipleListOr\ filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only)\ filterValues.annot pLoF,missense,synonymous,other\ filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation\ filterValuesDefault.FILTER PASS\ filterValuesDefault.annot pLoF,missense,synonymous\ html gnomadV4.1\ itemRgb on\ labelFields rsId,_displayName\ longLabel Genome Aggregation Database (gnomAD) Exomes Variants v4.1\ mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt)
TotalAF: ${AF} (${AC}/${AN})
Genes: $genes
Annotation: $annot
FILTER: ${FILTER}
PopMaxAF: ${grpmax}
Homozygous Individuals: ${nhomalt}
Hemizygous Individuals (only in chrX & chrY): ${nhemi}\ parent gnomadVariantsV4.1 on\ priority 2\ searchIndex name,_displayName,rsId\ shortLabel gnomAD v4.1 Exomes\ skipEmptyFields on\ skipFields _displayName\ track gnomadExomesVariantsV4_1\ type bigBed 9 +\ url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$-$?dataset=gnomad_r4\ urlLabel View this variant at gnomAD\ visibility squish\ gtexEqtlDapg GTEx DAP-G eQTLs bigBed 12 + GTEx High-Confidence cis-eQTLs from DAP-G (no chrX) 3 2 0 0 0 127 127 127 0 0 0 regulation 1 bigDataUrl /gbdb/hg38/gtex/eQtl/gtexDapg.bb\ filter.clusterPip 0\ filter.pip 0\ filterLabel.clusterPip SNP Cluster PIP (Posterior Inclusion Probability)\ filterLabel.geneName Gene Symbol\ filterLabel.pip SNP PIP (Posterior Inclusion Probability)\ filterLabel.tissue Tissue\ filterText.geneName *\ filterValues.tissue Adipose_Subcutaneous,Adipose_Visceral_Omentum,Adrenal_Gland,Artery_Aorta,Artery_Coronary,Artery_Tibial,Brain_Amygdala,Brain_Anterior_cingulate_cortex_BA24,Brain_Caudate_basal_ganglia,Brain_Cerebellar_Hemisphere,Brain_Cerebellum,Brain_Cortex,Brain_Frontal_Cortex_BA9,Brain_Hippocampus,Brain_Hypothalamus,Brain_Nucleus_accumbens_basal_ganglia,Brain_Putamen_basal_ganglia,Brain_Spinal_cord_cervical_c-1,Brain_Substantia_nigra,Breast_Mammary_Tissue,Cells_Cultured_fibroblasts,Cells_EBV-transformed_lymphocytes,Colon_Sigmoid,Colon_Transverse,Esophagus_Gastroesophageal_Junction,Esophagus_Mucosa,Esophagus_Muscularis,Heart_Atrial_Appendage,Heart_Left_Ventricle,Kidney_Cortex,Liver,Lung,Minor_Salivary_Gland,Muscle_Skeletal,Nerve_Tibial,Ovary,Pancreas,Pituitary,Prostate,Skin_Not_Sun_Exposed_Suprapubic,Skin_Sun_Exposed_Lower_leg,Small_Intestine_Terminal_Ileum,Spleen,Stomach,Testis,Thyroid,Uterus,Vagina,Whole_Blood\ itemRgb on\ longLabel GTEx High-Confidence cis-eQTLs from DAP-G (no chrX)\ maxItems 100000\ mergeSpannedItems on\ mouseOver $name; SNP PIP: $pip; Cluster PIP: $clusterPip\ parent gtexEqtlHighConf off\ shortLabel GTEx DAP-G eQTLs\ showCfg on\ track gtexEqtlDapg\ type bigBed 12 +\ urls eqtlName="https://gtexportal.org/home/snp/$$" geneName="https://gtexportal.org/home/locusBrowserPage/$$" eqtlPos="hgTracks?db=$D&position=$$" genePos="hgTracks?db=$D&position=$$" geneId="https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=$$"\ visibility pack\ wgEncodeRegMarkH3k4me1H1hesc H1-hESC bigWig 0 8355 H3K4Me1 Mark (Often Found Near Regulatory Elements) on H1-hESC Cells from ENCODE 0 2 255 212 128 255 233 191 0 0 0 regulation 1 color 255,212,128\ longLabel H3K4Me1 Mark (Often Found Near Regulatory Elements) on H1-hESC Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k4me1\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel H1-hESC\ table wgEncodeBroadHistoneH1hescH3k4me1StdSig\ track wgEncodeRegMarkH3k4me1H1hesc\ type bigWig 0 8355\ wgEncodeRegMarkH3k4me3H1hesc H1-hESC bigWig 0 6957 H3K4Me3 Mark (Often Found Near Promoters) on H1-hESC Cells from ENCODE 0 2 255 212 128 255 233 191 0 0 0 regulation 1 color 255,212,128\ longLabel H3K4Me3 Mark (Often Found Near Promoters) on H1-hESC Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k4me3\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel H1-hESC\ table wgEncodeBroadHistoneH1hescH3k4me3StdSig\ track wgEncodeRegMarkH3k4me3H1hesc\ type bigWig 0 6957\ wgEncodeRegTxnCaltechRnaSeqH1hescR2x75Il200SigPooled H1-hESC bigWig 0 65535 Transcription of H1-hESC cells from ENCODE 0 2 255 212 128 255 233 191 0 0 0 regulation 1 color 255,212,128\ longLabel Transcription of H1-hESC cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegTxn\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ priority 2\ shortLabel H1-hESC\ track wgEncodeRegTxnCaltechRnaSeqH1hescR2x75Il200SigPooled\ type bigWig 0 65535\ wgEncodeRegMarkH3k27acH1hesc H1-hESC bigWig 0 14898 H3K27Ac Mark (Often Found Near Regulatory Elements) on H1-hESC Cells from ENCODE 2 2 255 212 128 255 233 191 0 0 0 regulation 1 color 255,212,128\ longLabel H3K27Ac Mark (Often Found Near Regulatory Elements) on H1-hESC Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k27ac\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel H1-hESC\ table wgEncodeBroadHistoneH1hescH3k27acStdSig\ track wgEncodeRegMarkH3k27acH1hesc\ type bigWig 0 14898\ h1hescMicroC H1-hESC Micro-C hic Micro-C Chromatin Structure on H1-hESC 0 2 0 0 0 127 127 127 0 0 0 regulation 1 bigDataUrl /gbdb/hg38/bbi/hic/4DNFI2TK7L2F.hic\ longLabel Micro-C Chromatin Structure on H1-hESC\ parent hicAndMicroC on\ shortLabel H1-hESC Micro-C\ track h1hescMicroC\ type hic\ netHprcGCA_018466845v1 HG02257.mat netAlign GCA_018466845.1 chainHprcGCA_018466845v1 HG02257.mat HG02257.pri.mat.f1_v2 (May 2021 GCA_018466845.1_HG02257.pri.mat.f1_v2) HPRC project computed Chain Nets 1 2 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02257.mat HG02257.pri.mat.f1_v2 (May 2021 GCA_018466845.1_HG02257.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018466845.1\ parent hprcChainNetViewnet off\ priority 18\ shortLabel HG02257.mat\ subGroups view=net sample=s018 population=afr subpop=acb hap=mat\ track netHprcGCA_018466845v1\ type netAlign GCA_018466845.1 chainHprcGCA_018466845v1\ highlyReproducible Highly Reproducible Regions bed 3 Highly Reproducible genomic regions for sequencing 0 2 0 0 0 127 127 127 0 0 0

Description

\ \

\ \ \

Problematic Regions

\ The Problematic Regions track contains the following subtracks:\

\ The UCSC Unusual Regions subtrack contains annotations collected at UCSC, \ put together from other tracks, our experiences and support email list\ requests over the years. For example, it contains the most well-known gene\ clusters (IGH, IGL, PAR1/2, TCRA, TCRB, etc) and annotations for the GRC\ fixed sequences, alternate haplotypes, unplaced\ contigs, pseudo-autosomal regions, and mitochondria. These loci can yield alignments with\ low-quality mapping scores and discordant read pairs, especially for short-read sequencing data.\ This data set was manually curated, based on the Genome Browser's\ assembly description, the FAQs about assembly, and the\ NCBI RefSeq "other" annotations\ track data.\
\ The ENCODE Blacklist subtrack contains a comprehensive set of regions which are troublesome\ for high-throughput Next-Generation Sequencing (NGS) aligners. These regions tend to have a very\ high ratio of multi-mapping to unique mapping reads and high variance in mappability due to\ repetitive elements such as satellite, centromeric and telomeric repeats. \
\ The GRC Exclusions subtrack contains a set of regions that have been flagged by the GRC to\ contain false duplications or contamination sequences. The GRC has now removed these sequences from\ the files that it uses to generate the reference assembly, however, removing the sequences from the\ GRCh38/hg38 assembly would trigger the next major release of the human assembly. In order to\ help users recognize these regions and avoid them in their analyses, the GRC have produced a masking\ file to be used as a companion to GRCh38, and the BED file is available from the\ GenBank FTP site.\

\ \

Highly Reproducible Regions

a Chinese Quartet, samples CQ-5, CQ-6, CQ-7, CQ-8
a HapMap Trio, samples NA10385, NA12248, NA12249
a Genome in a Bottle sample, NA12878s

\ \ Please refer to the Pan et al reference for more information on how\ these regions were defined.\

\ \

GIAB Problematic Regions

\ \

\ \ \ \

Display Conventions and Configuration

\ \

Data access

\ The raw data can be explored interactively with the Table Browser\ or the Data Integrator.\ \

\ \

Methods

\ \

MetaDome

\ \

\ \ \ \ \ \ \ \ \ \
Classification MetaDome Tolerance Score
Highly intolerant ≤ 0.175
Intolerant ≤ 0.525
Slightly intolerant ≤ 0.7
\

Classification	MetaDome Tolerance Score
Highly intolerant	≤ 0.175
Intolerant	≤ 0.525
Slightly intolerant	≤ 0.7

\ \

MTR

\ \

Green items MTR percentiles over 75\
Black items MTR percentiles between 25 and 75\
Red items MTR percentiles below 25\
Blue items No MTR score\

\ \

Methods

\ \

JARVIS

\ Scores were downloaded and converted to a single bigWig file. See the\ hg19 makeDoc and the\ hg38 makeDoc for more info.\

\ \

HMC

\ Scores were downloaded and converted to .bedGraph files with a custom Python \ script. The bedGraph files were then converted to bigWig files, as documented in our \ makeDoc hg19 build log.

\ \

MetaDome

\ See the hg19 makeDoc for details including the build script.

\ The raw MetaDome data can also be accessed via their Zenodo handle.

\ \

MTR

\ See the hg19 makeDoc entry on MTR for more info.

\ \

Data Access

\ \

\ Please refer to our\ Data Access FAQ\ for more information.\

\ \ \

Credits

\ \

\ \

\ Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and\ repeat libraries used to generate this track.\

\ \

References

\ \

\ Smit AFA, Hubley R, Green P.\ RepeatMasker Open-3.0.\ \ http://www.repeatmasker.org. 1996-2010.\

\ \

\ Repbase Update is described in:\

\ \

\ Jurka J.\ \ Repbase Update: a database and an electronic journal of repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-420.\ PMID: 10973072\

\ \

\ For a discussion of repeats in mammalian genomes, see:\

\ \

\ Smit AF.\ \ Interspersed repeats and other mementos of transposable elements in mammalian genomes.\ Curr Opin Genet Dev. 1999 Dec;9(6):657-63.\ PMID: 10607616\

\ \

\ Smit AF.\ \ The origin of interspersed repeats in the human genome.\ Curr Opin Genet Dev. 1996 Dec;6(6):743-8.\ PMID: 8994846\

\ rep 1 exonNumbers off\ group rep\ longLabel Fragments of Interrupted Repeats Joined by RepeatMasker ID\ priority 2\ shortLabel Interrupted Rpts\ track nestedRepeats\ type bed 12 +\ useScore 1\ visibility hide\ jaspar2022 JASPAR 2022 TFBS bigBed 6 + JASPAR CORE 2022 - Predicted Transcription Factor Binding Sites 0 2 0 0 0 127 127 127 1 0 0 http://jaspar.genereg.net/search?q=$$&collection=all&tax_group=all&tax_id=all&type=all&class=all&family=all&version=all regulation 1 bigDataUrl /gbdb/hg38/jaspar/JASPAR2022.bb\ filterValues.TFName Ahr::Arnt,Alx1,ALX3,Alx4,Ar,ARGFX,Arid3a,Arid3b,Arid5a,Arnt,ARNT2,ARNT::HIF1A,Arntl,Arx,ASCL1,Ascl2,Atf1,ATF2,Atf3,ATF3,ATF4,ATF6,ATF7,Atoh1,ATOH7,BACH1,Bach1::Mafk,BACH2,BARHL1,BARHL2,BARX1,BARX2,BATF,BATF3,BATF::JUN,Bcl11B,BCL6,BCL6B,Bhlha15,BHLHA15,BHLHE22,BHLHE23,BHLHE40,BHLHE41,BNC2,BSX,CDX1,CDX2,CDX4,CEBPA,CEBPB,CEBPD,CEBPE,CEBPG,CLOCK,CREB1,CREB3,CREB3L1,Creb3l2,CREB3L4,Creb5,CREM,Crx,CTCF,CTCFL,CUX1,CUX2,DBP,Ddit3::Cebpa,DLX1,Dlx2,Dlx3,Dlx4,Dlx5,DLX6,Dmbx1,Dmrt1,DMRT3,DMRTA1,DMRTA2,DMRTC2,DPRX,DRGX,Dux,DUX4,DUXA,E2F1,E2F2,E2F3,E2F4,E2F6,E2F7,E2F8,EBF1,Ebf2,EBF3,EGR1,EGR2,EGR3,EGR4,EHF,ELF1,ELF2,ELF3,ELF4,Elf5,ELK1,ELK1::HOXA1,ELK1::HOXB13,ELK1::SREBF2,ELK3,ELK4,EMX1,EMX2,EN1,EN2,EOMES,ERF,ERF::FIGLA,ERF::FOXI1,ERF::FOXO1,ERF::HOXB13,ERF::NHLH1,ERF::SREBF2,Erg,ESR1,ESR2,ESRRA,ESRRB,Esrrg,ESX1,ETS1,ETS2,ETV1,ETV2,ETV2::DRGX,ETV2::FIGLA,ETV2::FOXI1,ETV2::HOXB13,ETV3,ETV4,ETV5,ETV5::DRGX,ETV5::FIGLA,ETV5::FOXI1,ETV5::FOXO1,ETV5::HOXA2,ETV6,ETV7,EVX1,EVX2,EWSR1-FLI1,FERD3L,FEV,FIGLA,FLI1,FLI1::DRGX,FLI1::FOXI1,FOS,FOSB::JUN,FOSB::JUNB,FOS::JUN,FOS::JUNB,FOS::JUND,FOSL1,FOSL1::JUN,FOSL1::JUNB,FOSL1::JUND,FOSL2,FOSL2::JUN,FOSL2::JUNB,FOSL2::JUND,FOXA1,FOXA2,FOXA3,FOXB1,FOXC1,FOXC2,FOXD1,FOXD2,FOXD3,FOXE1,Foxf1,FOXF2,FOXG1,FOXH1,FOXI1,Foxj2,FOXJ2::ELF1,Foxj3,FOXK1,FOXK2,FOXL1,Foxl2,Foxn1,FOXN3,Foxo1,FOXO1::ELF1,FOXO1::ELK1,FOXO1::ELK3,FOXO1::FLI1,Foxo3,FOXO4,FOXO6,FOXP1,FOXP2,FOXP3,Foxq1,GABPA,GATA1,GATA1::TAL1,GATA2,Gata3,GATA4,GATA5,GATA6,GBX1,GBX2,GCM1,GCM2,GFI1,Gfi1B,Gli1,Gli2,GLI3,GLIS1,GLIS2,GLIS3,Gmeb1,GMEB2,GRHL1,GRHL2,GSC,GSC2,GSX1,GSX2,Hand1::Tcf3,HAND2,HES1,HES2,HES5,HES6,HES7,HESX1,HEY1,HEY2,Hic1,HIC2,HIF1A,HINFP,HLF,HMBOX1,Hmx1,Hmx2,Hmx3,Hnf1A,HNF1A,HNF1B,HNF4A,HNF4G,HOXA1,HOXA10,Hoxa11,Hoxa13,HOXA2,HOXA4,HOXA5,HOXA6,HOXA7,HOXA9,HOXB13,HOXB2,HOXB2::ELK1,HOXB3,HOXB4,HOXB5,HOXB6,HOXB7,HOXB8,HOXB9,HOXC10,HOXC11,HOXC12,HOXC13,HOXC4,HOXC8,HOXC9,HOXD10,HOXD11,HOXD12,HOXD12::ELK1,Hoxd13,HOXD3,HOXD4,HOXD8,HOXD9,HSF1,HSF2,HSF4,IKZF1,Ikzf3,INSM1,Irf1,IRF2,IRF3,IRF4,IRF5,IRF6,IRF7,IRF8,IRF9,Isl1,ISL2,ISX,JDP2,Jun,JUN,JUNB,JUND,JUN::JUNB,KLF1,KLF10,KLF11,KLF12,KLF13,KLF14,KLF15,KLF16,KLF17,KLF2,KLF3,KLF4,KLF5,KLF6,KLF7,KLF9,LBX1,LBX2,Lef1,Lhx1,LHX2,Lhx3,Lhx4,LHX5,LHX6,Lhx8,LHX9,LIN54,LMX1A,LMX1B,MAF,MAFA,Mafb,MAFF,Mafg,MAFG::NFE2L1,MAFK,MAF::NFE2,MAX,MAX::MYC,MAZ,Mecom,MEF2A,MEF2B,MEF2C,MEF2D,MEIS1,MEIS2,MEIS3,MEOX1,MEOX2,MGA,MGA::EVX1,MITF,mix-a,MIXL1,MLX,Mlxip,MLXIPL,MNT,MNX1,MSANTD3,MSC,Msgn1,MSX1,MSX2,Msx3,MTF1,MXI1,MYB,MYBL1,MYBL2,MYC,MYCN,MYF5,MYF6,MYOD1,MYOG,MZF1,NEUROD1,Neurod2,NEUROG1,NEUROG2,Nfat5,Nfatc1,Nfatc2,NFATC3,NFATC4,NFE2,Nfe2l2,NFIA,NFIB,NFIC,NFIC::TLX1,NFIL3,NFIX,NFKB1,NFKB2,NFYA,NFYB,NFYC,NHLH1,NHLH2,Nkx2-1,NKX2-2,NKX2-3,NKX2-4,NKX2-5,NKX2-8,Nkx3-1,Nkx3-2,NKX6-1,NKX6-2,NKX6-3,Nobox,NOTO,Npas2,Npas4,NR1D1,NR1D2,Nr1H2,NR1H2::RXRA,Nr1h3::Rxra,Nr1H4,NR1H4::RXRA,NR1I2,NR1I3,NR2C1,NR2C2,Nr2e1,Nr2e3,NR2F1,NR2F2,Nr2f6,Nr2F6,NR2F6,NR3C1,NR3C2,NR4A1,NR4A2,NR4A2::RXRA,NR5A1,Nr5A2,NR6A1,Nrf1,NRL,OLIG1,Olig2,OLIG2,OLIG3,ONECUT1,ONECUT2,ONECUT3,OSR1,OSR2,OTX1,OTX2,OVOL1,OVOL2,PATZ1,PAX1,PAX2,PAX3,PAX4,PAX5,PAX6,Pax7,PAX9,PBX1,PBX2,PBX3,PDX1,PHOX2A,PHOX2B,PITX1,PITX2,PITX3,PKNOX1,PKNOX2,PLAG1,Plagl1,PLAGL2,POU1F1,POU2F1,POU2F1::SOX2,POU2F2,POU2F3,POU3F1,POU3F2,POU3F3,POU3F4,POU4F1,POU4F2,POU4F3,POU5F1,POU5F1B,Pou5f1::Sox2,POU6F1,POU6F2,PPARA::RXRA,PPARD,PPARG,Pparg::Rxra,PRDM1,Prdm14,Prdm15,Prdm4,Prdm5,PRDM9,PROP1,PROX1,PRRX1,PRRX2,Ptf1a,Ptf1A,RARA,RARA::RXRA,RARA::RXRG,Rarb,RARB,Rarg,RARG,RAX,RAX2,RBPJ,Rbpjl,REL,RELA,RELB,REST,RFX1,RFX2,RFX3,RFX4,RFX5,Rfx6,RFX7,Rhox11,RHOXF1,RORA,RORB,RORC,RREB1,Runx1,RUNX2,RUNX3,Rxra,RXRA::VDR,RXRB,RXRG,SATB1,SCRT1,SCRT2,Sf1,SHOX,Shox2,SIX1,SIX2,Six3,Six4,SMAD2,Smad2::Smad3,SMAD2::SMAD3::SMAD4,SMAD3,Smad4,SMAD5,SNAI1,SNAI2,SNAI3,SOHLH2,Sox1,SOX10,Sox11,SOX12,SOX13,SOX14,SOX15,Sox17,SOX18,SOX2,SOX21,Sox3,SOX4,Sox5,Sox6,SOX8,SOX9,SP1,SP2,SP3,SP4,SP5,SP8,SP9,SPDEF,Spi1,SPIB,SPIC,Spz1,SREBF1,SREBF2,SRF,SRY,STAT1,STAT1::STAT2,Stat2,STAT3,Stat4,Stat5a,Stat5a::Stat5b,Stat5b,Stat6,TAL1::TCF3,TBP,TBR1,TBX1,TBX15,TBX18,TBX19,TBX2,TBX20,TBX21,TBX3,TBX4,TBX5,Tbx6,TBXT,Tcf12,TCF12,Tcf21,TCF21,TCF3,TCF4,TCF7,TCF7L1,TCF7L2,TCFL5,TEAD1,TEAD2,TEAD3,TEAD4,TEF,TFAP2A,TFAP2B,TFAP2C,TFAP2E,TFAP4,TFAP4::ETV1,TFAP4::FLI1,TFCP2,Tfcp2l1,TFDP1,TFE3,TFEB,TFEC,TGIF1,TGIF2,TGIF2LX,TGIF2LY,THAP1,Thap11,THRA,THRB,TLX2,TP53,TP63,TP73,TRPS1,TWIST1,Twist2,UNCX,USF1,USF2,VAX1,VAX2,Vdr,VENTX,VEZF1,VSX1,VSX2,Wt1,XBP1,Yy1,YY2,ZBED1,ZBED2,ZBTB12,ZBTB14,ZBTB18,ZBTB26,ZBTB32,ZBTB33,ZBTB6,ZBTB7A,ZBTB7B,ZBTB7C,ZEB1,ZFP14,Zfp335,ZFP42,ZFP57,Zfx,ZIC1,Zic1::Zic2,Zic2,Zic3,ZIC4,ZIC5,ZIM3,ZKSCAN1,ZKSCAN3,ZKSCAN5,ZNF135,ZNF136,ZNF140,ZNF143,ZNF148,ZNF16,ZNF189,ZNF211,ZNF214,ZNF24,ZNF257,ZNF263,ZNF274,ZNF281,ZNF282,ZNF317,ZNF320,ZNF324,ZNF331,ZNF341,ZNF343,ZNF354A,ZNF354C,ZNF382,ZNF384,ZNF410,ZNF416,ZNF417,ZNF418,Znf423,ZNF449,ZNF454,ZNF460,ZNF528,ZNF530,ZNF549,ZNF574,ZNF582,ZNF610,ZNF652,ZNF667,ZNF669,ZNF675,ZNF680,ZNF682,ZNF684,ZNF692,ZNF701,ZNF707,ZNF708,ZNF740,ZNF75D,ZNF76,ZNF768,ZNF784,ZNF8,ZNF816,ZNF85,ZNF93,ZSCAN29,ZSCAN31,ZSCAN4\ labelFields TFName\ longLabel JASPAR CORE 2022 - Predicted Transcription Factor Binding Sites\ motifPwmTable hgFixed.jasparCore2022\ parent jaspar off\ priority 2\ shortLabel JASPAR 2022 TFBS\ track jaspar2022\ type bigBed 6 +\ visibility hide\ lovdLong LOVD Variants >= 50 bp bigBed 9 + LOVD: Leiden Open Variation Database Public Variants, long >= 50 bp variants 0 2 0 0 0 127 127 127 0 0 0 phenDis 1 bigDataUrl /gbdb/hg38/lovd/lovd.hg38.long.bb\ group phenDis\ longLabel LOVD: Leiden Open Variation Database Public Variants, long >= 50 bp variants\ mergeSpannedItems on\ noScoreFilter on\ parent lovdComp\ shortLabel LOVD Variants >= 50 bp\ track lovdLong\ type bigBed 9 +\ urls id="https://varcache.lovd.nl/redirect/$$"\ visibility hide\ alllowmapandsegdupregions LowMap+SegDup bigBed 3 Genome In a Bottle: lowMap+SegDup regions 1 2 0 0 0 127 127 127 0 0 0 map 1 bigDataUrl /gbdb/hg38/problematic/GIAB/alllowmapandsegdupregions.bb\ longLabel Genome In a Bottle: lowMap+SegDup regions\ parent problematicGIAB on\ shortLabel LowMap+SegDup\ track alllowmapandsegdupregions\ type bigBed 3\ visibility dense\ tgpNA19675_m004_MXL m004 MXL Trio vcfPhasedTrio 1000 Genomes m004 Mexican Ancestry from Los Angeles Trio 2 2 0 0 0 127 127 127 0 0 23 chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX, varRep 0 longLabel 1000 Genomes m004 Mexican Ancestry from Los Angeles Trio\ parent tgpTrios\ shortLabel m004 MXL Trio\ track tgpNA19675_m004_MXL\ type vcfPhasedTrio\ vcfChildSample NA19675|child\ vcfParentSamples NA19678|mother,NA19679|father\ visibility full\ MaxCounts_Rev Max counts of CAGE reads (rev) bigWig Max counts of CAGE reads reverse 2 2 0 0 255 127 127 255 0 0 0 regulation 0 bigDataUrl /gbdb/hg38/fantom5/ctssMaxCounts.rev.bw\ color 0,0,255\ dataVersion FANTOM5 reprocessed7\ longLabel Max counts of CAGE reads reverse\ parent Max_counts_multiwig\ shortLabel Max counts of CAGE reads (rev)\ subGroups category=max strand=reverse\ track MaxCounts_Rev\ type bigWig\ cadd1_7_C Mutation: C bigWig CADD 1.7 Score: Mutation is C 1 2 100 130 160 177 192 207 0 0 0 phenDis 0 bigDataUrl /gbdb/hg38/cadd1.7/c.bw\ longLabel CADD 1.7 Score: Mutation is C\ maxHeightPixels 128:20:8\ parent cadd1_7 on\ shortLabel Mutation: C\ track cadd1_7_C\ type bigWig\ viewLimits 10:50\ viewLimitsMax 0:100\ visibility dense\ revelC Mutation: C bigWig REVEL: Mutation is C 1 2 150 80 200 202 167 227 0 0 0 phenDis 0 bigDataUrl /gbdb/hg38/revel/c.bw\ longLabel REVEL: Mutation is C\ maxHeightPixels 128:20:8\ maxWindowToDraw 10000000\ maxWindowToQuery 500000\ mouseOverFunction noAverage\ parent revel on\ shortLabel Mutation: C\ track revelC\ type bigWig\ viewLimits 0:1.0\ viewLimitsMax 0:1.0\ visibility dense\ caddC Mutation: C bigWig CADD 1.6 Score: Mutation is C 1 2 100 130 160 177 192 207 0 0 0 phenDis 0 bigDataUrl /gbdb/hg38/cadd/c.bw\ longLabel CADD 1.6 Score: Mutation is C\ maxHeightPixels 128:20:8\ parent cadd on\ shortLabel Mutation: C\ track caddC\ type bigWig\ viewLimits 10:50\ viewLimitsMax 0:100\ visibility dense\ platinumNA12877 NA12877 vcfTabix Platinum genome variant NA12877 3 2 0 0 0 127 127 127 0 0 23 chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX, varRep 1 bigDataUrl /gbdb/hg38/platinumGenomes/NA12877.vcf.gz\ chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX\ configureByPopup off\ group varRep\ longLabel Platinum genome variant NA12877\ maxWindowToDraw 200000\ parent platinumGenomes\ shortLabel NA12877\ showHardyWeinberg on\ track platinumNA12877\ type vcfTabix\ vcfDoFilter off\ vcfDoMaf off\ visibility pack\ refSeqComposite NCBI RefSeq genePred RefSeq genes from NCBI 1 2 0 0 0 127 127 127 0 0 0

Description

\ The NCBI RefSeq Genes composite track shows human protein-coding and non-protein-coding\ genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use\ coordinates provided by RefSeq, except for the UCSC RefSeq track, which UCSC produces by\ realigning the RefSeq RNAs to the genome. This realignment may result in occasional differences\ between the annotation coordinates provided by UCSC and NCBI. For RNA-seq analysis, we advise\ using NCBI aligned tables like RefSeq All or RefSeq Curated. See the \ Methods section for more details about how the different tracks were \ created.

\ Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, \ submit additions and corrections, or ask for help concerning RefSeq records.

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ This track is a composite track that contains differing data sets.\ To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to \ hide. Note: Not all subtracts are available on all assemblies.

\ \ The possible subtracks include:\

RefSeq aligned annotations and UCSC alignment of RefSeq annotations\

\ \

\ The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq HGMD,\ RefSeq Select/MANE and UCSC RefSeq tracks follow the display conventions for\ gene prediction tracks.\ The color shading indicates the level of review the RefSeq record has undergone:\ predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq.

\ \

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Color Level of review
Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information.
Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff.
Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted.
\

Color	Level of review
	Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information.
	Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff.
	Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted.

\ \

\ The item labels and codon display properties for features within this track can be configured \ through the check-box controls at the top of the track description page. To adjust the settings \ for an individual subtrack, click the wrench icon next to the track name in the subtrack list .

\ Label: By default, items are labeled by gene name. Click the appropriate Label \ option to display the accession name or OMIM identifier instead of the gene name, show all or a \ subset of these labels including the gene name, OMIM identifier and accession names, or turn off \ the label completely.
\ Codon coloring: This track has an optional codon coloring feature that \ allows users to quickly validate and compare gene predictions. To display codon colors, select the\ genomic codons option from the Color track by codons pull-down menu. For more \ information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.

\ \

The RefSeq Diffs track contains five different types of inconsistency between the\ reference genome sequence and the RefSeq transcript sequences. The five types of differences are\ as follows:\

\ mismatch – aligned but mismatching bases, plus HGVS g. \ to show the genomic change required to match the transcript and HGVS c./n. \ to show the transcript change required to match the genome.
\ short gap – genomic gaps that are too small to be introns (arbitrary cutoff of\ \ < 45 bp), most likely insertions/deletion variants or errors, with HGVS g. and c./n. \ \ showing differences.
\ shift gap – shortGap items whose placement could be shifted left and/or right on\ \ the genome due to repetitive sequence, with HGVS c./n. position range of ambiguous region \ \ in transcript. Here, thin and thick lines are used -- the thin line shows the span of the\ \ repetitive sequence, and the thick line shows the rightmost shifted gap.\
\ double gap – genomic gaps that are long enough to be introns but that skip over \ \ transcript sequence (invisible in default setting), with HGVS c./n. deletion.
\ skipped – sequence at the beginning or end of a transcript that is not aligned to\ the genome\ (invisible in default setting), with HGVS c./n. deletion

\ \ HGVS Terminology (Human Genome Variation Society):\ \ g. = genomic sequence ; c. = coding DNA sequence ; n. = non-coding RNA reference sequence.\

\ \

\ When reporting HGVS with RefSeq sequences, to make sure that results from\ research articles can be mapped to the genome unambiguously, \ please specify the RefSeq annotation release displayed on the transcript's\ Genome Browser details page and also the RefSeq transcript ID with version\ (e.g. NM_012309.4 not NM_012309). \

\ \ \ \

Methods

\ Tracks contained in the RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using \ data from the NCBI RefSeq project. Data files were downloaded from RefSeq in GFF file format and \ converted to the genePred and PSL table formats for display in the Genome Browser. Information about\ the NCBI annotation pipeline can be found \ here.

\ \

The RefSeq Diffs track is generated by UCSC using NCBI's RefSeq RNA alignments.

\ The UCSC RefSeq Genes track is constructed using the same methods as previous RefSeq Genes tracks.\ RefSeq RNAs were aligned against the human genome using BLAT. Those with an alignment of\ less than 15% were discarded. When a single RNA aligned in multiple places, the alignment\ having the highest base identity was identified. Only alignments having a base identity\ level within 0.1% of the best and at least 96% base identity with the genomic sequence were\ kept.

\ \

Data Access

\ The raw data for these tracks can be accessed in multiple ways. It can be explored interactively \ using the REST API,\ Table Browser or\ Data Integrator. The tables can also be accessed programmatically through our\ public MySQL server or downloaded from our\ downloads server for local processing. The previous track versions are available\ in the archives of our downloads server. You can also access any RefSeq table\ entries in JSON format through our \ JSON API.

\ The data in the RefSeq Other and RefSeq Diffs tracks are organized in \ bigBed file format; more\ information about accessing the information in this bigBed file can be found\ below. The other subtracks are associated with database tables as follows:

genePred format:
PSL format:

\ The first column of each of these tables is "bin". This column is designed\ to speed up access for display in the Genome Browser, but can be safely ignored in downstream\ analysis. You can read more about the bin indexing system\ here.

\ The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed \ files, which can be obtained from our downloads server here,\ ncbiRefSeqOther.bb and \ ncbiRefSeqDiffs.bb.\ Individual regions or the whole set of genome-wide annotations can be obtained using our tool\ bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system from the utilities directory linked below. For example, to extract only\ annotations in a given region, you could use the following command:

\ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/ncbiRefSeq/ncbiRefSeqOther.bb\ -chrom=chr16 -start=34990190 -end=36727467 stdout

\ You can download a GTF format version of the RefSeq All table from the \ GTF downloads directory.\ The genePred format tracks can also be converted to GTF format using the\ genePredToGtf utility, available from the\ utilities directory on the UCSC downloads \ server. The utility can be run from the command line like so:

\ genePredToGtf hg38 ncbiRefSeqPredicted ncbiRefSeqPredicted.gtf\

\ Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore \ must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access\ section.

\ A file containing the RNA sequences in FASTA format for all items in the RefSeq All, RefSeq Curated, \ and RefSeq Predicted tracks can be found on our downloads server\ here.

\ Please refer to our mailing list archives for questions.

\ \

\ Previous versions of the ncbiRefSeq set of tracks can be found on our archive download server.\

\ \

Credits

\ This track was produced at UCSC from data generated by scientists worldwide and curated by the\ NCBI RefSeq project.

\ \

References

\ Kent WJ.\ BLAT - the BLAST-like \ alignment tool. Genome Res. 2002 Apr;12(4):656-64.\ PMID: 11932250; PMC: PMC187518

\ Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\ Landrum MJ, McGarvey KM et al.\ RefSeq: an update on mammalian reference sequences.\ Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63.\ PMID: 24259432; PMC: \ PMC3965018

\ Pruitt KD, Tatusova T, Maglott DR.\ \ NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts \ and proteins.\ Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.\ PMID: 15608248; PMC: PMC539979

\ genes 1 allButtonPair on\ compositeTrack on\ dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqVersion.txt\ dbPrefixLabels hg="HGNC" dm="FlyBase" ce="WormBase" rn="RGD" sacCer="SGD" danRer="ZFIN" mm="MGI" xenTro="XenBase"\ dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="http://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="http://www.informatics.jax.org/marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$"\ dragAndDrop subTracks\ group genes\ longLabel RefSeq genes from NCBI\ noInherit on\ priority 2\ shortLabel NCBI RefSeq\ track refSeqComposite\ type genePred\ visibility dense\ chainHg19ReMap NCBI ReMap hg19 chain hg19 NCBI ReMap alignments to hg19/GRCh37 0 2 0 0 0 127 127 127 0 0 0 map 1 chainLinearGap medium\ chainMinScore 3000\ longLabel NCBI ReMap alignments to hg19/GRCh37\ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb hg19\ parent liftHg19\ priority 2\ shortLabel NCBI ReMap hg19\ track chainHg19ReMap\ type chain hg19\ omimGene2 OMIM Genes bed 4 OMIM Gene Phenotypes - Dark Green Can Be Disease-causing 1 2 0 80 0 127 167 127 0 0 0 http://www.omim.org/entry/

Description

\ \

\ \ \

\ \

\ The OMIM data are separated into three separate tracks:\

\ \

OMIM Alleles \
Variants in the OMIM database that have associated \ dbSNP identifiers. This track is currently unavailable on the hg38 assembly,\ as it depends on dbSNP data that has not been released yet.\ \

OMIM Genes\
The genomic positions of gene entries in the OMIM \ database. The coloring indicates the associated OMIM phenotype map key.\

\ \

OMIM Phenotypes - Gene Unknown\
Regions known to be associated with a phenotype, \ but for which no specific gene is known to be causative. This track \ also includes known multi-gene syndromes.\

\ \

\ \ \

\ This track shows the genomic positions of all gene entries in the Online Mendelian\ Inheritance in Man (OMIM) database.\

\ \

Display Conventions and Configuration

\ \

Genomic locations of OMIM gene entries are displayed as solid blocks. The entries are colored\ according to the associated OMIM phenotype map key (if any):\

Lighter Green for phenotype map key 1 OMIM records\ - the disorder has been placed on the map based on its association with\ a gene, but the underlying defect is not known.\
Light Green for phenotype map key 2 OMIM records\ - the disorder has been placed on the map by linkage; no mutation has\ been found.\
Dark Green for phenotype map key 3 OMIM records\ - the molecular basis for the disorder is known; a mutation has been\ found in the gene.\
Purple for phenotype map key 4 OMIM records\ - a contiguous gene deletion or duplication syndrome; multiple genes\ are deleted or duplicated causing the phenotype.\
Light Gray for Others\ - no associated OMIM phenotype map key info available.\

Gene symbol and disease information, when available, are displayed on the details page for an\ item, and links to related RefSeq Genes and UCSC Genes are given.\

The descriptions of the OMIM entries are shown on the main browser display when Full display\ mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry. Items\ displayed can be filtered according to phenotype map key on the track controls page. \

\ \

Methods

\ The mappings displayed in this track are based on OMIM gene entries, their Entrez Gene IDs, and\ the corresponding RefSeq Gene locations:\

The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap.\
The data file mim2gene.txt from OMIM was processed and loaded into the MySQL table omim2gene.\
Entries in genemap.txt having disorder info were parsed and loaded into the \ omimPhenotype table.\
For each OMIM gene in the omim2gene table, the\ Entrez Gene ID was used to get the\ corresponding RefSeq Gene ID via\ the ncbiRefLink table, and the RefSeq ID was used to get the genomic location from the\ ncbiRefSeq table. The OMIM gene IDs and corresponding RefSeq Gene locations were loaded into\ the omimGene2 table, the primary table for this track.\
\

\ \

Data Access

\ If you need the OMIM data in exactly the format of the UCSC Genome Browser,\ for example if you are running a UCSC Genome Browser local installation (a partial "mirror"),\ please create a user account on omim.org and contact OMIM via\ https://omim.org/contact. Send them your OMIM\ account name and request access to the UCSC Genome Browser "entitlement". They will\ then grant you access to a MySQL/MariaDB data dump that contains all UCSC\ Genome Browser OMIM tables.

\ Please refer to our searchable\ mailing list archives\ for more questions and example queries, or our\ Data Access FAQ\ for more information.

\ \

Example: Retrieve phenotype, Mode of Inheritance, and other OMIM data within a range

Go to Table Browser, make sure the right dataset is selected:\ group: Phenotype and Literature, track: OMIM Genes, table: omimGene2.
Define region of interest by entering coordinates or a gene symbol into the "Position" textbox, such as\ chr1:11,106,535-11,262,551 or MTOR, or upload a list.
Format your data by setting the "Output format" dropdown to "selected fields from primary\ and related Tables" and click . This \ brings up the data field and linked table selection page.
Select chrom, chromStart, chromEnd, and name from omimGene2 table. Then select the related tables omim2gene\ and omimPhenotype and click .\ This brings up the fields of the linked tables, where you can select approvedGeneSymbol,\ omimID, description, omimPhenotypeMapKey, and inhMode.

Click on the to proceed to the results page:\

chr1\	11106534\	11262551\	MTOR\	601231,\	Smith-Kingsmore syndrome,Focal cortical dysplasia, type II, somatic,\	3,\	Autosomal dominant

For a quick link to pre-fill these options, click \ \ this session link.\ \

\ \

Credits

\ Thanks to OMIM and NCBI for the use of their data. This track was\ constructed by Fan Hsu, Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group.

\ \

References

Amberger J, Bocchini CA, Scott AF, Hamosh A. \ McKusick's Online Mendelian Inheritance in Man (OMIM®). \ Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. Epub 2008 Oct 8.\

\ Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. \ Online Mendelian Inheritance in Man (OMIM), a knowledgebase of \ human genes and genetic disorders. \ Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7.\

Description

\ \

\ Below is a schematic diagram of the types of regulatory regions: \

ReMap 2022 Atlas (all peaks for each analyzed data set)
ReMap 2022 Non-redundant peaks (merged similar target)
ReMap 2022 Cis Regulatory Modules

\ \

Display Conventions and Configuration

\ Each transcription factor follows a specific RGB color.\
\ ChIP-seq peak summits are represented by vertical bars.\
\ Hsap: A data set is defined as a ChIP/Exo-seq experiment in a given\ GEO/ArrayExpress/ENCODE series (e.g. GSE41561), for a given TF (e.g. ESR1), in\ a particular biological condition (e.g. MCF-7).\
Data sets are labeled with the concatenation of these three pieces of\ information (e.g. GSE41561.ESR1.MCF-7).\
\ Atha: The data set is defined as a ChIP-seq experiment in a given series\ (e.g. GSE94486), for a given target (e.g. ARR1), in a particular biological\ condition (i.e. ecotype, tissue type, experimental conditions; e.g.\ Col-0_seedling_3d-6BA-4h).\
Data sets are labeled with the concatenation of these three pieces of\ information (e.g. GSE94486.ARR1.Col-0_seedling_3d-6BA-4h).\

\ \

Methods

\ \

GEO & ArrayExpress

\ \

ENCODE

Assay: "ChIP-seq"
Organism: "Homo sapiens"
Target of assay: "transcription factor"
Available data: "fastq" on 2016 June 21st

\ Metadata information in JSON format and FASTQ files\ were retrieved using the Python requests module.\

\ The underlying expression matrix and TSI values can be obtained from the\ miRNA tissue atlas website, in the\ data_matrix_quantile.txt and tsi_quantile.csv files.\

\ \

References

\ expression 1 barChartBars adipocyte artery colon dura_mater kidney liver lung muscle myocardium skin spleen stomach testis thyroid small_intestine_duodenum small_intestine_jejunum pancreas kidney_glandula_suprarenalis kidney_cortex_renalis kidney_medulla_renalis esophagus prostate bone_marrow vein lymph_node nerve_not_specified pleura brain_pituitary_gland spinal_cord brain_thalamus brain_white_matter brain_nucleus_caudatus brain_gray_matter brain_cerebral_cortex_temporal brain_cerebral_cortex_frontal brain_cerebral_cortex_occipital brain_cerebellum\ barChartColors #F7A028 #F73528 #DEBE98 #86BF80 #CDB79E #CDB79E #9ACD32 #7A67AE #9745AC #1E90FF \\#CDB79E #FFD39B #A6A6A6 #008B45 #CDB79E #CDB79E #CD9B1D \\#CDB79E #CDB79E #CDB79E #AC8F69 #D9D9D9 #BD3487 \\#FF00FF #EE82EE #F7E300 #73A585 #B4EEB4 #EEEE00 \\#EEEE00 #EEEE00 #EEEE00 #EEEE00 \\#EEEE00 #EEEE00 \\#EEEE00 #EEEE00\ barChartLabel Tissue\ barChartMatrixUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample2Matrix.txt\ barChartSampleUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample2.txt\ barChartUnit Quantile_Norm_Expr\ bigDataUrl /gbdb/hg38/bbi/miRnaAtlasSample2.bb\ configurable on\ group expression\ html miRnaAtlas\ longLabel miRNA Tissue Atlas microRna Expression\ maxLimit 52000\ parent miRnaAtlasSample2\ searchIndex name\ shortLabel Sample 2\ subGroups view=b_B\ track miRnaAtlasSample2BarChart\ url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$\ url2Label miRBase v21 Precursor Accession:\ visibility full\ snpediaText SNPedia with text bed 4 SNPedia pages with manually typed text 0 2 50 0 100 152 127 177 0 0 0 https://www.snpedia.com/index.php/$$ phenDis 1 color 50,0,100\ exonNumbers off\ itemDetailsHtmlTable snpediaTextHtml\ longLabel SNPedia pages with manually typed text\ parent snpedia\ shortLabel SNPedia with text\ track snpediaText\ type bed 4\ url https://www.snpedia.com/index.php/$$\ urlLabel Link to SNPedia page:\ TotalCounts_Rev Total counts of CAGE reads (rev) bigWig Total counts of CAGE reads reverse 2 2 0 0 255 127 127 255 0 0 0 regulation 0 bigDataUrl /gbdb/hg38/fantom5/ctssTotalCounts.rev.bw\ color 0,0,255\ dataVersion FANTOM5 reprocessed7\ longLabel Total counts of CAGE reads reverse\ parent Total_counts_multiwig\ shortLabel Total counts of CAGE reads (rev)\ subGroups category=total strand=reverse\ track TotalCounts_Rev\ type bigWig\ pliByTranscript Transcript LoF v2 bigBed 12 + gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v2.1.1 3 2 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r2_1 varRep 1 bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.bb\ filter._pli 0:1\ filterByRange._pli on\ filterLabel._pli Show only items between this pLI range\ itemRgb on\ labelFields name,geneName\ longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v2.1.1\ mouseOverField _mouseOver\ parent constraintV2 off\ priority 2\ searchIndex name,geneName\ shortLabel Transcript LoF v2\ subGroups view=v2\ track pliByTranscript\ type bigBed 12 +\ url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r2_1\ urlLabel View this Transcript on the gnomAD browser\ pliByTranscriptV4 Transcript LoF v4 bigBed 12 + gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4 0 2 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4 varRep 1 bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.v4.bb\ filter._pli 0:1\ filterByRange._pli on\ filterLabel._pli Show only items between this pLI range\ itemRgb on\ labelFields name,geneName\ longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4\ mouseOverField _mouseOver\ parent constraintV4\ priority 2\ searchIndex name,geneName\ shortLabel Transcript LoF v4\ subGroups view=v4\ track pliByTranscriptV4\ type bigBed 12 +\ url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4\ urlLabel View this Transcript on the gnomAD browser\ pliByTranscriptV4_1 Transcript LoF v4.1 bigBed 12 + gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4.1 3 2 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4 varRep 1 bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.v4.1.bb\ filter._pli 0:1\ filterByRange._pli on\ filterLabel._pli Show only items between this pLI range\ itemRgb on\ labelFields name,geneName\ longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4.1\ mouseOverField _mouseOver\ parent constraintV4_1\ pennantIcon New red ../goldenPath/newsarch.html#093024 "September 30, 2024"\ priority 2\ searchIndex name,geneName\ shortLabel Transcript LoF v4.1\ subGroups view=v4_1\ track pliByTranscriptV4_1\ type bigBed 12 +\ url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4\ urlLabel View this Transcript on the gnomAD browser\ missenseByTranscript Transcript Missense v2 bigBed 12 + gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v2.1.1 3 2 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r2_1 varRep 1 bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.bb\ filter._zscore -20:11\ filterByRange._zscore on\ filterLabel._zscore Show only items between this Z-score range\ labelFields name,geneName\ longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v2.1.1\ mouseOverField _mouseOver\ parent constraintV2 off\ priority 2\ searchIndex name,geneName\ shortLabel Transcript Missense v2\ subGroups view=v2\ track missenseByTranscript\ type bigBed 12 +\ url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r2_1\ urlLabel View this Transcript on the gnomAD browser\ missenseByTranscriptV4 Transcript Missense v4 bigBed 12 + gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4 0 2 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4 varRep 1 bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.v4.bb\ filter._zscore -20:11\ filterByRange._zscore on\ filterLabel._zscore Show only items between this Z-score range\ labelFields name,geneName\ longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4\ mouseOverField _mouseOver\ parent constraintV4\ priority 2\ searchIndex name,geneName\ shortLabel Transcript Missense v4\ subGroups view=v4\ track missenseByTranscriptV4\ type bigBed 12 +\ url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4\ urlLabel View this Transcript on the gnomAD browser\ missenseByTranscriptV4_1 Transcript Missense v4.1 bigBed 12 + gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4.1 3 2 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4 varRep 1 bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.v4.1.bb\ filter._zscore -20:11\ filterByRange._zscore on\ filterLabel._zscore Show only items between this Z-score range\ labelFields name,geneName\ longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4.1\ mouseOverField _mouseOver\ parent constraintV4_1\ pennantIcon New red ../goldenPath/newsarch.html#093024 "September 30, 2024"\ priority 2\ searchIndex name,geneName\ shortLabel Transcript Missense v4.1\ subGroups view=v4_1\ track missenseByTranscriptV4_1\ type bigBed 12 +\ url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4\ urlLabel View this Transcript on the gnomAD browser\ unipAliTrembl TrEMBL Aln. bigPsl UCSC alignment of TrEMBL proteins to genome 0 2 0 0 0 127 127 127 0 0 0 genes 1 baseColorDefault genomicCodons\ baseColorTickColor contrastingColor\ baseColorUseCds given\ bigDataUrl /gbdb/hg38/uniprot/unipAliTrembl.bb\ indelDoubleInsert on\ indelQueryInsert on\ itemRgb on\ labelFields name,acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt\ longLabel UCSC alignment of TrEMBL proteins to genome\ mouseOverField protFullNames\ parent uniprot off\ priority 2\ searchIndex name,acc\ shortLabel TrEMBL Aln.\ showDiffBasesAllScales on\ skipFields isMain\ track unipAliTrembl\ type bigPsl\ urls acc="https://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" refseq="https://www.ncbi.nlm.nih.gov/nuccore/$$" refSeqProt="https://www.ncbi.nlm.nih.gov/protein/$$" ncbiGene="https://www.ncbi.nlm.nih.gov/gene/$$" entrezGene="https://www.ncbi.nlm.nih.gov/gene/$$" ensGene="https://www.ensembl.org/Gene/Summary?g=$$"\ visibility hide\ TSS_activity_read_counts TSS activity - read counts bigWig FANTOM5: TSS activity per sample read counts 0 2 0 0 0 127 127 127 0 0 0

Description

\ \

Display Conventions and Configuration

\ \

Items in this track are colored according to their strand orientation. Blue\ indicates alignment to the negative strand, and red indicates\ alignment to the positive strand.\

\ \

Methods

Protocol

hCAGE
LQhCAGE

Samples

Primary cell
Tissue
Cell Line
Time course
Fractionation

TSS peaks

TSS (CAGE) peaks\
- the robust peaks
\
TSS summary profiles\
- Total counts and TPM (tags per million) in all the samples
- Maximum counts and TPM among the samples
\

\ \

TSS activity

\ \

Categories of individual samples: - Cell Line hCAGE; - Cell Line LQhCAGE; - fractionation hCAGE; - Primary cell hCAGE; - Primary cell LQhCAGE; - Time course hCAGE; - Tissue hCAGE

\ \

Data Access

\ \

\ The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website.

\ \

Credits

\ \

References

\ \

\ regulation 0 boxedCfg on\ compositeTrack on\ dataVersion FANTOM5 reprocessed7\ dimensions dimX=sequenceTech dimY=category dimA=strand\ html fantom5.html\ longLabel FANTOM5: TSS activity per sample read counts\ priority 2\ shortLabel TSS activity - read counts\ showSubtrackColorOnUi off\ sortOrder category=+ sequenceTech=+\ subGroup1 sequenceTech Sequence_Tech hCAGE=hCAGE LQhCAGE=LQhCAGE\ subGroup2 category Category cellLine=cellLine fractionation=fractionation primaryCell=primaryCell tissue=tissue AoSMC_response_to_FGF2=AoSMC_response_to_FGF2_timecourse AoSMC_response_to_IL1b=AoSMC_response_to_IL1b_timecourse ES_to_cardiomyocyte=ES_to_cardiomyocyte_timecourse Embryoid_body_to_melanocyte=Embryoid_body_to_melanocyte_timecourse Epithelial_to_mesenchymal=Epithelial_to_mesenchymal_timecourse Human_iPS_to_neuron_Downs_syndrome_1=Human_iPS_to_neuron_Downs_syndrome_1_timecourse Human_iPS_to_neuron_Downs_syndrome_2=Human_iPS_to_neuron_Downs_syndrome_2_timecourse Human_iPS_to_neuron_wt_1=Human_iPS_to_neuron_wt_1_timecourse Human_iPS_to_neuron_wt_2=Human_iPS_to_neuron_wt_2_timecourse Lymphatic_EC_response_to_VEGFC=Lymphatic_EC_response_to_VEGFC_timecourse MCF7_response_to_EGF=MCF7_response_to_EGF_timecourse MCF7_response_to_HRG=MCF7_response_to_HRG_timecourse MSC_to_adipocyte_human=MSC_to_adipocyte_human_timecourse Macrophage_influenza_infection=Macrophage_influenza_infection_timecourse Macrophage_response_to_LPS=Macrophage_response_to_LPS_timecourse Myoblast_to_myotube_wt_and_DMD=Myoblast_to_myotube_wt_and_DMD_timecourse Preadipocyte_to_adipocyte=Preadipocyte_to_adipocyte_timecourse Rinderpest_infection_series=Rinderpest_infection_series_timecourse Saos_calcification=Saos_calcification_timecourse timecourse=other_samples_in_timecourse\ subGroup3 strand Strand forward=forward reverse=reverse\ superTrack fantom5\ track TSS_activity_read_counts\ type bigWig\ visibility hide\ umap36 Umap S36 bigBed 6 Single-read mappability with 36-mers 0 2 80 70 240 167 162 247 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k36.Unique.Mappability.bb\ color 80,70,240\ longLabel Single-read mappability with 36-mers\ parent umapBigBed off\ priority 2\ shortLabel Umap S36\ subGroups view=SR\ track umap36\ visibility hide\ cpgIslandExtUnmasked Unmasked CpG bed 4 + CpG Islands on All Sequence (Islands < 300 Bases are Light Green) 0 2 0 100 0 128 228 128 0 0 0

Description

\ \

\ The unmasked version of the track displays potential CpG islands\ that exist in repeat regions and would otherwise not be visible\ in the repeat masked version.\

\ \

\ By default, only the masked version of the track is displayed. To view the\ unmasked version, change the visibility settings in the track controls at\ the top of this page.\

\ \

Methods

\ \

GC content of 50% or greater
length greater than 200 bp
ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the \ \ basis of the number of Gs and Cs in the segment

\ \

    Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)

\ \ where N = length of sequence.

\ The calculation of the track data is performed by the following command sequence:\

\
twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\\
  | cpg_lh /dev/stdin 2> cpg_lh.err \\\
    |  awk '{$2 = $2 - 1; width = $3 - $2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\\
     | sort -k1,1 -k2,2n > cpgIsland.bed\

\ The unmasked track data is constructed from\ twoBitToFa -noMask output for the twoBitToFa command.\

\ This track set shows GWAS meta-analyses from the \ \ COVID-19 Host Genetics Initiative (HGI): \ a collaborative effort to facilitate \ the generation, analysis and sharing of COVID-19 host genetics research.\ The COVID-19 HGI organizes meta-analyses across multiple studies contributed by \ partners world-wide\ to identify the genetic determinants of SARS-CoV-2 infection susceptibility and disease severity \ and outcomes. Moreover, the COVID-19 HGI also aims to provide a platform for study partners to \ share analytical results in the form of summary statistics and/or individual level data where \ possible.\

\ \

\ The specific phenotypes studied by the COVID-19 HGI are those that benefit from maximal sample \ size: primary analysis on disease severity. Two meta-analyses are represented in this track:\

\ \

ANA_C2_V2: covid vs. population (6696 cases from 18 studies)
ANA_B2_V2: hospitalized covid vs. population (3199 cases from 8 studies)

\ \

Display Conventions

\ Displayed items are colored by GWAS effect: red for positive, blue for negative. \ The height of the item reflects the effect size. The effect size, defined as the \ contribution of a SNP to the genetic variance of the trait, was measured as beta coefficient \ (beta). The higher the absolute value of the beta coefficient, the stronger the effect.\ The color saturation indicates statistical significance: p-values smaller than 1e-5\ are brightly colored (bright red\ \ , bright blue\ \ ),\ those with less significance (p >= 1e-5) are paler (light red\ \ , light blue\ \ ). For better visualization of the data, only SNPs with p-values smaller than 1e-3 are \ displayed by default. \

\ \

Methods

\ COVID-19 Host Genetics Initiative (HGI) GWAS meta-analysis round 3 (July 2020) results were used \ in this study. Each participating study partner submitted GWAS summary statistics for up to four \ of the COVID-19 phenotype definitions.\

\ Data were generated from genome-wide SNP array and whole exome and genome\ sequencing, leveraging the impact of both common and rare variants. The statistical analysis\ performed takes into account differences between sex, ancestry, and date of sample collection. \ Alleles were harmonized across studies and reported allele frequencies are based on gnomAD \ version 3.0 reference data. Most study partners used the SAIGE GWAS pipeline in order \ to generate summary statistics used for the COVID-19 HGI meta-analysis. The summary statistics \ of individual studies were manually examined for inflation, \ deflation, and excessive number of false positives. Qualifying summary statistics were filtered for \ INFO > 0.6 and MAF > 0.0001 prior to meta-analyzing the entirety of the data. \ The meta-analysis was done using inverse variance weighting of effects method, accounting for \ strand differences and allele flips in the individual studies. \

\ The meta-analysis results of variants appearing in at least three studies (analysis C2) or two \ studies (all other analyses) were made publicly available.\ The meta-analysis software and workflow are available here. More information about the \ prospective studies, processing pipeline, results and data sharing can be found \ here.\

\ \ \

Data Access

\ The data underlying these tracks and summary statistics results are publicly available in \ COVID19-hg Release 3 (June 2020).\ The raw data can be explored interactively with the \ Table Browser, or the Data Integrator. \ Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.\

\ \

Credits

\ \

References

\ \

\ \ \ \ phenDis 1 autoScale on\ bedNameLabel SNP\ chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22\ compositeTrack on\ filter._effectSizeAbs 0\ filter.effectSize -13:21\ filter.pValueLog 3\ filter.sourceCount 1\ filterByRange.effectSize on\ filterLabel._effectSizeAbs Minimum effect size +-\ filterLabel.effectSize Effect size range\ filterLabel.sourceCount Minimum number of studies\ filterLimits.effectSize -13:21\ lollyField 21\ longLabel GWAS meta-analyses from the COVID-19 Host Genetics Initiative\ maxHeightPixels 48:75:128\ maxItems 500000\ mouseOver $name $ref/$alt effect $effectSize pval $pValue studies $sourceCount\ noScoreFilter on\ priority 2.1\ shortLabel COVID GWAS v3\ superTrack covid hide\ track covidHgiGwas\ type bigLolly 9 +\ viewLimits -13:21\ covidMuts COVID Rare Harmful Var bigBed 12 + Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort 3 2.2 179 0 0 217 127 127 0 0 0

Description

\ This track shows rare variants associated with monogenic congenital defects of immunity to \ the SARS-CoV-2 virus identified by the \ COVID Human Genetic Effort. \ This international consortium aims to discover truly causative variations: those underlying \ severe forms of COVID-19 in previously healthy individuals, and those that make certain \ individuals resistant to infection by the SARS-CoV2 virus despite repeated exposure.\

\ The major feature of the small set of variants in this track is that they are functionally tested\ to be deleterious and genetically tested to be disease-causing. \ Specifically, rare variants were predicted to be loss-of-function at human loci known to govern\ interferon (IFN) immunity to influenza virus in patients with life-threatening COVID-19 pneumonia, \ relative to subjects with asymptomatic or benign infection.\ These genetic defects display incomplete penetrance for influenza respiratory distress and only\ appear clinically upon infection with the more virulent SARS-CoV-2.\

\ \

Display Conventions

\ Only eight genes with 23 variants are contained in this track. \ Use the links below to navigate to the gene of interest or view \ all eight genes together using the following sessions for \ hg38 or\ hg19.\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

Gene Name	Human GRCh37/hg19 Assembly	Human GRCh38/hg38 Assembly
TLR3	\ chr4:186990309-187006252	\ chr4:186069152-186088069
IRF7	\ chr11:612555-615999	\ chr11:612591-615970
UNC93B1	\ chr11:67758575-67771593	\ chr11:67991100-68004097
TBK1	\ chr12:64845840-64895899	\ chr12:64452120-64502114
TICAM1	\ chr19:4815936-4831754	\ chr19:4815932-4831704
IRF3	\ chr19:50162826-50169132	\ chr19:49659570-49665875
IFNAR1	\ chr21:34697214-34732128	\ chr21:33324970-33359864
IFNAR2	\ chr21:34602231-34636820	\ chr21:33229974-33264525

\ \

\ Missing sequence in the assemblies is highlighted in the track display\ by regions of yellow when zoomed out and Ns displayed at base\ level (see Gap Annotation, below).

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Organism Species Release date UCSC version alignment type
Human Homo sapiens \ Dec. 2013 (GRCh38/hg38) Dec. 2013 (GRCh38/hg38) MAF Net
Chimp Pan troglodytes \ May 2016 (Pan_tro 3.0/panTro5) May 2016 (Pan_tro 3.0/panTro5) MAF Net
Bonobo Pan paniscus \ Aug. 2015 (MPI-EVA panpan1.1/panPan2) Aug. 2015 (MPI-EVA panpan1.1/panPan2) MAF Net
Gorilla Gorilla gorilla gorilla \ Mar. 2016 (GSMRT3/gorGor5) Mar. 2016 (GSMRT3/gorGor5) MAF Net
Orangutan Pongo pygmaeus abelii \ July 2007 (WUGSC 2.0.2/ponAbe2) July 2007 (WUGSC 2.0.2/ponAbe2) MAF Net
Gibbon Nomascus leucogenys \ Oct. 2012 (GGSC Nleu3.0/nomLeu3) Oct. 2012 (GGSC Nleu3.0/nomLeu3) MAF Net
Rhesus Macaca mulatta \ Nov. 2015 (BCM Mmul_8.0.1/rheMac8) Nov. 2015 (BCM Mmul_8.0.1/rheMac8) MAF Net
Crab-eating macaque Macaca fascicularis \ Jun. 2013 (Macaca_fascicularis_5.0/macFas5) Jun. 2013 (Macaca_fascicularis_5.0/macFas5) MAF Net
Pig-tailed macaque Macaca nemestrina \ Mar. 2015 (Mnem_1.0/macNem1) Mar. 2015 (Mnem_1.0/macNem1) MAF Net
Sooty mangabey Cercocebus atys \ Mar. 2015 (Caty_1.0/cerAty1) Mar. 2015 (Caty_1.0/cerAty1) MAF Net
Baboon Papio anubis \ Feb. 2013 (Baylor Panu_2.0/papAnu3) Feb. 2013 (Baylor Panu_2.0/papAnu3) MAF Net
Green monkey Chlorocebus sabaeus \ Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) MAF Net
Drill Mandrillus leucophaeus \ Mar. 2015 (Mleu.le_1.0/manLeu1) Mar. 2015 (Mleu.le_1.0/manLeu1) MAF Net
Proboscis monkey Nasalis larvatus \ Nov. 2014 (Charlie1.0/nasLar1) Nov. 2014 (Charlie1.0/nasLar1) MAF Net
Angolan colobus Colobus angolensis palliatus \ Mar. 2015 (Cang.pa_1.0/colAng1) Mar. 2015 (Cang.pa_1.0/colAng1) MAF Net
Golden snub-nosed monkey Rhinopithecus roxellana \ Oct. 2014 (Rrox_v1/rhiRox1) Oct. 2014 (Rrox_v1/rhiRox1) MAF Net
Black snub-nosed monkey Rhinopithecus bieti \ Aug. 2016 (ASM169854v1/rhiBie1) Aug. 2016 (ASM169854v1/rhiBie1) MAF Net
Marmoset Callithrix jacchus \ March 2009 (WUGSC 3.2/calJac3) March 2009 (WUGSC 3.2/calJac3) MAF Net
Squirrel monkey Saimiri boliviensis \ Oct. 2011 (Broad/saiBol1) Oct. 2011 (Broad/saiBol1) MAF Net
White-faced sapajou Cebus capucinus imitator \ Apr. 2016 (Cebus_imitator-1.0/cebCap1) Apr. 2016 (Cebus_imitator-1.0/cebCap1) MAF Net
Ma's night monkey Aotus nancymaae \ Jun. 2017 (Anan_2.0/aotNan1) Jun. 2017 (Anan_2.0/aotNan1) MAF Net
Tarsier Tarsius syrichta \ Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) MAF Net
Mouse lemur Microcebus murinus \ Feb. 2017 (Mmur_3.0/micMur3) Feb. 2017 (Mmur_3.0/micMur3) MAF Net
Coquerel's sifaka Propithecus coquereli \ Mar. 2015 (Pcoq_1.0/proCoq1) Mar. 2015 (Pcoq_1.0/proCoq1) MAF Net
Black lemur Eulemur macaco \ Aug. 2015 (Emacaco_refEf_BWA_oneround/eulMac1) Aug. 2015 (Emacaco_refEf_BWA_oneround/eulMac1) MAF Net
Sclater's lemur Eulemur flavifrons \ Aug. 2015 (Eflavifronsk33QCA/eulFla1) Aug. 2015 (Eflavifronsk33QCA/eulFla1) MAF Net
Bushbaby Otolemur garnettii \ Mar. 2011 (Broad/otoGar3) Mar. 2011 (Broad/otoGar3) MAF Net
Mouse Mus musculus \ Dec. 2011 (GRCm38/mm10) Dec. 2011 (GRCm38/mm10) MAF Net
Dog Canis lupus familiaris \ Sep. 2011 (Broad CanFam3.1/canFam3) Sep. 2011 (Broad CanFam3.1/canFam3) MAF Net
Armadillo Dasypus novemcinctus \ Dec. 2011 (Baylor/dasNov3) Dec. 2011 (Baylor/dasNov3) MAF Net

\ Table 1. Genome assemblies included in the 30-way Conservation track.\

\ \ Downloads for data in this track are available:\

\ Multiz alignments (MAF format), and phylogenetic trees\
\ PhyloP conservation (WIG format)\
\ PhastCons conservation (WIG format)\

\ \

Display Conventions and Configuration

\ In full and pack display modes, conservation scores are displayed as a\ wiggle track (histogram) in which the height reflects the\ value of the score.\ The conservation wiggles can be configured in a variety of ways to\ highlight different aspects of the displayed information.\ Click the Graph configuration help link for an explanation\ of the configuration options.

\ Checkboxes on the track configuration page allow selection of the\ species to include in the pairwise display.\ Configuration buttons are available to select all of the species\ (Set all), deselect all of the species (Clear all), or\ use the default settings (Set defaults).\ Note that excluding species from the pairwise display does not alter the\ the conservation score display.

\ To view detailed information about the alignments at a specific\ position, zoom the display in to 30,000 or fewer bases, then click on\ the alignment.

\ \

Gap Annotation

Single line: No bases in the aligned species. Possibly due to a\ lineage-specific insertion between the aligned blocks in the human genome\ or a lineage-specific deletion between the aligned blocks in the aligning\ species.\
Double line: Aligning species has one or more unalignable bases in\ the gap region. Possibly due to excessive evolutionary distance between\ species or independent indels in the region between the aligned blocks in both\ species.\
Pale yellow coloring: Aligning species has Ns in the gap region.\ Reflects uncertainty in the relationship between the DNA of both species, due\ to lack of sequence in relevant portions of the aligning species.\

\ \

Genomic Breaks

\ Discontinuities in the genomic context (chromosome, scaffold or region) of the\ aligned DNA in the aligning species are shown as follows:\

\ Vertical blue bar: Represents a discontinuity that persists indefinitely\ on either side, e.g. a large region of DNA on either side of the bar\ comes from a different chromosome in the aligned species due to a large scale\ rearrangement.\
\ Green square brackets: Enclose shorter alignments consisting of DNA from\ one genomic context in the aligned species nested inside a larger chain of\ alignments from a different genomic context. The alignment within the\ brackets may represent a short misalignment, a lineage-specific insertion of a\ transposon in the human genome that aligns to a paralogous copy somewhere\ else in the aligned species, or other similar occurrence.\

\ \

Base Level

\ When zoomed-in to the base-level display, the track shows the base\ composition of each alignment.\ The numbers and symbols on the Gaps\ line indicate the lengths of gaps in the human sequence at those\ alignment positions relative to the longest non-human sequence.\ If there is sufficient space in the display, the size of the gap is shown.\ If the space is insufficient and the gap size is a multiple of 3, a\ "*" is displayed; other gap sizes are indicated by "+".

\ No codon translation: The gene annotation is not used; the bases are\ displayed without translation.\
\ Use default species reading frames for translation: The annotations from\ the genome displayed in the Default species to establish reading frame\ pull-down menu are used to translate all the aligned species present in the\ alignment.\
\ Use reading frames for species if available, otherwise no translation:\ Codon translation is performed only for those species where the region is\ annotated as protein coding.\
Use reading frames for species if available, otherwise use default species:\ Codon translation is done on those species that are annotated as being protein\ coding over the aligned region using species-specific annotation; the remaining\ species are translated using the default species annotation.\

\ Codon translation uses the following gene tracks as the basis for\ translation, depending on the species chosen (Table 2).\ \

\ \ \ \ \ \
Gene Track Species
Known Genes human, mouse
Ensembl Genes v78 baboon, bushbaby, chimp, dog, gorilla, marmoset, mouse lemur, orangutan, tree shrew
RefSeq crab-eating macaque, rhesus
no annotation bonobo, green monkey, gibbon, proboscis monkey, golden snub-nosed monkey, squirrel monkey, tarsier
\ Table 2. Gene tracks used for codon translation.\

\ \

Methods

\ An additional filtering step was introduced in the generation of the 30-way\ conservation track to reduce the number of paralogs and pseudogenes from the\ high-quality assemblies and the suspect alignments from the low-quality\ assemblies.\

\ \ \ \
type of net alignment Species
Syntenic Net baboon, chimp, dog, gibbon, green monkey, crab-eating macaque, marmoset, mouse, orangutan, rhesus
Reciprocal best Net bushbaby, bonobo, gorilla, golden snub-nosed monkey, mouse lemur, proboscis monkey, squirrel monkey, tarsier, tree shrew
\ Table 3. Type of Net alignment\

\ \

Phylogenetic Tree Model

\ Both phastCons and phyloP are phylogenetic methods that rely\ on a tree model containing the tree topology, branch lengths representing\ evolutionary distance at neutrally evolving sites, the background distribution\ of nucleotides, and a substitution rate matrix.\ The\ all species tree model for this track was\ generated using the phyloFit program from the PHAST package\ (REV model, EM algorithm, medium precision) using multiple alignments of\ 4-fold degenerate sites extracted from the 30-way alignment\ (msa_view). The 4d sites were derived from the Xeno RefSeq gene set,\ filtered to select single-coverage long transcripts.\

\ This same tree model was used in the phyloP calculations, however their\ background frequencies were modified to maintain reversibility.\ The resulting tree model for\ all species.\

PhastCons Conservation

\ The phastCons parameters used were: expected-length=45,\ target-coverage=0.3, rho=0.3.

\ \

PhyloP Conservation

\ The phyloP program supports several different methods for computing\ p-values of conservation or acceleration, for individual nucleotides or\ larger elements\ (http://compgen.cshl.edu/phast/).\ Here it was used\ to produce separate scores at each base (--wig-scores option), considering\ all branches of the phylogeny rather than a particular subtree or lineage\ (i.e., the --subtree option was not used). The scores were computed by\ performing a likelihood ratio test at each alignment column (--method LRT),\ and scores for both conservation and acceleration were produced (--mode CONACC).\

Conserved Elements

\ \

Credits

This track was created using the following programs:\

Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb\ Miller of the Penn State Bioinformatics Group\
Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC\
Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and\ other programs in PHAST by\ Adam Siepel at Cold Spring Harbor Laboratory (original development\ done at the Haussler lab at UCSC).\
MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows\ by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC\
Tree image generator: phyloPng by Galt Barber, UCSC\
Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle\ display), and Brian Raney (gap annotation and codon framing) at UCSC\

The phylogenetic tree is based on Murphy et al. (2001) and general\ consensus in the vertebrate phylogeny community as of March 2007.\

\ \

References

\ \

Phylo-HMMs, phastCons, and phyloP:

\ \

\ Felsenstein J, Churchill GA.\ A Hidden Markov Model approach to\ variation among sites in rate of evolution.\ Mol Biol Evol. 1996 Jan;13(1):93-104.\ PMID: 8583911\

\ \

\ Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.\ \ Detection of nonneutral substitution rates on mammalian phylogenies.\ Genome Res. 3010 Jan;30(1):110-21.\ PMID: 19858363; PMC: PMC2798823\

\ \

\ Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,\ Clawson H, Spieth J, Hillier LW, Richards S, et al.\ Evolutionarily conserved elements in vertebrate, insect, worm,\ and yeast genomes.\ Genome Res. 2005 Aug;15(8):1034-50.\ PMID: 16024819; PMC: PMC1182216\

\ \

\ Siepel A, Haussler D.\ Phylogenetic Hidden Markov Models.\ In: Nielsen R, editor. Statistical Methods in Molecular Evolution.\ New York: Springer; 2005. pp. 325-351\

\ \

\ compGeno 1 compositeTrack on\ dragAndDrop subTracks\ group compGeno\ longLabel Mammals Multiz Alignment & Conservation (27 primates)\ priority 3\ shortLabel Cons 30 Primates\ subGroup1 view Views align=Multiz_Alignments phyloP=Basewise_Conservation_(phyloP) phastcons=Element_Conservation_(phastCons) elements=Conserved_Elements\ track cons30way\ type bed 4\ visibility hide\ cons30wayViewelements Conserved Elements bed 4 Mammals Multiz Alignment & Conservation (27 primates) 1 3 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Mammals Multiz Alignment & Conservation (27 primates)\ parent cons30way\ shortLabel Conserved Elements\ track cons30wayViewelements\ view elements\ visibility dense\ cq8Vcf CQ-8 Variants vcfTabix CQ-8 Variants 0 3 0 0 0 127 127 127 0 0 0 map 1 bigDataUrl /gbdb/hg38/problematic/highRepro/CQ-8.sort.vcf.gz\ longLabel CQ-8 Variants\ parent highReproVcfs\ shortLabel CQ-8 Variants\ subGroups view=vcfs\ track cq8Vcf\ type vcfTabix\ dbSnp153Mult dbSNP(153) Mult. bigDbSnp Short Genetic Variants from dbSNP Release 153 that Map to Multiple Genomic Loci 1 3 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 bigDataUrl /gbdb/hg38/snp/dbSnp153Mult.bb\ defaultGeneTracks knownGene\ longLabel Short Genetic Variants from dbSNP Release 153 that Map to Multiple Genomic Loci\ parent dbSnp153ViewVariants off\ priority 3\ shortLabel dbSNP(153) Mult.\ subGroups view=variants\ track dbSnp153Mult\ dbVar_common_global dbVar Curated All Populations bigBed 9 + . NCBI dbVar Curated Common SVs: all populations 3 3 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ varRep 1 bigDataUrl /gbdb/hg38/bbi/dbVar/common_global.bb\ longLabel NCBI dbVar Curated Common SVs: all populations\ parent dbVar_common on\ shortLabel dbVar Curated All Populations\ track dbVar_common_global\ type bigBed 9 + .\ url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$\ urlLabel NCBI Variant Page:\ cons30wayViewphastcons Element Conservation (phastCons) bed 4 Mammals Multiz Alignment & Conservation (27 primates) 2 3 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Mammals Multiz Alignment & Conservation (27 primates)\ parent cons30way\ shortLabel Element Conservation (phastCons)\ track cons30wayViewphastcons\ view phastcons\ visibility full\ knownGeneV45 GENCODE V45 bigGenePred knownGenePep knownGeneMrna GENCODE V45 3 3 0 0 0 127 127 127 0 0 0

Description

\ The GENCODE Genes track (version 45, January 2024) shows high-quality manual\ annotations merged with evidence-based automated annotations across the entire\ human genome generated by the\ GENCODE project.\ By default, only the basic gene set is\ displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts\ that GENCODE believes will be useful to the majority of users.

\ \

\ The following table provides statistics for the v45 release derived from the GTF file that contains\ annotations only on the main chromosomes. More information on how they were generated can be found\ in the GENCODE site.

\ \

\ \ \ \ \ \ \ \ \
GENCODE v45 Release Stats
Genes Observed Transcripts Observed
Protein-coding genes 19,395 Protein-coding transcripts 89,110
Long non-coding RNA genes 20,424 - full length protein-coding 64,028
Small non-coding RNA genes 7,565 - partial length protein-coding 25,082
Pseudogenes 14,719 Nonsense mediated decay transcripts 21,427
Immunoglobulin/T-cell receptor gene segments 648 Long non-coding RNA loci transcripts 59,719
Total No of distinct translations 65,357 Genes that have more than one distinct translations 13,600

\

GENCODE v45 Release Stats
Genes	Observed	Transcripts	Observed
Protein-coding genes	19,395	Protein-coding transcripts	89,110
Long non-coding RNA genes	20,424	- full length protein-coding	64,028
Small non-coding RNA genes	7,565	- partial length protein-coding	25,082
Pseudogenes	14,719	Nonsense mediated decay transcripts	21,427
Immunoglobulin/T-cell receptor gene segments	648	Long non-coding RNA loci transcripts	59,719
Total No of distinct translations	65,357	Genes that have more than one distinct translations	13,600

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ \

Coloring for the gene annotations is based on the annotation type:

coding: protein coding transcripts, including polymorphic\ pseudogenes\
non-coding: non-protein coding transcripts\
pseudogene: pseudogene transcript annotations\
problem: problem transcripts (Biotypes of\ retained_intron, TEC, or disrupted_domain)

\ \

\ \ \

Squishy-pack Display

\ Protein_coding genes\

MANE or Ensembl canonical\
- 1st: MANE Select / Ensembl canonical
- 2nd: MANE Plus Clinical
\
Coding biotypes\
- 1st: protein_coding and protein_coding_LoF
- 2nd: NMDs and NSDs
- 3rd: retained intron and protein_coding_CDS_not_defined
\
Completeness\
- 1st: full length
- 2nd: CDS start/end not found
\
CARS score (only for coding transcripts)
Transcript genomic span and length (only for non-coding transcripts)

\ Non-coding genes\

Transcript biotype\
- 1st: transcript biotype identical to gene biotype
\
Ensembl canonical
GENCODE basic
Transcript genomic span
Transcript length

\ \ \

Methods

\ The GENCODE v45 track was built from the GENCODE downloads file \ gencode.v45.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources\ were correlated with the GENCODE data to build association tables.

\ \

Related Data

\ The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a\ downloadable\ file.\ \

Description

\ \

\ \ \

Problematic Regions

\ The Problematic Regions track contains the following subtracks:\

\ The UCSC Unusual Regions subtrack contains annotations collected at UCSC, \ put together from other tracks, our experiences and support email list\ requests over the years. For example, it contains the most well-known gene\ clusters (IGH, IGL, PAR1/2, TCRA, TCRB, etc) and annotations for the GRC\ fixed sequences, alternate haplotypes, unplaced\ contigs, pseudo-autosomal regions, and mitochondria. These loci can yield alignments with\ low-quality mapping scores and discordant read pairs, especially for short-read sequencing data.\ This data set was manually curated, based on the Genome Browser's\ assembly description, the FAQs about assembly, and the\ NCBI RefSeq "other" annotations\ track data.\
\ The ENCODE Blacklist subtrack contains a comprehensive set of regions which are troublesome\ for high-throughput Next-Generation Sequencing (NGS) aligners. These regions tend to have a very\ high ratio of multi-mapping to unique mapping reads and high variance in mappability due to\ repetitive elements such as satellite, centromeric and telomeric repeats. \
\ The GRC Exclusions subtrack contains a set of regions that have been flagged by the GRC to\ contain false duplications or contamination sequences. The GRC has now removed these sequences from\ the files that it uses to generate the reference assembly, however, removing the sequences from the\ GRCh38/hg38 assembly would trigger the next major release of the human assembly. In order to\ help users recognize these regions and avoid them in their analyses, the GRC have produced a masking\ file to be used as a companion to GRCh38, and the BED file is available from the\ GenBank FTP site.\

\ \

Highly Reproducible Regions

a Chinese Quartet, samples CQ-5, CQ-6, CQ-7, CQ-8
a HapMap Trio, samples NA10385, NA12248, NA12249
a Genome in a Bottle sample, NA12878s

\ \ Please refer to the Pan et al reference for more information on how\ these regions were defined.\

\ \

GIAB Problematic Regions

\ \

\ \ \ \

Display Conventions and Configuration

\ \

Data access

\ The raw data can be explored interactively with the Table Browser\ or the Data Integrator.\ \

\ \

Methods

\ \

\ Files were downloaded from the respective databases and converted to bigBed format.\ The procedure is documented in our\ hg38 makeDoc file.\

\ Tissue-cell type combinations in the Full and Combined tracks are\ colored by which cell type they belong to in the below table:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Color Cell Type
Endothelial
Epithelial
Glia
Immune
Neuron
Stromal
Other
\

Color	Cell Type
	Endothelial
	Epithelial
	Glia
	Immune
	Neuron
	Stromal
	Other

\ \

Color	Cell Type
	Inflammatory Macrophage
	Lung Macrophage
	Monocyte/Macrophage FCGR3A High
	Monocyte/Macrophage FCGR3A Low
	Macrophage HLAII High
	Macrophage LYVE1 High
	Proliferating Macrophage
	Dendritic Cell 1
	Dendritic Cell 2
	Mature Dendritic Cell
	Langerhans
	CD14+ Monocyte
	CD16+ Monocyte
	LAM-like
	Other

Methods

\ \

\ For detailed methods, please refer to Eraslan et al, or the\ \ GTEx portal website.\

\ \

UCSC Methods

\ \

Data Access

\ \

Credits

Thanks to the GTEx Consortium for creating and analyzing these data.

\ \

References

\ singleCell 1 barChartCategoryUrl /gbdb/hg38/bbi/gtexImmuneAtlas/facet_detailed.categories\ barChartFacets tissue,cell_type,cell_class,sex,donor\ barChartMerge on\ barChartMetric gene/genome\ barChartStatsUrl /gbdb/hg38/bbi/gtexImmuneAtlas/facet_detailed_class.facets\ barChartStretchToItem on\ barChartUnit parts per million\ bigDataUrl /gbdb/hg38/bbi/gtexImmuneAtlas/facet_detailed_class.bb\ defaultLabelFields name\ html crossTissueMaps\ labelFields name,name2\ longLabel GTEx single nuclei immune expression\ parent crossTissueMaps\ priority 3\ shortLabel GTEx Immune Atlas\ track gtexImmuneAtlasFullDetails\ type bigBarChart\ url https://cells.ucsc.edu/?ds=tabula-sapiens+all&gene=$\ urlLabel View on the UCSC Cell Browser: $\ visibility pack\ wgEncodeRegTxnCaltechRnaSeqHelas3R2x75Il200SigPooled HeLa-S3 bigWig 0 65535 Transcription of HeLa-S3 cells from ENCODE 0 3 227 255 128 241 255 191 0 0 0 regulation 1 color 227,255,128\ longLabel Transcription of HeLa-S3 cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegTxn\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ priority 3\ shortLabel HeLa-S3\ track wgEncodeRegTxnCaltechRnaSeqHelas3R2x75Il200SigPooled\ type bigWig 0 65535\ hffc6Insitu HFFc6 In situ hic In situ Hi-C Chromatin Structure on HFFc6 0 3 0 0 0 127 127 127 0 0 0 regulation 1 bigDataUrl /gbdb/hg38/bbi/hic/4DNFIFLJLIS5.hic\ longLabel In situ Hi-C Chromatin Structure on HFFc6\ parent hicAndMicroC off\ shortLabel HFFc6 In situ\ track hffc6Insitu\ type hic\ chainHprcGCA_018466985v1 HG02559.mat chain GCA_018466985.1 HG02559.mat HG02559.pri.mat.f1_v2 (May 2021 GCA_018466985.1_HG02559.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 3 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02559.mat HG02559.pri.mat.f1_v2 (May 2021 GCA_018466985.1_HG02559.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018466985.1\ parent hprcChainNetViewchain off\ priority 20\ shortLabel HG02559.mat\ subGroups view=chain sample=s020 population=afr subpop=acb hap=mat\ track chainHprcGCA_018466985v1\ type chain GCA_018466985.1\ wgEncodeRegMarkH3k4me1Hsmm HSMM bigWig 0 6265 H3K4Me1 Mark (Often Found Near Regulatory Elements) on HSMM Cells from ENCODE 0 3 120 235 204 187 245 229 0 0 0 regulation 1 color 120,235,204\ longLabel H3K4Me1 Mark (Often Found Near Regulatory Elements) on HSMM Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k4me1\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel HSMM\ table wgEncodeBroadHistoneHsmmH3k4me1StdSig\ track wgEncodeRegMarkH3k4me1Hsmm\ type bigWig 0 6265\ wgEncodeRegMarkH3k4me3Hsmm HSMM bigWig 0 25995 H3K4Me3 Mark (Often Found Near Promoters) on HSMM Cells from ENCODE 0 3 120 235 204 187 245 229 0 0 0 regulation 1 color 120,235,204\ longLabel H3K4Me3 Mark (Often Found Near Promoters) on HSMM Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k4me3\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel HSMM\ table wgEncodeBroadHistoneHsmmH3k4me3StdSig\ track wgEncodeRegMarkH3k4me3Hsmm\ type bigWig 0 25995\ wgEncodeRegMarkH3k27acHsmm HSMM bigWig 0 5448 H3K27Ac Mark (Often Found Near Regulatory Elements) on HSMM Cells from ENCODE 2 3 120 235 204 187 245 229 0 0 0 regulation 1 color 120,235,204\ longLabel H3K27Ac Mark (Often Found Near Regulatory Elements) on HSMM Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k27ac\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel HSMM\ table wgEncodeBroadHistoneHsmmH3k27acStdSig\ track wgEncodeRegMarkH3k27acHsmm\ type bigWig 0 5448\ xGen_Research_Probes_V2 IDT xGen V2 P bigBed IDT - xGen Exome Research Panel V2 Probes 1 3 100 143 255 177 199 255 0 0 0 map 1 bigDataUrl /gbdb/hg38/exomeProbesets/xgen-exome-research-panel-v2-probes-hg38.bb\ color 100,143,255\ longLabel IDT - xGen Exome Research Panel V2 Probes\ parent exomeProbesets on\ shortLabel IDT xGen V2 P\ track xGen_Research_Probes_V2\ type bigBed\ visibility dense\ jaspar2020 JASPAR 2020 TFBS bigBed 6 + JASPAR CORE 2020 - Predicted Transcription Factor Binding Sites 0 3 0 0 0 127 127 127 1 0 0 http://jaspar.genereg.net/search?q=$$&collection=all&tax_group=all&tax_id=all&type=all&class=all&family=all&version=all regulation 1 bigDataUrl /gbdb/hg38/jaspar/JASPAR2020.bb\ filterValues.name Ahr::Arnt,Alx1,ALX3,Alx4,Ar,ARGFX,Arid3a,Arid3b,Arid5a,Arnt,ARNT2,ARNT::HIF1A,Arntl,Arx,ASCL1,ASCL1(var.2),Ascl2,Atf1,ATF2,ATF3,ATF4,ATF6,ATF7,Atoh1,ATOH1(var.2),ATOH7,BACH1,Bach1::Mafk,BACH2,BACH2(var.2),BARHL1,BARHL2,BARX1,BARX2,BATF,BATF3,BATF::JUN,BCL6,BCL6B,Bhlha15,BHLHA15(var.2),BHLHE22,BHLHE22(var.2),BHLHE23,BHLHE40,BHLHE41,BSX,CDX1,CDX2,CDX4,CEBPA,CEBPB,CEBPD,CEBPE,CEBPG,CEBPG(var.2),CENPB,CLOCK,CREB1,CREB3,CREB3L1,Creb3l2,CREB3L4,CREB3L4(var.2),Creb5,CREM,Crx,CTCF,CTCFL,CUX1,CUX2,DBP,Ddit3::Cebpa,Dlx1,Dlx2,Dlx3,Dlx4,DLX5,DLX6,Dmbx1,Dmrt1,DMRT3,DMRTA2,DMRTC2,DPRX,DRGX,Dux,DUX4,DUXA,E2F1,E2F2,E2F3,E2F4,E2F6,E2F7,E2F8,EBF1,Ebf2,EBF3,EGR1,EGR2,EGR3,EGR4,EHF,ELF1,ELF2,ELF3,ELF4,ELF5,ELK1,ELK3,ELK4,EMX1,EMX2,EN1,EN2,EOMES,ERF,ERG,ESR1,ESR2,ESRRA,ESRRB,Esrrg,ESX1,ETS1,ETS2,ETV1,ETV2,ETV3,ETV4,ETV5,ETV6,EVX1,EVX2,EWSR1-FLI1,FERD3L,FEV,FIGLA,FLI1,FOS,FOSB::JUN,FOSB::JUNB,FOSB::JUNB(var.2),FOS::JUN,FOS::JUNB,FOS::JUND,FOS::JUN(var.2),FOSL1,FOSL1::JUN,FOSL1::JUNB,FOSL1::JUND,FOSL1::JUND(var.2),FOSL1::JUN(var.2),FOSL2,FOSL2::JUN,FOSL2::JUNB,FOSL2::JUNB(var.2),FOSL2::JUND,FOSL2::JUND(var.2),FOSL2::JUN(var.2),FOXA1,FOXA2,FOXA3,FOXB1,FOXC1,FOXC2,FOXD1,FOXD2,Foxd3,FOXE1,Foxf1,FOXF2,FOXG1,FOXH1,FOXI1,Foxj2,Foxj3,FOXK1,FOXK2,FOXL1,Foxl2,FOXN3,Foxo1,FOXO3,FOXO4,FOXO6,FOXP1,FOXP2,FOXP3,Foxq1,GABPA,GATA1,GATA1::TAL1,GATA2,GATA3,GATA4,GATA5,GATA6,GBX1,GBX2,GCM1,GCM2,GFI1,Gfi1b,GLI2,GLI3,GLIS1,GLIS2,GLIS3,Gmeb1,GMEB2,GRHL1,GRHL2,GSC,GSC2,GSX1,GSX2,Hand1::Tcf3,HAND2,HES1,HES2,HES5,HES6,HES7,HESX1,HEY1,HEY2,Hic1,HIC2,HIF1A,HINFP,HLF,HLTF,HMBOX1,Hmx1,Hmx2,Hmx3,HNF1A,HNF1B,HNF4A,HNF4A(var.2),HNF4G,HOXA1,HOXA10,Hoxa11,HOXA13,HOXA2,HOXA4,HOXA5,HOXA6,HOXA7,HOXA9,HOXB13,HOXB2,HOXB3,HOXB4,HOXB5,HOXB6,HOXB7,HOXB8,HOXB9,HOXC10,HOXC11,HOXC12,HOXC13,HOXC4,HOXC8,HOXC9,HOXD10,HOXD11,HOXD12,HOXD13,HOXD3,HOXD4,HOXD8,HOXD9,HSF1,HSF2,HSF4,IKZF1,INSM1,IRF1,IRF2,IRF3,IRF4,IRF5,IRF6,IRF7,IRF8,IRF9,Isl1,ISL2,ISX,JDP2,JDP2(var.2),JUN,JUNB,JUNB(var.2),JUND,JUND(var.2),JUN::JUNB,JUN::JUNB(var.2),JUN(var.2),Klf1,KLF10,KLF11,Klf12,KLF13,KLF14,KLF15,KLF16,KLF17,KLF2,KLF3,KLF4,KLF5,KLF6,KLF9,LBX1,LBX2,LEF1,LHX1,LHX2,Lhx3,Lhx4,LHX5,LHX6,Lhx8,LHX9,LIN54,LMX1A,LMX1B,MAF,MAFA,Mafb,MAFF,MAFG,MAFK,MAF::NFE2,MAX,MAX::MYC,MAZ,Mecom,MEF2A,MEF2B,MEF2C,MEF2D,MEIS1,MEIS1(var.2),MEIS2,MEIS2(var.2),MEIS3,MEOX1,MEOX2,MGA,MITF,mix-a,MIXL1,MLX,Mlxip,MLXIPL,MNT,MNX1,MSANTD3,MSC,MSGN1,MSX1,MSX2,Msx3,MTF1,MXI1,MYB,MYBL1,MYBL2,MYC,MYCN,MYF5,MYF6,MYOD1,MYOG,MZF1,MZF1(var.2),NEUROD1,NEUROD2,NEUROG1,NEUROG2,NEUROG2(var.2),NFAT5,NFATC1,NFATC2,NFATC3,NFATC4,NFE2,NFE2L1,Nfe2l2,NFIA,NFIB,NFIC,NFIC::TLX1,NFIC(var.2),NFIL3,NFIX,NFIX(var.2),NFKB1,NFKB2,NFYA,NFYB,NFYC,NHLH1,NHLH2,NKX2-2,NKX2-3,NKX2-5,Nkx2-5(var.2),NKX2-8,Nkx3-1,Nkx3-2,NKX6-1,NKX6-2,NKX6-3,Nobox,NOTO,Npas2,NR1D1,NR1D2,NR1H2::RXRA,Nr1h3::Rxra,NR1H4,NR1H4::RXRA,NR1I2,NR1I3,NR2C1,NR2C2,NR2C2(var.2),Nr2e1,Nr2e3,NR2F1,NR2F1(var.2),NR2F1(var.3),NR2F2,Nr2f6,Nr2f6(var.2),NR2F6(var.3),NR3C1,NR3C2,NR4A1,NR4A2,NR4A2::RXRA,NR5A1,Nr5a2,NR6A1,NRF1,NRL,OLIG1,OLIG2,OLIG3,ONECUT1,ONECUT2,ONECUT3,OSR1,OSR2,OTX1,OTX2,OVOL1,OVOL2,PAX1,Pax2,PAX3,PAX3(var.2),PAX4,PAX5,PAX6,PAX7,PAX9,PBX1,PBX2,PBX3,PDX1,PHOX2A,PHOX2B,PITX1,PITX2,PITX3,PKNOX1,PKNOX2,PLAG1,Plagl1,PLAGL2,POU1F1,POU2F1,POU2F2,POU2F3,POU3F1,POU3F2,POU3F3,POU3F4,POU4F1,POU4F2,POU4F3,POU5F1,POU5F1B,Pou5f1::Sox2,POU6F1,POU6F1(var.2),POU6F2,PPARA::RXRA,PPARD,PPARG,Pparg::Rxra,PRDM1,Prdm15,PRDM4,PROP1,PROX1,PRRX1,PRRX2,Ptf1a,Ptf1a(var.2),Ptf1a(var.3),RARA,RARA::RXRA,RARA::RXRG,RARA(var.2),Rarb,Rarb(var.2),RARB(var.3),Rarg,Rarg(var.2),RARG(var.3),RAX,RAX2,RBPJ,Rbpjl,REL,RELA,RELB,REST,RFX1,RFX2,RFX3,RFX4,RFX5,RFX7,Rhox11,RHOXF1,RORA,RORA(var.2),RORB,RORC,RREB1,RUNX1,RUNX2,RUNX3,Rxra,RXRA::VDR,RXRB,RXRB(var.2),RXRG,RXRG(var.2),SCRT1,SCRT2,SHOX,Shox2,SIX1,SIX2,Six3,Smad2::Smad3,SMAD2::SMAD3::SMAD4,SMAD3,Smad4,SMAD5,SNAI1,SNAI2,SNAI3,SOHLH2,Sox1,SOX10,Sox11,SOX12,SOX13,SOX14,SOX15,Sox17,SOX18,SOX2,SOX21,Sox3,SOX4,Sox5,Sox6,SOX8,SOX9,SP1,SP2,SP3,SP4,SP8,SP9,SPDEF,SPI1,SPIB,SPIC,Spz1,SREBF1,SREBF1(var.2),SREBF2,SREBF2(var.2),SRF,SRY,STAT1,STAT1::STAT2,Stat2,STAT3,Stat4,Stat5a,Stat5a::Stat5b,Stat5b,Stat6,TAL1::TCF3,TBP,TBR1,TBX1,TBX15,TBX18,TBX19,TBX2,TBX20,TBX21,TBX3,TBX4,TBX5,TBX6,TBXT,Tcf12,TCF12(var.2),Tcf21,TCF21(var.2),TCF3,TCF4,TCF7,TCF7L1,TCF7L2,TCFL5,TEAD1,TEAD2,TEAD3,TEAD4,TEF,TFAP2A,TFAP2A(var.2),TFAP2A(var.3),TFAP2B,TFAP2B(var.2),TFAP2B(var.3),TFAP2C,TFAP2C(var.2),TFAP2C(var.3),TFAP2E,TFAP4,TFAP4(var.2),TFCP2,TFDP1,TFE3,TFEB,TFEC,TGIF1,TGIF2,TGIF2LX,TGIF2LY,THAP1,THAP11,THRB,THRB(var.2),THRB(var.3),TLX2,TP53,TP63,TP73,TWIST1,Twist2,UNCX,USF1,USF2,VAX1,VAX2,VDR,VENTX,VEZF1,VSX1,VSX2,Wt1,XBP1,YY1,YY2,ZBED1,ZBTB12,ZBTB14,ZBTB18,ZBTB26,ZBTB32,ZBTB33,ZBTB6,ZBTB7A,ZBTB7B,ZBTB7C,ZEB1,ZFP42,ZFP57,Zfx,ZIC1,Zic1::Zic2,Zic2,ZIC3,ZIC4,ZIC5,ZKSCAN1,ZKSCAN5,ZNF135,ZNF136,ZNF140,ZNF143,ZNF148,ZNF16,ZNF24,ZNF263,ZNF274,Znf281,ZNF282,ZNF317,ZNF341,ZNF354C,ZNF382,ZNF384,ZNF410,Znf423,ZNF449,ZNF460,ZNF528,ZNF652,ZNF682,ZNF684,ZNF740,ZNF75D,ZSCAN29,ZSCAN4\ longLabel JASPAR CORE 2020 - Predicted Transcription Factor Binding Sites\ motifPwmTable hgFixed.jasparVertebrates2020\ parent jaspar off\ priority 3\ shortLabel JASPAR 2020 TFBS\ track jaspar2020\ type bigBed 6 +\ visibility hide\ wgEncodeRegDnaseUwLncapPeak LNCaP Pk narrowPeak LNCaP prostate adenocarcinoma cell line DNaseI Peaks from ENCODE 1 3 255 102 85 255 178 170 1 0 0 regulation 1 color 255,102,85\ longLabel LNCaP prostate adenocarcinoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel LNCaP Pk\ subGroups view=a_Peaks cellType=LNCaP treatment=n_a tissue=prostate cancer=cancer\ track wgEncodeRegDnaseUwLncapPeak\ wgEncodeRegDnaseUwLncapWig LNCaP Sg bigWig 0 37372.7 LNCaP prostate adenocarcinoma cell line DNaseI Signal from ENCODE 0 3 255 102 85 255 178 170 0 0 0 regulation 1 color 255,102,85\ longLabel LNCaP prostate adenocarcinoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.01793\ shortLabel LNCaP Sg\ subGroups cellType=LNCaP treatment=n_a tissue=prostate cancer=cancer\ table wgEncodeRegDnaseUwLncapSignal\ track wgEncodeRegDnaseUwLncapWig\ type bigWig 0 37372.7\ tgpNA19685_m011_MXL m011 MXL Trio vcfPhasedTrio 1000 Genomes m011 Mexican Ancestry from Los Angeles Trio 2 3 0 0 0 127 127 127 0 0 23 chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX, varRep 0 longLabel 1000 Genomes m011 Mexican Ancestry from Los Angeles Trio\ parent tgpTrios\ shortLabel m011 MXL Trio\ track tgpNA19685_m011_MXL\ type vcfPhasedTrio\ vcfChildSample NA19685|child\ vcfParentSamples NA19660|mother,NA19661|father\ visibility full\ microsat Microsatellite bed 4 Microsatellites - Di-nucleotide and Tri-nucleotide Repeats 0 3 0 0 0 127 127 127 0 0 0

Description

\ This track displays regions that are likely to be useful as microsatellite\ markers. These are sequences of at least 15 perfect di-nucleotide and \ tri-nucleotide repeats and tend to be highly polymorphic in the\ population.\

\ \

Methods

Contact

If you have questions or comments, please write to:\

Huang Muyao, \ \ 2171272903@edu.k.u-tokyo.ac.jp\ \

\ \

References

\ \

\ Kleine T, Maier UG, Leister D.\ \ DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis.\ Annu Rev Plant Biol. 2009;60:115-38.\ DOI: 10.1146/annurev.arplant.043008.092119; PMID: 19014347\

\ Zhang GJ, Dong R, Lan LN, Li SF, Gao WJ, Niu HX.\ \ Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants.\ Int J Mol Sci. 2020 Jan 21;21(3).\ DOI: 10.3390/ijms21030707; PMID:\ 31973163; PMC: PMC7037861\

\ Yao Y, Frith MC.\ \ Improved DNA-Versus-Protein Homology Search for Protein Fossils.\ IEEE/ACM Trans Comput Biol Bioinform. 2023 May-Jun;20(3):1691-1699.\ DOI: 10.1109/TCBB.2022.3177855; PMID: 35617174\

\ Frith MC.\ \ A simple method for finding related sequences by adding probabilities of alternative alignments.\ Genome Res. 2024 Sep 13;.\ DOI: 10.1101/gr.279464.124;\ PMID: 39152037\

\ rep 1 bigDataUrl /gbdb/hg38/bbi/nuMtSeq/nuMtSeq_hg38.bb\ group rep\ longLabel Nuclear mitochondrial DNA segments\ priority 3\ scoreMax 100\ shortLabel NuMTs Sequence\ spectrum on\ track nuMtSeq\ type bigBed 6\ omimLocation OMIM Cyto Loci bed 4 OMIM Cytogenetic Loci Phenotypes - Gene Unknown 0 3 0 80 0 127 167 127 0 0 0 http://www.omim.org/entry/

Description

\ \

\ \ \

\ \

\ The OMIM data are separated into three separate tracks:\

\ \

OMIM Genes\
The genomic positions of gene entries in the OMIM \ database. The coloring indicates the associated OMIM phenotype map key.\

\ \

OMIM Phenotypes - Gene Unknown\
Regions known to be associated with a phenotype, \ but for which no specific gene is known to be causative. This track \ also includes known multi-gene syndromes.\

\ \

\ \ \

\ This track shows the cytogenetic locations of phenotype entries in the Online Mendelian\ Inheritance in Man (OMIM) database for which\ the gene is unknown.\

\ \

Display Conventions and Configuration

\ \

Cytogenetic locations of OMIM entries are displayed as solid\ blocks. The entries are colored according to the OMIM phenotype map key of associated disorders:\ \

Lighter Green for phenotype map key 1 OMIM records\ - the disorder has been placed on the map based on its association with\ a gene, but the underlying defect is not known.\
Light Green for phenotype map key 2 OMIM records\ - the disorder has been placed on the map by linkage; no mutation has\ been found.\
Dark Green for phenotype map key 3 OMIM records\ - the molecular basis for the disorder is known; a mutation has been\ found in the gene.\
Purple for phenotype map key 4 OMIM records\ - a contiguous gene deletion or duplication syndrome; multiple genes\ are deleted or duplicated causing the phenotype.\

Gene symbols and disease information, when available, are displayed on the details pages.\

The descriptions of OMIM entries are shown on the main browser display when Full display\ mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry. Items\ displayed can be filtered according to phenotype map key on the track controls page.\

\ \

Methods

\ This track was constructed as follows: \

The data file genemap.txt from OMIM was loaded into the MySQL table\ omimGeneMap.\
Entries in genemap.txt having disorder info were parsed and loaded into the\ omimPhenotype table. The phenotype map keys (the numbers (1)(2)(3)(4) from the\ disorder columns) were placed into a separate field.\
The cytogenetic location data (from the location column in omimGeneMap) were\ parsed and converted into genomic start and end positions based on the cytoBand table.\ These genomic positions, together with the corresponding OMIM IDs, were loaded into the\ omimLocation table.\
All entries with no associated phenotype map key and all OMIM gene entries as reported in the\ "OMIM Genes" track were then excluded from the omimLocation table.\

\ \

Data Access

\ Please refer to our searchable\ mailing list archives\ for more questions and example queries, or our\ Data Access FAQ\ for more information.

\ \

Credits

\ Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu,\ Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group.

\ \

References

Amberger J, Bocchini CA, Scott AF, Hamosh A.\ McKusick's Online Mendelian Inheritance in Man (OMIM®).\ Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. Epub 2008 Oct 8.\

\ Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA.\ Online Mendelian Inheritance in Man (OMIM), a knowledgebase of\ human genes and genetic disorders.\ Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7.\

Description

\ \

Display Conventions and Configuration

\ \

Items in this track are colored according to their strand orientation. Blue\ indicates alignment to the negative strand, and red indicates\ alignment to the positive strand.\

\ \

Methods

Protocol

hCAGE
LQhCAGE

Samples

Primary cell
Tissue
Cell Line
Time course
Fractionation

TSS peaks

TSS (CAGE) peaks\
- the robust peaks
\
TSS summary profiles\
- Total counts and TPM (tags per million) in all the samples
- Maximum counts and TPM among the samples
\

\ \

TSS activity

\ \

Categories of individual samples: - Cell Line hCAGE; - Cell Line LQhCAGE; - fractionation hCAGE; - Primary cell hCAGE; - Primary cell LQhCAGE; - Time course hCAGE; - Tissue hCAGE

\ \

Data Access

\ \

gnomAD v4.1

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

\ \

gnomAD v3.1.1

\ The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,\ except as noted below.

\ \

There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).\
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one\ variant, with additional information available on the details page, which has roughly halved the\ number of items in the bigBed.\
The bigBed has been split into two files, one with the information necessary for the track\ display, and one with the information necessary for the details page. For more information on\ this data format, please see the Data Access section below.\
The VEP annotation is shown as a table instead of spread across multiple fields.\
Intergenic variants have not been pre-filtered.\

\ \

gnomAD v3.1

\ By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters\ described below), before the track switches to dense display mode.\

\ \

\ Mouse hover on an item will display many details about each variant, including the affected gene(s),\ the variant type, and annotation (missense, synonymous, etc).\

\ \

\ Clicking on an item will display additional details on the variant, including a population frequency\ table showing allele count in each sub-population.\

\ \

\ Following the conventions on the gnomAD browser, items are shaded according to their Annotation\ type:\ \ \ \ \ \
pLoF
Missense
Synonymous
Other
\

\ Four filters are available for these tracks, the same as the underlying VCF:\

AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))\
InbreedingCoeff: Inbreeding Coefficient < -0.3\
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)\
Pass: Variant passes all 3 filters\

\ \

\ There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.\

\ \ \

UCSC Methods

\ The gnomAD v3.1.1 and v4.1 data is unfiltered.

\ For the v3.1 update only, in order to cut \ down on the amount of displayed data, the following variant\ types have been filtered out, but are still viewable in the gnomAD browser:\

Regulatory Region Variants\
Downstream/Upstream Gene Variants\
Transcription Factor Binding Site Variants\

\ \

\ For the full steps used to create the gnomAD tracks at UCSC, please see the\ hg38 gnomad makedoc.\

\ \ \

Data Access

\ \

\
# find item of interest:\
bigBedToBed genomes.bb stdout | head -4 | tail -1\
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted for brevity..]    chr1-12417-G-A    67293    902\
\
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:\
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz\
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant",  [..omitted for brevity..]\

\ \

\ The data can also be found directly from the gnomAD downloads page. Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.\

\ \

\ Please note that some annotations within the provided files may have restrictions on usage. See here for more information. \

\ \

References

\ \

\ varRep 1 bigDataUrl /gbdb/hg38/gnomAD/v3.1.1/genomes.bb\ dataVersion Release v3.1.1 (March 20, 2021) and v3.1 chrM Release (November 17, 2020)\ defaultLabelFields _displayName\ detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies\ detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v3.1.1/gnomad.v3.1.1.details.tab.gz\ filter.AF 0.0\ filterLabel.AF Minor Allele Frequency Filter\ filterType.AC_non_cancer single\ filterType.FILTER multipleListAnd\ filterType.variation_type multipleListOr\ filterValues.AC_non_cancer Non-Cancer\ filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only)\ filterValues.annot pLoF,missense,synonymous,other\ filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation\ filterValuesDefault.AC_non_cancer Non-Cancer\ filterValuesDefault.FILTER PASS\ filterValuesDefault.annot pLoF,missense,synonymous\ html gnomadV4.1\ itemRgb on\ labelFields rsId,_displayName\ longLabel Genome Aggregation Database (gnomAD) Genome Variants v3.1.1\ maxItems 50000\ mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); rsId: $rsId; Genes: $genes; Annotation: $annot; FILTER: $FILTER; Variation: $variation_type\ parent gnomadVariants\ priority 3.1\ searchIndex name,_displayName,rsId\ shortLabel gnomAD v3.1.1\ skipEmptyFields on\ skipFields _displayName\ track gnomadGenomesVariantsV3_1_1\ type bigBed 9 +\ url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$-$?dataset=gnomad_r3&ignore=$\ urlLabel View this variant at gnomAD\ visibility hide\ gnomadGenomesVariantsV3_1 gnomAD v3.1 bigBed 9 + Genome Aggregation Database (gnomAD) Genome Variants v3.1 0 3.2 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$-$?dataset=gnomad_r3&ignore=$

Description

\ \

\ gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the\ GRCh38/hg38 lift-over provided by gnomAD on their downloads site.\

\ \

\ For questions on the gnomAD data, also see the gnomAD FAQ.

\ More details on the Variant type(s) can be found on the Sequence Ontology page.

\ \

Display Conventions and Configuration

gnomAD v4.1

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

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gnomAD v3.1.1

\ The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,\ except as noted below.

\ \

There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).\
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one\ variant, with additional information available on the details page, which has roughly halved the\ number of items in the bigBed.\
The bigBed has been split into two files, one with the information necessary for the track\ display, and one with the information necessary for the details page. For more information on\ this data format, please see the Data Access section below.\
The VEP annotation is shown as a table instead of spread across multiple fields.\
Intergenic variants have not been pre-filtered.\

\ \

gnomAD v3.1

\ By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters\ described below), before the track switches to dense display mode.\

\ \

\ Mouse hover on an item will display many details about each variant, including the affected gene(s),\ the variant type, and annotation (missense, synonymous, etc).\

\ \

\ Clicking on an item will display additional details on the variant, including a population frequency\ table showing allele count in each sub-population.\

\ \

\ Following the conventions on the gnomAD browser, items are shaded according to their Annotation\ type:\ \ \ \ \ \
pLoF
Missense
Synonymous
Other
\

\ Four filters are available for these tracks, the same as the underlying VCF:\

AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))\
InbreedingCoeff: Inbreeding Coefficient < -0.3\
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)\
Pass: Variant passes all 3 filters\

\ \

\ There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.\

\ \ \

UCSC Methods

\ The gnomAD v3.1.1 and v4.1 data is unfiltered.

\ For the v3.1 update only, in order to cut \ down on the amount of displayed data, the following variant\ types have been filtered out, but are still viewable in the gnomAD browser:\

Regulatory Region Variants\
Downstream/Upstream Gene Variants\
Transcription Factor Binding Site Variants\

\ \

\ For the full steps used to create the gnomAD tracks at UCSC, please see the\ hg38 gnomad makedoc.\

\ \ \

Data Access

\ \

\
# find item of interest:\
bigBedToBed genomes.bb stdout | head -4 | tail -1\
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted for brevity..]    chr1-12417-G-A    67293    902\
\
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:\
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz\
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant",  [..omitted for brevity..]\

\ \

\ The data can also be found directly from the gnomAD downloads page. Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.\

\ \

\ Please note that some annotations within the provided files may have restrictions on usage. See here for more information. \

\ \

References

\ \

\ varRep 1 bigDataUrl /gbdb/hg38/gnomAD/v3.1/variants/genomes.bb\ dataVersion Release 3.1 (October 29, 2020)\ defaultLabelFields name\ detailsStaticTable Population Frequencies|/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt\ filter.AF 0.0\ filterLabel.AF Minor Allele Frequency Filter\ filterType.FILTER multipleListAnd\ filterType.annot multiple\ filterType.variation_type multipleListOr\ filterValues.FILTER PASS,InbreedingCoeff,RF,AC0\ filterValues.annot pLoF,missense,synonymous,other\ filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,TFBS_ablation,TF_binding_site_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intergenic_variant,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation\ filterValuesDefault.FILTER PASS\ html gnomadV4.1\ itemRgb on\ labelFields name,rsId\ longLabel Genome Aggregation Database (gnomAD) Genome Variants v3.1\ maxItems 50000\ mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); Genes: $genes; Type: $annot; Tag: $FILTER; Allele Frequency: $AF ($AC/$AN)\ parent gnomadVariants\ priority 3.2\ sepFields AC_afr\ shortLabel gnomAD v3.1\ track gnomadGenomesVariantsV3_1\ type bigBed 9 +\ url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$-$?dataset=gnomad_r3&ignore=$\ urlLabel View this variant at gnomAD\ visibility hide\ gnomadGenomesVariantsV3 gnomAD v3 vcfTabix Genome Aggregation Database (gnomAD) Genome Variants v3 0 3.3 0 0 0 127 127 127 0 0 0 http://gnomad.broadinstitute.org/variant/$s-$-$-$?dataset=gnomad_r3&ignore=$$ varRep 1 bigDataUrl /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r3.0.sites.vcf.gz\ configureByPopup off\ dataVersion Release 3.0 (October 16, 2019)\ html gnomad4.1\ longLabel Genome Aggregation Database (gnomAD) Genome Variants v3\ maxWindowToDraw 200000\ parent gnomadVariants\ priority 3.3\ shortLabel gnomAD v3\ showHardyWeinberg on\ track gnomadGenomesVariantsV3\ type vcfTabix\ url http://gnomad.broadinstitute.org/variant/$s-$-$-$?dataset=gnomad_r3&ignore=$$\ urlLabel gnomAD:\ visibility hide\ netMelGal5 Turkey Net netAlign melGal5 chainMelGal5 Turkey (Nov. 2014 (Turkey_5.0/melGal5)) Alignment Net 1 4 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Turkey (Nov. 2014 (Turkey_5.0/melGal5)) Alignment Net\ otherDb melGal5\ parent vertebrateChainNetViewnet off\ shortLabel Turkey Net\ subGroups view=net species=s006 clade=c01\ track netMelGal5\ type netAlign melGal5 chainMelGal5\ netPanPan3 Bonobo Net netAlign panPan3 chainPanPan3 Bonobo (May 2020 (Mhudiblu_PPA_v0/panPan3)) Alignment Net 1 4 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Bonobo (May 2020 (Mhudiblu_PPA_v0/panPan3)) Alignment Net\ otherDb panPan3\ parent primateChainNetViewnet off\ shortLabel Bonobo Net\ subGroups view=net species=s007b clade=c00\ track netPanPan3\ type netAlign panPan3 chainPanPan3\ netGalVar1 Malayan flying lemur Net netAlign galVar1 chainGalVar1 Malayan flying lemur (Jun. 2014 (G_variegatus-3.0.2/galVar1)) Alignment Net 1 4 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Malayan flying lemur (Jun. 2014 (G_variegatus-3.0.2/galVar1)) Alignment Net\ otherDb galVar1\ parent placentalChainNetViewnet off\ shortLabel Malayan flying lemur Net\ subGroups view=net species=s006 clade=c00\ track netGalVar1\ type netAlign galVar1 chainGalVar1\ wgEncodeGencode2wayConsPseudoV20 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 20 (Ensembl 76) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 20 (Ensembl 76)\ parent wgEncodeGencodeV20View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV20\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV22 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 22 (Ensembl 79) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 22 (Ensembl 79)\ parent wgEncodeGencodeV22View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV22\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV23 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 23 (Ensembl 81) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 23 (Ensembl 81)\ parent wgEncodeGencodeV23View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV23\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV24 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 24 (Ensembl 83) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 24 (Ensembl 83)\ parent wgEncodeGencodeV24View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV24\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV25 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 25 (Ensembl 85) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 25 (Ensembl 85)\ parent wgEncodeGencodeV25View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV25\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV26 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 26 (Ensembl 88) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 26 (Ensembl 88)\ parent wgEncodeGencodeV26View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV26\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV27 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 27 (Ensembl 90) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 27 (Ensembl 90)\ parent wgEncodeGencodeV27View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV27\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV28 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 28 (Ensembl 92) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 28 (Ensembl 92)\ parent wgEncodeGencodeV28View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV28\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV29 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 29 (Ensembl 94) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 29 (Ensembl 94)\ parent wgEncodeGencodeV29View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV29\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV30 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 30 (Ensembl 96) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 30 (Ensembl 96)\ parent wgEncodeGencodeV30View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV30\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV31 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 31 (Ensembl 97) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 31 (Ensembl 97)\ parent wgEncodeGencodeV31View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV31\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV32 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 32 (Ensembl 98) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 32 (Ensembl 98)\ parent wgEncodeGencodeV32View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV32\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV33 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 33 (Ensembl 99) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 33 (Ensembl 99)\ parent wgEncodeGencodeV33View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV33\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV34 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 34 (Ensembl 100) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 34 (Ensembl 100)\ parent wgEncodeGencodeV34View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV34\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV35 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 35 (Ensembl 101) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 35 (Ensembl 101)\ parent wgEncodeGencodeV35View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV35\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV36 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 36 (Ensembl 102) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 36 (Ensembl 102)\ parent wgEncodeGencodeV36View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV36\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV37 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 37 (Ensembl 103) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 37 (Ensembl 103)\ parent wgEncodeGencodeV37View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV37\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV38 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 38 (Ensembl 104) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 38 (Ensembl 104)\ parent wgEncodeGencodeV38View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV38\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV39 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 39 (Ensembl 105) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 39 (Ensembl 105)\ parent wgEncodeGencodeV39View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV39\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV40 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 40 (Ensembl 106) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 40 (Ensembl 106)\ parent wgEncodeGencodeV40View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV40\ trackHandler wgEncodeGencode\ type genePred\ wgEncodeGencode2wayConsPseudoV41 2-way Pseudogenes genePred 2-way Pseudogene Annotation Set from GENCODE Version 41 (Ensembl 107) 0 4 255 51 255 255 153 255 0 0 0 genes 1 color 255,51,255\ longLabel 2-way Pseudogene Annotation Set from GENCODE Version 41 (Ensembl 107)\ parent wgEncodeGencodeV41View2Way off\ priority 4\ shortLabel 2-way Pseudogenes\ subGroups view=b2-way name=yTwo-way\ track wgEncodeGencode2wayConsPseudoV41\ trackHandler wgEncodeGencode\ type genePred\ phyloP447wayLRT 447 phyloP primates LRT bigWig -20 1.951 447 mammals Basewise Conservation by PhyloP, primates subset LRT 2 4 60 60 140 140 60 60 0 0 0 compGeno 0 altColor 140,60,60\ autoScale off\ bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP447way/hg38.phyloP447wayLRT.bw\ color 60,60,140\ configurable on\ longLabel 447 mammals Basewise Conservation by PhyloP, primates subset LRT\ maxHeightPixels 100:50:11\ noInherit on\ parent cons447wayViewphyloP\ priority 4\ shortLabel 447 phyloP primates LRT\ spanList 1\ subGroups view=phyloP\ track phyloP447wayLRT\ type bigWig -20 1.951\ viewLimits -4.5:2\ windowingFunction mean\ phyloP470wayBW 470 phyloP bigWig -20 11.936 470 mammals Basewise Conservation by PhyloP 2 4 60 60 140 140 60 60 0 0 0 compGeno 0 altColor 140,60,60\ autoScale off\ bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP470way/hg38.phyloP470way.bw\ color 60,60,140\ configurable on\ logoMaf https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf\ longLabel 470 mammals Basewise Conservation by PhyloP\ maxHeightPixels 100:50:11\ parent cons470wayViewphyloP\ priority 4\ shortLabel 470 phyloP\ spanList 1\ subGroups view=phyloP\ track phyloP470wayBW\ type bigWig -20 11.936\ viewLimits -4.5:7.5\ windowingFunction mean\ encTfChipPkENCFF330OCU A549 CBX8 narrowPeak Transcription Factor ChIP-seq Peaks of CBX8 in A549 from ENCODE 3 (ENCFF330OCU) 0 4 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of CBX8 in A549 from ENCODE 3 (ENCFF330OCU)\ parent encTfChipPk off\ shortLabel A549 CBX8\ subGroups cellType=A549 factor=CBX8\ track encTfChipPkENCFF330OCU\ cloneEndABC13 ABC13 bed 12 Agencourt fosmid library 13 0 4 0 0 0 127 127 127 0 0 0 map 1 colorByStrand 0,0,128 0,128,0\ longLabel Agencourt fosmid library 13\ parent cloneEndSuper off\ priority 4\ shortLabel ABC13\ subGroups source=agencourt\ track cloneEndABC13\ type bed 12\ visibility hide\ covidHgiGwasR4PvalC2 All COVID vars bigLolly 9 + COVID risk variants from the COVID-19 HGI GWAS Analysis C2 (17965 cases, 33 studies, Rel 4: Oct 2020) 0 4 0 0 0 127 127 127 0 0 22 chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, phenDis 1 bigDataUrl /gbdb/hg38/covidHgiGwas/covidHgiGwasR4.C2.hg38.bb\ longLabel COVID risk variants from the COVID-19 HGI GWAS Analysis C2 (17965 cases, 33 studies, Rel 4: Oct 2020)\ parent covidHgiGwasR4Pval on\ priority 4\ shortLabel All COVID vars\ track covidHgiGwasR4PvalC2\ dbSnp153 All dbSNP(153) bigDbSnp All Short Genetic Variants from dbSNP Release 153 1 4 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 bigDataUrl /gbdb/hg38/snp/dbSnp153.bb\ defaultGeneTracks knownGene\ longLabel All Short Genetic Variants from dbSNP Release 153\ maxWindowToDraw 1000000\ parent dbSnp153ViewVariants off\ priority 4\ shortLabel All dbSNP(153)\ subGroups view=variants\ track dbSnp153\ dbSnp155 All dbSNP(155) bigDbSnp All Short Genetic Variants from dbSNP Release 155 1 4 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/snp/$$ varRep 1 bigDataUrl /gbdb/hg38/snp/dbSnp155.bb\ defaultGeneTracks knownGene\ longLabel All Short Genetic Variants from dbSNP Release 155\ maxWindowToDraw 1000000\ parent dbSnp155ViewVariants off\ priority 4\ shortLabel All dbSNP(155)\ subGroups view=variants\ track dbSnp155\ AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep2LK2_CNhs13358_tpm_rev AorticSmsToFgf2_00hr00minBr2- bigWig Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_reverse 1 4 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12740-135I4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr00min%2c%20biol_rep2%20%28LK2%29.CNhs13358.12740-135I4.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12740-135I4 sequence_tech=hCAGE\ parent TSS_activity_TPM on\ shortLabel AorticSmsToFgf2_00hr00minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep2LK2_CNhs13358_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12740-135I4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep2LK2_CNhs13358_ctss_rev AorticSmsToFgf2_00hr00minBr2- bigWig Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_reverse 0 4 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12740-135I4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr00min%2c%20biol_rep2%20%28LK2%29.CNhs13358.12740-135I4.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12740-135I4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_00hr00minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep2LK2_CNhs13358_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12740-135I4\ urlLabel FANTOM5 Details:\ gtexCovArteryAorta Artery Aorta bigWig Artery Aorta 0 4 139 28 98 197 141 176 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-WYVS-0426-SM-4ONDL.Artery_Aorta.RNAseq.bw\ color 139,28,98\ longLabel Artery Aorta\ parent gtexCov\ shortLabel Artery Aorta\ track gtexCovArteryAorta\ phyloP241wayBW Basewise Cons bigWig -20 9.28 PhyloP Basewise Conservation of Zoonomia 241 Placental Mammals 2 4 60 60 140 140 60 60 0 0 0 compGeno 0 altColor 140,60,60\ autoScale off\ bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/cactus241way.phyloP.bw\ color 60,60,140\ configurable on\ logoMaf https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/cactus241way.bigMaf\ longLabel PhyloP Basewise Conservation of Zoonomia 241 Placental Mammals\ maxHeightPixels 100:50:11\ parent cons241wayViewphyloP\ priority 4\ shortLabel Basewise Cons\ spanList 1\ subGroups view=phyloP clade=all\ track phyloP241wayBW\ type bigWig -20 9.28\ viewLimits -4.5:7.5\ windowingFunction mean\ iscaBenignLossCum Benign Loss bedGraph 4 ClinGen CNVs: Benign Loss Coverage 2 4 200 0 0 227 127 127 0 0 0 phenDis 0 color 200,0,0\ longLabel ClinGen CNVs: Benign Loss Coverage\ parent iscaViewTotal\ shortLabel Benign Loss\ subGroups view=cov class=ben level=sub\ track iscaBenignLossCum\ bismap100Pos Bismap S100 + bigBed 6 Single-read mappability with 100-mers after bisulfite conversion (forward strand) 0 4 240 170 80 247 212 167 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k100.C2T-Converted.bb\ color 240,170,80\ longLabel Single-read mappability with 100-mers after bisulfite conversion (forward strand)\ parent bismapBigBed off\ priority 4\ shortLabel Bismap S100 +\ subGroups view=SR\ track bismap100Pos\ visibility hide\ lincRNAsCTBrain_R Brain_R bed 5 + lincRNAs from brain_r 1 4 0 60 120 127 157 187 1 0 0 genes 1 longLabel lincRNAs from brain_r\ origAssembly hg19\ parent lincRNAsAllCellType on\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel Brain_R\ subGroups view=lincRNAsRefseqExp tissueType=brain_r\ track lincRNAsCTBrain_R\ BRCA BRCA bigLolly 12 + Breast invasive carcinoma 0 4 0 0 0 127 127 127 0 0 0 phenDis 1 autoScale on\ bigDataUrl /gbdb/hg38/gdcCancer/BRCA.bb\ configurable off\ group phenDis\ lollyField 13\ longLabel Breast invasive carcinoma\ parent gdcCancer off\ priority 4\ shortLabel BRCA\ track BRCA\ type bigLolly 12 +\ urls case_id=https://portal.gdc.cancer.gov/cases/193294\ phyloP100way Cons 100 Verts wig -20 7.532 100 vertebrates Basewise Conservation by PhyloP 2 4 60 60 140 140 60 60 0 0 0 compGeno 0 altColor 140,60,60\ autoScale off\ color 60,60,140\ configurable on\ logoMaf multiz100way\ longLabel 100 vertebrates Basewise Conservation by PhyloP\ maxHeightPixels 100:50:11\ noInherit on\ parent cons100wayViewphyloP on\ priority 4\ shortLabel Cons 100 Verts\ spanList 1\ subGroups view=phyloP\ track phyloP100way\ type wig -20 7.532\ viewLimits -0.5:4\ windowingFunction mean\ phyloP30way Cons 30 Mammals wig -20 1.312 30 mammals Basewise Conservation by PhyloP (27 primates) 2 4 60 60 140 140 60 60 0 0 0 compGeno 0 altColor 140,60,60\ autoScale off\ color 60,60,140\ configurable on\ logoMaf multiz30way\ longLabel 30 mammals Basewise Conservation by PhyloP (27 primates)\ maxHeightPixels 100:50:11\ noInherit on\ parent cons30wayViewphyloP on\ priority 4\ shortLabel Cons 30 Mammals\ spanList 1\ subGroups view=phyloP\ track phyloP30way\ type wig -20 1.312\ viewLimits -3:1\ windowingFunction mean\ dbVar_common_decipher dbVar Curated DECIPHER SVs bigBed 9 + . NCBI dbVar Curated Common SVs: all populations from DECIPHER 3 4 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ varRep 1 bigDataUrl /gbdb/hg38/bbi/dbVar/common_decipher.bb\ longLabel NCBI dbVar Curated Common SVs: all populations from DECIPHER\ parent dbVar_common on\ shortLabel dbVar Curated DECIPHER SVs\ track dbVar_common_decipher\ type bigBed 9 + .\ url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$\ urlLabel NCBI Variant Page:\ unipLocExtra Extracellular bigBed 12 + UniProt Extracellular Domain 1 4 0 150 255 127 202 255 0 0 0 genes 1 bigDataUrl /gbdb/hg38/uniprot/unipLocExtra.bb\ color 0,150,255\ filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)\ itemRgb off\ longLabel UniProt Extracellular Domain\ parent uniprot\ priority 4\ shortLabel Extracellular\ track unipLocExtra\ type bigBed 12 +\ visibility dense\ knownGeneV44 GENCODE V44 bigGenePred knownGenePep knownGeneMrna GENCODE V44 0 4 0 0 0 127 127 127 0 0 0

Description

\ The GENCODE Genes track (version 44, July 2023) shows high-quality manual\ annotations merged with evidence-based automated annotations across the entire\ human genome generated by the\ GENCODE project.\ By default, only the basic gene set is\ displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts\ that GENCODE believes will be useful to the majority of users.

\ \

\ The following table provides statistics for the v44 release derived from the GTF file that contains\ annotations only on the main chromosomes. More information on how they were generated can be found\ in the GENCODE site.

\ \

\ \ \ \ \ \ \ \ \
GENCODE v44 Release Stats
Genes Observed Transcripts Observed
Protein-coding genes 19,396 Protein-coding transcripts 89,067
Long non-coding RNA genes 19,922 - full length protein-coding 63,968
Small non-coding RNA genes 7,566 - partial length protein-coding 25,099
Pseudogenes 14,735 Nonsense mediated decay transcripts 21,384
Immunoglobulin/T-cell receptor gene segments 647 Long non-coding RNA loci transcripts 58,246
Total No of distinct translations 65,342 Genes that have more than one distinct translations 13,594

\

GENCODE v44 Release Stats
Genes	Observed	Transcripts	Observed
Protein-coding genes	19,396	Protein-coding transcripts	89,067
Long non-coding RNA genes	19,922	- full length protein-coding	63,968
Small non-coding RNA genes	7,566	- partial length protein-coding	25,099
Pseudogenes	14,735	Nonsense mediated decay transcripts	21,384
Immunoglobulin/T-cell receptor gene segments	647	Long non-coding RNA loci transcripts	58,246
Total No of distinct translations	65,342	Genes that have more than one distinct translations	13,594

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ \

Coloring for the gene annotations is based on the annotation type:

coding: protein coding transcripts, including polymorphic\ pseudogenes\
non-coding: non-protein coding transcripts\
pseudogene: pseudogene transcript annotations\
problem: problem transcripts (Biotypes of\ retained_intron, TEC, or disrupted_domain)

\ \

\ \ \

Squishy-pack Display

\ Protein_coding genes\

MANE or Ensembl canonical\
- 1st: MANE Select / Ensembl canonical
- 2nd: MANE Plus Clinical
\
Coding biotypes\
- 1st: protein_coding and protein_coding_LoF
- 2nd: NMDs and NSDs
- 3rd: retained intron and protein_coding_CDS_not_defined
\
Completeness\
- 1st: full length
- 2nd: CDS start/end not found
\
CARS score (only for coding transcripts)
Transcript genomic span and length (only for non-coding transcripts)

\ Non-coding genes\

Transcript biotype\
- 1st: transcript biotype identical to gene biotype
\
Ensembl canonical
GENCODE basic
Transcript genomic span
Transcript length

\ \ \

Methods

\ The GENCODE v44 track was built from the GENCODE downloads file \ gencode.v44.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources\ were correlated with the GENCODE data to build association tables.

\ \

Related Data

\ The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a\ downloadable\ file.\ \

Description

\ \

\ gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the\ GRCh38/hg38 lift-over provided by gnomAD on their downloads site.\

\ \

\ For questions on the gnomAD data, also see the gnomAD FAQ.

\ More details on the Variant type(s) can be found on the Sequence Ontology page.

\ \

Display Conventions and Configuration

gnomAD v4.1

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

\ \

gnomAD v3.1.1

\ The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,\ except as noted below.

\ \

There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).\
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one\ variant, with additional information available on the details page, which has roughly halved the\ number of items in the bigBed.\
The bigBed has been split into two files, one with the information necessary for the track\ display, and one with the information necessary for the details page. For more information on\ this data format, please see the Data Access section below.\
The VEP annotation is shown as a table instead of spread across multiple fields.\
Intergenic variants have not been pre-filtered.\

\ \

gnomAD v3.1

\ By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters\ described below), before the track switches to dense display mode.\

\ \

\ Mouse hover on an item will display many details about each variant, including the affected gene(s),\ the variant type, and annotation (missense, synonymous, etc).\

\ \

\ Clicking on an item will display additional details on the variant, including a population frequency\ table showing allele count in each sub-population.\

\ \

\ Following the conventions on the gnomAD browser, items are shaded according to their Annotation\ type:\ \ \ \ \ \
pLoF
Missense
Synonymous
Other
\

\ Four filters are available for these tracks, the same as the underlying VCF:\

AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))\
InbreedingCoeff: Inbreeding Coefficient < -0.3\
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)\
Pass: Variant passes all 3 filters\

\ \

\ There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.\

\ \ \

UCSC Methods

\ The gnomAD v3.1.1 and v4.1 data is unfiltered.

\ For the v3.1 update only, in order to cut \ down on the amount of displayed data, the following variant\ types have been filtered out, but are still viewable in the gnomAD browser:\

Regulatory Region Variants\
Downstream/Upstream Gene Variants\
Transcription Factor Binding Site Variants\

\ \

\ For the full steps used to create the gnomAD tracks at UCSC, please see the\ hg38 gnomad makedoc.\

\ \ \

Data Access

\ \

\
# find item of interest:\
bigBedToBed genomes.bb stdout | head -4 | tail -1\
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted for brevity..]    chr1-12417-G-A    67293    902\
\
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:\
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz\
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant",  [..omitted for brevity..]\

\ \

\ The data can also be found directly from the gnomAD downloads page. Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.\

\ \

\ Please note that some annotations within the provided files may have restrictions on usage. See here for more information. \

\ \

References

\ \

\ varRep 1 compositeTrack on\ configureByPopup off\ dataVersion Release 2.1.1 (March 6, 2019)\ html gnomadV4.1\ longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1\ maxWindowToDraw 200000\ parent gnomadVariants\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ priority 4\ shortLabel gnomAD v2\ showHardyWeinberg on\ track gnomadVariantsV2\ type vcfTabix\ visibility hide\ wgEncodeRegTxnCaltechRnaSeqHepg2R2x75Il200SigPooled HepG2 bigWig 0 65535 Transcription of HepG2 cells from ENCODE 0 4 128 255 149 191 255 202 0 0 0 regulation 1 color 128,255,149\ longLabel Transcription of HepG2 cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegTxn\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ priority 4\ shortLabel HepG2\ track wgEncodeRegTxnCaltechRnaSeqHepg2R2x75Il200SigPooled\ type bigWig 0 65535\ hffc6MicroC HFFc6 Micro-C hic Micro-C Chromatin Structure on HFFc6 0 4 0 0 0 127 127 127 0 0 0 regulation 1 bigDataUrl /gbdb/hg38/bbi/hic/4DNFI18Q799K.hic\ longLabel Micro-C Chromatin Structure on HFFc6\ parent hicAndMicroC off\ shortLabel HFFc6 Micro-C\ track hffc6MicroC\ type hic\ netHprcGCA_018466985v1 HG02559.mat netAlign GCA_018466985.1 chainHprcGCA_018466985v1 HG02559.mat HG02559.pri.mat.f1_v2 (May 2021 GCA_018466985.1_HG02559.pri.mat.f1_v2) HPRC project computed Chain Nets 1 4 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02559.mat HG02559.pri.mat.f1_v2 (May 2021 GCA_018466985.1_HG02559.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018466985.1\ parent hprcChainNetViewnet off\ priority 20\ shortLabel HG02559.mat\ subGroups view=net sample=s020 population=afr subpop=acb hap=mat\ track netHprcGCA_018466985v1\ type netAlign GCA_018466985.1 chainHprcGCA_018466985v1\ highReproRegions Highly Reproducible Regions bigBed 9 + Highly Reproducible Regions 1 4 0 0 0 127 127 127 0 0 0 map 1 bigDataUrl /gbdb/hg38/problematic/highRepro/highRepro.bb\ filterType.sampleNames multipleListOr\ filterValues.sampleNames CQ-56,CQ-7,CQ-8,HR_NA10835,HR_NA12248,HR_NA12249,HR_NA12878\ longLabel Highly Reproducible Regions\ parent highReproBeds\ shortLabel Highly Reproducible Regions\ subGroups view=beds\ track highReproRegions\ type bigBed 9 +\ wgEncodeRegDnaseUwHmecPeak HMEC Pk narrowPeak HMEC mammary epithelium DNaseI Peaks from ENCODE 1 4 255 112 85 255 183 170 1 0 0 regulation 1 color 255,112,85\ longLabel HMEC mammary epithelium DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMEC Pk\ subGroups view=a_Peaks cellType=HMEC treatment=n_a tissue=breast cancer=normal\ track wgEncodeRegDnaseUwHmecPeak\ wgEncodeRegDnaseUwHmecWig HMEC Sg bigWig 0 32097.2 HMEC mammary epithelium DNaseI Signal from ENCODE 0 4 255 112 85 255 183 170 0 0 0 regulation 1 color 255,112,85\ longLabel HMEC mammary epithelium DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.02847\ shortLabel HMEC Sg\ subGroups cellType=HMEC treatment=n_a tissue=breast cancer=normal\ table wgEncodeRegDnaseUwHmecSignal\ track wgEncodeRegDnaseUwHmecWig\ type bigWig 0 32097.2\ wgEncodeRegMarkH3k4me1Huvec HUVEC bigWig 0 4666 H3K4Me1 Mark (Often Found Near Regulatory Elements) on HUVEC Cells from ENCODE 0 4 128 212 255 191 233 255 0 0 0 regulation 1 color 128,212,255\ longLabel H3K4Me1 Mark (Often Found Near Regulatory Elements) on HUVEC Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k4me1\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel HUVEC\ table wgEncodeBroadHistoneHuvecH3k4me1StdSig\ track wgEncodeRegMarkH3k4me1Huvec\ type bigWig 0 4666\ wgEncodeRegMarkH3k4me3Huvec HUVEC bigWig 0 7852 H3K4Me3 Mark (Often Found Near Promoters) on HUVEC Cells from ENCODE 0 4 128 212 255 191 233 255 0 0 0 regulation 1 color 128,212,255\ longLabel H3K4Me3 Mark (Often Found Near Promoters) on HUVEC Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k4me3\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel HUVEC\ table wgEncodeBroadHistoneHuvecH3k4me3StdSig\ track wgEncodeRegMarkH3k4me3Huvec\ type bigWig 0 7852\ wgEncodeRegMarkH3k27acHuvec HUVEC bigWig 0 3721 H3K27Ac Mark (Often Found Near Regulatory Elements) on HUVEC Cells from ENCODE 2 4 128 212 255 191 233 255 0 0 0 regulation 1 color 128,212,255\ longLabel H3K27Ac Mark (Often Found Near Regulatory Elements) on HUVEC Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k27ac\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel HUVEC\ table wgEncodeBroadHistoneHuvecH3k27acStdSig\ track wgEncodeRegMarkH3k27acHuvec\ type bigWig 0 3721\ xGen_Research_Targets_V2 IDT xGen V2 T bigBed IDT - xGen Exome Research Panel V2 Target Regions 1 4 100 143 255 177 199 255 0 0 0 map 1 bigDataUrl /gbdb/hg38/exomeProbesets/xgen-exome-research-panel-v2-targets-hg38.bb\ color 100,143,255\ longLabel IDT - xGen Exome Research Panel V2 Target Regions\ parent exomeProbesets on\ shortLabel IDT xGen V2 T\ track xGen_Research_Targets_V2\ type bigBed\ visibility dense\ snpArrayIllumina450k Illumina 450k bigBed 6 Illumina 450k Methylation Array 3 4 0 0 0 127 127 127 0 0 0

Description

Agilent Arrays

\ The arrays listed in this track are probes from the\ Agilent Catalog Oligonucleotide Microarrays.\

Please note that more microarray tracks are available on the hg19 genome assembly. \ To view those tracks, please \ click this link for hg19 microarrays.\ Microarrays that are not listed can be added as Custom Tracks with data from the companies.\

\ Agilent GenetiSure Cyto\

\ Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables the\ study of genome-wide DNA copy number changes at a high resolution. The CGH probes on Agilent\ CGH microarrays are 60-mer oligonucleotides synthesized in situ using Agilent's inkjet\ SurePrint technology. The probes represented on the Agilent CGH microarrays have been\ selected using algorithms developed specifically for the CGH application, assuring optimal\ performance of these probes in detecting DNA copy number changes.\

\ \

Illumina 450k and 850k Methylation Arrays

\ With the Infinium MethylationEPIC BeadChip Kit, researchers can interrogate over 850,000\ methylation sites quantitatively across the genome at single-nucleotide resolution. Multiple\ samples, including FFPE, can be analyzed in parallel to deliver high-throughput power while\ minimizing the cost per sample. These tracks show positions being measured on the Illumina 450k and\ 850k (EPIC) microarray tracks. More information about the arrays can be found on the\ Infinium MethylationEPIC Kit website.\ \

Illumina CytoSNP 850K Probe Array

\ The Infinium CytoSNP-850K v1.2 BeadChip provides comprehensive coverage of\ cytogenetically relevant genes on a proven platform, helping researchers find valuable information\ that may be missed by other technologies. It contains approximately 850,000 empirically selected\ single nucleotide polymorphisms (SNPs) spanning the entire genome with enriched coverage for 3,262\ genes of known cytogenetics relevance in both constitutional and cancer applications. \

\ \

Affymetrix Cytoscan HD GeneChip Array

\ The CytoScan HD Array, which is included in the\ CytoScan HD Suite, provides the broadest coverage and highest performance for\ detecting chromosomal aberrations. CytoScan HD Suite has greater than 99% sensitivity and can\ reliably detect 25-50kb copy number changes across the genome at high specificity with\ single-nucleotide polymorphism (SNP) allelic corroboration. With more than 2.6 million copy number\ markers, CytoScan HD Suite covers all OMIM and RefSeq genes.\

\ \ \ \

Display Conventions and Configuration

\ \

\ Items in this track are colored according to their strand orientation. Blue\ indicates alignment to the negative strand, and red indicates\ alignment to the positive strand.\

\ \ \

Methods

\ The Agilent arrays were downloaded from their \ Agilent SureDesign website tool on March 2022.

\ The Illumina 450k and 850k (EPIC) tracks were created using a few columns from the\ Infinium MethylationEPIC v1.0 B5 Manifest File (CSV Format)\ and was then converted into a bigBed.

\ The Illumina CytoSNP-850K track was created by downloading the\ CytoSNP-850K v1.2 Manifest File (CSV Format) (GRCh38) file and then converted\ into a bigBed file.\

\ The Affymetrix Cytoscan HD GeneChip Array track was created by converting the \ CytoScanHD_Accel_Array.na36.bed.zip\ into a bigBed file.\

\ \

Data Access

\ The raw data can be explored interactively with the\ Table Browser or the\ Data Integrator.\ For automated analysis, the data may be queried from our\ REST API \ or downloaded from our \ Downloads site. Please refer to our\ \ mailing list archives for questions, or our\ \ Data Access FAQ for more information.\

\ \

Credits

\ Thanks to the Aliglent and Illumina support teams for sharing the data and the UCSC Genome Browser\ engineers for configuring the data.

Description

\ \

\ This track was created using Arian Smit's\ RepeatMasker\ program, which screens DNA sequences\ for interspersed repeats and low complexity DNA sequences. The program\ outputs a detailed annotation of the repeats that are present in the\ query sequence (represented by this track), as well as a modified version\ of the query sequence in which all the annotated repeats have been masked\ (generally available on the\ Downloads page). RepeatMasker uses a separately curated version of the \ Repbase Update repeat library from the\ Genetic \ Information Research Institute (GIRI).\ Repbase Update is described in Jurka (2000) in the References section below.

\ Alternatively, RepeatMasker can use the new\ Dfam database of repeat profile HMMs.\ Profile HMMs provide a richer description of the repeat families and when used with\ RepeatMasker + nhmmer provide a more\ sensitive approach to identifying repeats. Dfam is described in Wheeler et al. (2012)\ in the References section below.\

\ \

Display Conventions and Configuration

\ \

\ In dense display mode, a single line is displayed denoting the coverage of repeats using a series\ of black boxes. \

\ In full display mode, the track view is controlled by the scale of the view. At scales between 10 Mb\ and 30 kb, this track displays up to ten different classes of repeats (see below) one class per\ line. The repeat ranges are denoted as grayscale boxes, reflecting both the size of the repeat and\ the amount of base mismatch, base deletion, and base insertion associated with a repeat element.\ The higher the combined number of these, the lighter the shading.\

\ In full display mode and at scales less than 30 kb, a new detailed display mode is used. Repeats\ are displayed as arrow boxes, indicating the size and orientation of the repeat. The interior\ grayscale shading represents the divergence of the repeat (see above) while the outline color\ represents the class of the repeat. Dotted lines above the repeat and extending left or right\ indicate the length of unaligned repeat consensus sequence. If the length of the unaligned sequence\ is large, a double interruption line is used to indicate that the unaligned sequence is not to scale. \

\ For example, the following repeat is a SINE element in the forward orientation with average\ divergence. Only the 5' proximal fragment of the consensus sequence is aligned to the genome.\ The 3' unaligned length (384bp) is not drawn to scale and is instead displayed using a set of\ interruption lines along with the length of the unaligned sequence.\

\ \ \ \

\ Repeats that have been fragmented by insertions or large internal deletions are now represented\ by join lines. In the example below, a LINE element is found as two fragments. The solid\ connection lines indicate that there are no unaligned consensus bases between the two fragments.\ Also note these fragments represent the end of the repeat, as there is no unaligned consensus\ sequence following the last fragment.\

\ \ \ \

\ In cases where there is unaligned consensus sequence between the fragments, the repeat will look like\ the following. The dotted line indicates the length of the unaligned sequence between the two\ fragments. In this case the unaligned consensus is longer than the actual genomic distance between\ these two fragments.\

\ \ \ \

\ If there is consensus overlap between the two fragments, the joining lines will be drawn to indicate\ how much of the left fragment is repeated in the right fragment. \

\ \ \ \

\ The following table lists the repeat class colors:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

Color	Repeat Class
	SINE - Short Interspersed Nuclear Element
	LINE - Long Interspersed Nuclear Element
	LTR - Long Terminal Repeat
	DNA - DNA Transposon
	Simple - Single Nucleotide Stretches and Tandem Repeats
	Low_complexity - Low Complexity DNA
	Satellite - Satellite Repeats
	RNA - RNA Repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
	Other - Other Repeats (including class RC - Rolling Circle)
	Unknown - Unknown Classification

\ \

\ A "?" at the end of the "Family" or "Class" (for example, DNA?)\ signifies that the curator was unsure of the classification. At some point in the future,\ either the "?" will be removed or the classification will be changed.

\ \

Methods

\ \

Credits

\ \

\ Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and\ repeat libraries used to generate this track.\

\ \

References

\ \

\ Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0.\ \ http://www.repeatmasker.org. 1996-2010.\

\ \

\ Dfam is described in:\

\ Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.\ \ Dfam: a database of repetitive DNA based on profile hidden Markov models.\ Nucleic Acids Res. 2013 Jan;41(Database issue):D70-82.\ PMID: 23203985; PMC: PMC3531169\

\ \

\ Repbase Update is described in:\

\ Jurka J.\ \ Repbase Update: a database and an electronic journal of repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-420.\ PMID: 10973072\

\ \

\ For a discussion of repeats in mammalian genomes, see:\

\ Smit AF.\ \ Interspersed repeats and other mementos of transposable elements in mammalian genomes.\ Curr Opin Genet Dev. 1999 Dec;9(6):657-63.\ PMID: 10607616\

\ \

\ Smit AF.\ \ The origin of interspersed repeats in the human genome.\ Curr Opin Genet Dev. 1996 Dec;6(6):743-8.\ PMID: 8994846\

\ rep 0 allButtonPair on\ canPack off\ compositeTrack on\ group rep\ html joinedRmsk\ longLabel Detailed Visualization of RepeatMasker Annotations\ maxWindowToDraw 10000000\ priority 4\ shortLabel RepeatMasker Viz.\ spectrum on\ track joinedRmsk\ type bed 3 +\ visibility hide\ rmskJoinedBaseline RepeatMasker Viz. bed 3 + RepeatMasker v3.0.1 db20100302 : Browser Baseline Dataset 0 4 0 0 0 127 127 127 1 0 0 rep 0 group rep\ longLabel RepeatMasker v3.0.1 db20100302 : Browser Baseline Dataset\ parent joinedRmsk on\ priority 4\ shortLabel RepeatMasker Viz.\ track rmskJoinedBaseline\ visibility hide\ umap100 Umap S100 bigBed 6 Single-read mappability with 100-mers 0 4 80 170 240 167 212 247 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k100.Unique.Mappability.bb\ color 80,170,240\ longLabel Single-read mappability with 100-mers\ parent umapBigBed off\ priority 4\ shortLabel Umap S100\ subGroups view=SR\ track umap100\ visibility hide\ chainGalGal6 Chicken Chain chain galGal6 Chicken (Mar. 2018 (GRCg6a/galGal6)) Chained Alignments 3 5 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)) Chained Alignments\ otherDb galGal6\ parent vertebrateChainNetViewchain off\ shortLabel Chicken Chain\ subGroups view=chain species=s008a clade=c01\ track chainGalGal6\ type chain galGal6\ chainGorGor6 Gorilla Chain chain gorGor6 Gorilla (Aug. 2019 (Kamilah_GGO_v0/gorGor6)) Chained Alignments 3 5 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Gorilla (Aug. 2019 (Kamilah_GGO_v0/gorGor6)) Chained Alignments\ otherDb gorGor6\ parent primateChainNetViewchain off\ shortLabel Gorilla Chain\ subGroups view=chain species=s009a clade=c00\ track chainGorGor6\ type chain gorGor6\ chainMm39 Mouse Chain chain mm39 Mouse (Jun. 2020 (GRCm39/mm39)) Chained Alignments 3 5 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Chained Alignments\ otherDb mm39\ parent placentalChainNetViewchain off\ shortLabel Mouse Chain\ subGroups view=chain species=s012a clade=c00\ track chainMm39\ type chain mm39\ encTfChipPkENCFF047UIF A549 CEBPB narrowPeak Transcription Factor ChIP-seq Peaks of CEBPB in A549 from ENCODE 3 (ENCFF047UIF) 0 5 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of CEBPB in A549 from ENCODE 3 (ENCFF047UIF)\ parent encTfChipPk off\ shortLabel A549 CEBPB\ subGroups cellType=A549 factor=CEBPB\ track encTfChipPkENCFF047UIF\ cloneEndABC14 ABC14 bed 12 Agencourt fosmid library 14 0 5 0 0 0 127 127 127 0 0 0 map 1 colorByStrand 0,0,128 0,128,0\ longLabel Agencourt fosmid library 14\ parent cloneEndSuper off\ priority 5\ shortLabel ABC14\ subGroups source=agencourt\ track cloneEndABC14\ type bed 12\ visibility hide\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_tpm_fwd AorticSmsToFgf2_00hr15minBr1+ bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_forward 1 5 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12643-134G6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep1%20%28LK4%29.CNhs13340.12643-134G6.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12643-134G6 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_00hr15minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12643-134G6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_ctss_fwd AorticSmsToFgf2_00hr15minBr1+ bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_forward 0 5 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12643-134G6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep1%20%28LK4%29.CNhs13340.12643-134G6.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12643-134G6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_00hr15minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12643-134G6\ urlLabel FANTOM5 Details:\ gtexCovArteryCoronary Artery Coron bigWig Artery Coronary 0 5 238 106 80 246 180 167 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1GMR3-0626-SM-9WYT3.Artery_Coronary.RNAseq.bw\ color 238,106,80\ longLabel Artery Coronary\ parent gtexCov\ shortLabel Artery Coron\ track gtexCovArteryCoronary\ bismap24Neg Bismap S24 - bigBed 6 Single-read mappability with 24-mers after bisulfite conversion (reverse strand) 1 5 240 20 80 247 137 167 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k24.G2A-Converted.bb\ color 240,20,80\ longLabel Single-read mappability with 24-mers after bisulfite conversion (reverse strand)\ parent bismapBigBed on\ priority 5\ shortLabel Bismap S24 -\ subGroups view=SR\ track bismap24Neg\ visibility dense\ lincRNAsCTBreast Breast bed 5 + lincRNAs from breast 1 5 0 60 120 127 157 187 1 0 0 genes 1 longLabel lincRNAs from breast\ origAssembly hg19\ parent lincRNAsAllCellType on\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel Breast\ subGroups view=lincRNAsRefseqExp tissueType=breast\ track lincRNAsCTBreast\ CESC CESC bigLolly 12 + Cervical squamous cell carcinoma and endocervical adenocarcinoma 0 5 0 0 0 127 127 127 0 0 0 phenDis 1 autoScale on\ bigDataUrl /gbdb/hg38/gdcCancer/CESC.bb\ configurable off\ group phenDis\ lollyField 13\ longLabel Cervical squamous cell carcinoma and endocervical adenocarcinoma\ parent gdcCancer off\ priority 5\ shortLabel CESC\ track CESC\ type bigLolly 12 +\ urls case_id=https://portal.gdc.cancer.gov/cases/193294\ dbVar_common_european dbVar Curated European SVs bigBed 9 + . NCBI dbVar Curated Common SVs: European 3 5 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ varRep 1 bigDataUrl /gbdb/hg38/bbi/dbVar/common_european.bb\ longLabel NCBI dbVar Curated Common SVs: European\ parent dbVar_common on\ shortLabel dbVar Curated European SVs\ track dbVar_common_european\ type bigBed 9 + .\ url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$\ urlLabel NCBI Variant Page:\ knownGeneV43 GENCODE V43 bigGenePred GENCODE V43 0 5 0 0 0 127 127 127 0 0 0

Description

\ The GENCODE Genes track (version 43, February 2023) shows high-quality manual\ annotations merged with evidence-based automated annotations across the entire\ human genome generated by the\ GENCODE project.\ By default, only the basic gene set is\ displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts\ that GENCODE believes will be useful to the majority of users.

\ \

\ The following table provides statistics for the v43 release derived from the GTF file that contains\ annotations only on the main chromosomes. More information on how they were generated can be found\ in the GENCODE site.

\ \

\ \ \ \ \ \ \ \ \
GENCODE v43 Release Stats
Genes Observed Transcripts Observed
Protein-coding genes 19,393 Protein-coding transcripts 89,411
Long non-coding RNA genes 19,928 - full length protein-coding 64,004
Small non-coding RNA genes 7,566 - partial length protein-coding 25,407
Pseudogenes 14,737 Nonsense mediated decay transcripts 21,354
Immunoglobulin/T-cell receptor gene segments 410 Long non-coding RNA loci transcripts 58,023
Total No of distinct translations 65,519 Genes that have more than one distinct translations 13,618

\

GENCODE v43 Release Stats
Genes	Observed	Transcripts	Observed
Protein-coding genes	19,393	Protein-coding transcripts	89,411
Long non-coding RNA genes	19,928	- full length protein-coding	64,004
Small non-coding RNA genes	7,566	- partial length protein-coding	25,407
Pseudogenes	14,737	Nonsense mediated decay transcripts	21,354
Immunoglobulin/T-cell receptor gene segments	410	Long non-coding RNA loci transcripts	58,023
Total No of distinct translations	65,519	Genes that have more than one distinct translations	13,618

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ \

Coloring for the gene annotations is based on the annotation type:

coding: protein coding transcripts, including polymorphic\ pseudogenes\
non-coding: non-protein coding transcripts\
pseudogene: pseudogene transcript annotations\
problem: problem transcripts (Biotypes of\ retained_intron, TEC, or disrupted_domain)

\ \

\ \ \

Squishy-pack Display

\ Protein_coding genes\

MANE or Ensembl canonical\
- 1st: MANE Select / Ensembl canonical
- 2nd: MANE Plus Clinical
\
Coding biotypes\
- 1st: protein_coding and protein_coding_LoF
- 2nd: NMDs and NSDs
- 3rd: retained intron and protein_coding_CDS_not_defined
\
Completeness\
- 1st: full length
- 2nd: CDS start/end not found
\
CARS score (only for coding transcripts)
Transcript genomic span and length (only for non-coding transcripts)

\ Non-coding genes\

Transcript biotype\
- 1st: transcript biotype identical to gene biotype
\
Ensembl canonical
GENCODE basic
Transcript genomic span
Transcript length

\ \ \

Methods

\ The GENCODE v43 track was built from the GENCODE downloads file \ gencode.v43.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources \ were correlated with the GENCODE data to build association tables.

\ \

Related Data

GENCODE data are available for use without restrictions.

Methods

\ The Agilent arrays were downloaded from their \ Agilent SureDesign website tool on March 2022.

\ The Illumina 450k and 850k (EPIC) tracks were created using a few columns from the\ Infinium MethylationEPIC v1.0 B5 Manifest File (CSV Format)\ and was then converted into a bigBed.

\ The Illumina CytoSNP-850K track was created by downloading the\ CytoSNP-850K v1.2 Manifest File (CSV Format) (GRCh38) file and then converted\ into a bigBed file.\

\ The Affymetrix Cytoscan HD GeneChip Array track was created by converting the \ CytoScanHD_Accel_Array.na36.bed.zip\ into a bigBed file.\

\ \

Data Access

\ \

Credits

\ Thanks to the Aliglent and Illumina support teams for sharing the data and the UCSC Genome Browser\ engineers for configuring the data.

Description

\ This track shows regions detected as putative genomic duplications within the\ golden path. The following display conventions are used to distinguish\ levels of similarity:\

\ Light to dark gray: 90 - 98% similarity\
\ Light to dark yellow: 98 - 99% similarity\
\ Light to dark orange: greater than 99% similarity \
\ Red: duplications of greater than 98% similarity that lack sufficient \ Segmental Duplication Database evidence (most likely missed overlaps) \

\ For a region to be included in the track, at least 1 Kb of the total \ sequence (containing at least 500 bp of non-RepeatMasked sequence) had to \ align and a sequence identity of at least 90% was required.

\ \

Methods

\ Segmental duplications play an important role in both genomic disease \ and gene evolution. This track displays an analysis of the global \ organization of these long-range segments of identity in genomic sequence.\

\ \

Large recent duplications (>= 1 kb and >= 90% identity) were detected\ by identifying high-copy repeats, removing these repeats from the genomic \ sequence ("fuguization") and searching all sequence for similarity. The\ repeats were then reinserted into the pairwise alignments, the ends of \ alignments trimmed, and global alignments were generated.\ For a full description of the "fuguization" detection method, see Bailey\ et al., 2001. This method has become\ known as WGAC (whole-genome assembly comparison); for example, see Bailey \ et al., 2002.\ \

Credits

\ These data were provided by Ginger Cheng, Xinwei She,\ Archana Raja,\ Tin Louie and\ Evan Eichler \ at the University of Washington.

\ \

References

\ Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, \ Myers EW, Li PW, Eichler EE.\ Recent segmental duplications in the human genome.\ Science. 2002 Aug 9;297(5583):1003-7.\ PMID: 12169732\

\ \

\ Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE.\ Segmental duplications: organization and impact within the \ current human genome project assembly.\ Genome Res. 2001 Jun;11(6):1005-17.\ PMID: 11381028; PMC: PMC311093\

\ rep 1 group rep\ longLabel Duplications of >1000 Bases of Non-RepeatMasked Sequence\ noScoreFilter .\ priority 5\ shortLabel Segmental Dups\ track genomicSuperDups\ type bed 6 +\ visibility hide\ tgpHG00702_SH089_CHS SH089 CHS Trio vcfPhasedTrio 1000 Genomes Southern Han Chinese Trio 2 5 0 0 0 127 127 127 0 0 23 chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX, varRep 0 longLabel 1000 Genomes Southern Han Chinese Trio\ parent tgpTrios\ shortLabel SH089 CHS Trio\ track tgpHG00702_SH089_CHS\ type vcfPhasedTrio\ vcfChildSample HG00702|child\ vcfParentSamples HG00657|mother,HG00656|father\ visibility full\ wgEncodeRegDnaseUwT47dPeak T-47D Pk narrowPeak T-47D mammary ductal carcinoma cell line DNaseI Peaks from ENCODE 1 5 255 124 85 255 189 170 1 0 0 regulation 1 color 255,124,85\ longLabel T-47D mammary ductal carcinoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel T-47D Pk\ subGroups view=a_Peaks cellType=T-47D treatment=n_a tissue=breast cancer=cancer\ track wgEncodeRegDnaseUwT47dPeak\ wgEncodeRegDnaseUwT47dWig T-47D Sg bigWig 0 34214.8 T-47D mammary ductal carcinoma cell line DNaseI Signal from ENCODE 0 5 255 124 85 255 189 170 0 0 0 regulation 1 color 255,124,85\ longLabel T-47D mammary ductal carcinoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.04106\ shortLabel T-47D Sg\ subGroups cellType=T-47D treatment=n_a tissue=breast cancer=cancer\ table wgEncodeRegDnaseUwT47dSignal\ track wgEncodeRegDnaseUwT47dWig\ type bigWig 0 34214.8\ unipLocTransMemb Transmembrane bigBed 12 + UniProt Transmembrane Domains 1 5 0 150 0 127 202 127 0 0 0 genes 1 bigDataUrl /gbdb/hg38/uniprot/unipLocTransMemb.bb\ color 0,150,0\ filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)\ itemRgb off\ longLabel UniProt Transmembrane Domains\ parent uniprot\ priority 5\ shortLabel Transmembrane\ track unipLocTransMemb\ type bigBed 12 +\ visibility dense\ umap24Quantitative Umap M24 bigWig 0.041667 1.0 Multi-read mappability with 24-mers 2 5 80 20 240 167 137 247 0 0 0 map 0 bigDataUrl /gbdb/hg38/hoffmanMappability/k24.Umap.MultiTrackMappability.bw\ color 80,20,240\ longLabel Multi-read mappability with 24-mers\ parent umapBigWig on\ priority 5\ shortLabel Umap M24\ subGroups view=MR\ track umap24Quantitative\ type bigWig 0.041667 1.0\ iscaLikelyBenign Uncert Ben gvf ClinGen CNVs: Uncertain: Likely Benign 3 5 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/?term=$$ phenDis 1 longLabel ClinGen CNVs: Uncertain: Likely Benign\ parent iscaViewDetail off\ shortLabel Uncert Ben\ subGroups view=cnv class=likB level=sub\ track iscaLikelyBenign\ chainMm10 Mouse Chain chain mm10 Mouse (Dec. 2011 (GRCm38/mm10)) Chained Alignments 3 6 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Mouse (Dec. 2011 (GRCm38/mm10)) Chained Alignments\ otherDb mm10\ parent placentalChainNetViewchain off\ shortLabel Mouse Chain\ subGroups view=chain species=s012a clade=c00\ track chainMm10\ type chain mm10\ netGalGal6 Chicken Net netAlign galGal6 chainGalGal6 Chicken (Mar. 2018 (GRCg6a/galGal6)) Alignment Net 1 6 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Chicken (Mar. 2018 (GRCg6a/galGal6)) Alignment Net\ otherDb galGal6\ parent vertebrateChainNetViewnet on\ shortLabel Chicken Net\ subGroups view=net species=s008a clade=c01\ track netGalGal6\ type netAlign galGal6 chainGalGal6\ netGorGor6 Gorilla Net netAlign gorGor6 chainGorGor6 Gorilla (Aug. 2019 (Kamilah_GGO_v0/gorGor6)) Alignment Net 1 6 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Gorilla (Aug. 2019 (Kamilah_GGO_v0/gorGor6)) Alignment Net\ otherDb gorGor6\ parent primateChainNetViewnet off\ shortLabel Gorilla Net\ subGroups view=net species=s009a clade=c00\ track netGorGor6\ type netAlign gorGor6 chainGorGor6\ encTfChipPkENCFF766YPH A549 CHD4 narrowPeak Transcription Factor ChIP-seq Peaks of CHD4 in A549 from ENCODE 3 (ENCFF766YPH) 0 6 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of CHD4 in A549 from ENCODE 3 (ENCFF766YPH)\ parent encTfChipPk off\ shortLabel A549 CHD4\ subGroups cellType=A549 factor=CHD4\ track encTfChipPkENCFF766YPH\ cloneEndABC16 ABC16 bed 12 Agencourt fosmid library 16 0 6 0 0 0 127 127 127 0 0 0 map 1 colorByStrand 0,0,128 0,128,0\ longLabel Agencourt fosmid library 16\ parent cloneEndSuper off\ priority 6\ shortLabel ABC16\ subGroups source=agencourt\ track cloneEndABC16\ type bed 12\ visibility hide\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_tpm_rev AorticSmsToFgf2_00hr15minBr1- bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_reverse 1 6 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12643-134G6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep1%20%28LK4%29.CNhs13340.12643-134G6.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12643-134G6 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_00hr15minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12643-134G6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_ctss_rev AorticSmsToFgf2_00hr15minBr1- bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_reverse 0 6 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12643-134G6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep1%20%28LK4%29.CNhs13340.12643-134G6.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12643-134G6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_00hr15minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12643-134G6\ urlLabel FANTOM5 Details:\ gtexCovArteryTibial Artery Tibia bigWig Artery Tibial 0 6 255 0 0 255 127 127 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-XPT6-2226-SM-4B66R.Artery_Tibial.RNAseq.bw\ color 255,0,0\ longLabel Artery Tibial\ parent gtexCov\ shortLabel Artery Tibia\ track gtexCovArteryTibial\ bismap36Neg Bismap S36 - bigBed 6 Single-read mappability with 36-mers after bisulfite conversion (reverse strand) 0 6 240 70 80 247 162 167 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k36.G2A-Converted.bb\ color 240,70,80\ longLabel Single-read mappability with 36-mers after bisulfite conversion (reverse strand)\ parent bismapBigBed off\ priority 6\ shortLabel Bismap S36 -\ subGroups view=SR\ track bismap36Neg\ visibility hide\ CHOL CHOL bigLolly 12 + Cholangiocarcinoma 0 6 0 0 0 127 127 127 0 0 0 phenDis 1 autoScale on\ bigDataUrl /gbdb/hg38/gdcCancer/CHOL.bb\ configurable off\ group phenDis\ lollyField 13\ longLabel Cholangiocarcinoma\ parent gdcCancer off\ priority 6\ shortLabel CHOL\ track CHOL\ type bigLolly 12 +\ urls case_id=https://portal.gdc.cancer.gov/cases/193294\ lincRNAsCTColon Colon bed 5 + lincRNAs from colon 1 6 0 60 120 127 157 187 1 0 0 genes 1 longLabel lincRNAs from colon\ origAssembly hg19\ parent lincRNAsAllCellType on\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel Colon\ subGroups view=lincRNAsRefseqExp tissueType=colon\ track lincRNAsCTColon\ unipLocCytopl Cytoplasmic bigBed 12 + UniProt Cytoplasmic Domains 1 6 255 150 0 255 202 127 0 0 0 genes 1 bigDataUrl /gbdb/hg38/uniprot/unipLocCytopl.bb\ color 255,150,0\ filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)\ itemRgb off\ longLabel UniProt Cytoplasmic Domains\ parent uniprot\ priority 6\ shortLabel Cytoplasmic\ track unipLocCytopl\ type bigBed 12 +\ visibility dense\ snpArrayCytoSnp850k CytoSNP 850k bigBed 6 + Illumina 850k CytoSNP Array 3 6 0 0 0 127 127 127 0 0 0

Description

Agilent Arrays

\ The arrays listed in this track are probes from the\ Agilent Catalog Oligonucleotide Microarrays.\

\ Agilent GenetiSure Cyto\

\ \

Illumina 450k and 850k Methylation Arrays

Credits

\ Thanks to the Aliglent and Illumina support teams for sharing the data and the UCSC Genome Browser\ engineers for configuring the data.

\ varRep 1 bigDataUrl /gbdb/hg38/bbi/cytoSnp/cytoSnp850k.bb\ colorByStrand 255,0,0 0,0,255\ html genotypeArrays\ longLabel Illumina 850k CytoSNP Array\ noScoreFilter on\ parent genotypeArrays on\ priority 6\ shortLabel CytoSNP 850k\ track snpArrayCytoSnp850k\ type bigBed 6 +\ urls rsID="https://www.ncbi.nlm.nih.gov/snp/?term=$$"\ visibility pack\ dbVar_common_gnomad dbVar Curated gnomAD SVs bigBed 9 + . NCBI dbVar Curated Common SVs: all populations from gnomAD 3 6 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ varRep 1 bigDataUrl /gbdb/hg38/bbi/dbVar/common_gnomad.bb\ longLabel NCBI dbVar Curated Common SVs: all populations from gnomAD\ parent dbVar_common on\ shortLabel dbVar Curated gnomAD SVs\ track dbVar_common_gnomad\ type bigBed 9 + .\ url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$\ urlLabel NCBI Variant Page:\ knownGeneV39 GENCODE V39 bigGenePred GENCODE V39 0 6 0 0 0 127 127 127 0 0 0

Description

\ The GENCODE Genes track (version 39, December 2021) shows high-quality manual\ annotations merged with evidence-based automated annotations across the entire\ human genome generated by the\ GENCODE project.\ By default, only the basic gene set is\ displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts\ that GENCODE believes will be useful to the majority of users.

\ \

\ The following table provides statistics for the v39 release derived from the GTF file that contains\ annotations only on the main chromosomes. More information on how they were generated can be found\ in the GENCODE site.

\ \

\ \ \ \ \ \ \ \
GENCODE v39 Release Stats
Genes Observed Transcripts Observed
Protein-coding genes 19,982 Protein-coding transcripts 87,151
Long non-coding RNA genes 18,811 - full length protein-coding 61,516
Small non-coding RNA genes 7,567 - partial length protein-coding 25,635
Pseudogenes 14,763 Nonsense mediated decay transcripts 19,762
Immunoglobulin/T-cell receptor gene segments 409 Long non-coding RNA loci transcripts 53,009

\

GENCODE v39 Release Stats
Genes	Observed	Transcripts	Observed
Protein-coding genes	19,982	Protein-coding transcripts	87,151
Long non-coding RNA genes	18,811	- full length protein-coding	61,516
Small non-coding RNA genes	7,567	- partial length protein-coding	25,635
Pseudogenes	14,763	Nonsense mediated decay transcripts	19,762
Immunoglobulin/T-cell receptor gene segments	409	Long non-coding RNA loci transcripts	53,009

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ \

Coloring for the gene annotations is based on the annotation type:

coding\
non-coding\
pseudogene\
problem\

\ \ \ \

\ \

Methods

\ The GENCODE v39 track was built from the GENCODE downloads file \ gencode.v39.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources \ were correlated with the GENCODE data to build association tables.

\ \

Related Data

\ The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a\ downloadable\ file.\ \

\ One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list\ is then available on the table menu.\ \ \

Data access

\ \

Credits

\ The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a\ computational pipeline developed by Jim Kent and Brian Raney.

\ \

References

\ \

A full list of GENCODE publications is available\ at The GENCODE\ Project web site.\

\ \

Data Release Policy

GENCODE data are available for use without restrictions.

Description

\ This track shows alignments of the human genome with itself, using\ a gap scoring system that allows longer gaps than traditional\ affine gap scoring systems. The system can also tolerate gaps\ in both sets of sequence simultaneously. After filtering out the \ "trivial" alignments produced when identical locations of the \ genome map to one another (e.g. chrN mapping to chrN), \ the remaining alignments point out areas of duplication within the \ human genome. The pseudoautosomal regions of chrX and chrY are an \ exception: in this assembly, these regions have been copied from chrX into \ chrY, resulting in a large amount of self chains aligning in these positions \ on both chromosomes.

\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions. Single lines indicate \ gaps that are largely due to a deletion in the query assembly or an \ insertion in the target assembly. Double lines represent more complex gaps \ that involve substantial sequence in both the query and target assemblies. \ This may result from inversions, overlapping deletions, an abundance of local \ mutation, or an unsequenced gap in one of the assemblies. In cases where \ multiple chains align over a particular region of the human genome, the \ chains with single-lined gaps are often due to processed pseudogenes, while \ chains with double-lined gaps are more often due to paralogs and unprocessed \ pseudogenes.

\ Chains have both a score and a normalized score. The score is derived by \ comparing sequence similarity, while penalizing both mismatches and gaps\ in a per base fashion. This leads to longer chains having greater scores, \ even if a smaller chain provides a better match. The normalized score divides\ the score by the length of the alignment, providing a more comparable score value\ not dependent on the match length.

\ \

Display Conventions and Configuration

By default, the chains are colored by the normalized score. This can be changed\ to color based on which chromosome they map to in the aligning organism. There is also\ an option to color all the chains black.

\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.

\ By default, chains with a score of 20,000 or more are displayed. This default value provides\ a conservative cutoff, filtering out many false-positive alignments with low sequence \ similarity, or high penalties. It should be noted however, that alignments below this \ threshold may still be indicative of homology.

\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.

\ \

Methods

\ The genome was aligned to itself using blastz. Trivial alignments were \ filtered out, and the remaining alignments were converted into axt format\ using the lavToAxt program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single target chromosome and a single\ query chromosome into a group and creates a kd-tree out of the gapless \ subsections (blocks) of the alignments. A dynamic program was then run over \ the kd-trees to find the maximally scoring chains of these blocks. Chains \ scoring below a threshold were discarded; the remaining chains are displayed \ in this track.

\ \

Credits

\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.

\ Lineage-specific repeats were identified by Arian Smit and his\ RepeatMasker\ program.

\ The axtChain program was developed at the University of California\ at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.\

\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.

\ \

References

\ \

\ Chiaromonte F, Yap VB, Miller W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput 2002, 115-26 (2002).\

\ \

\ Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\ \ Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.\ Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.\

\ \

\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W.\ \ Human-mouse alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.\

\ rep 1 altColor 255,240,200\ chainColor Normalized Score\ chainNormScoreAvailable yes\ color 100,50,0\ group rep\ longLabel Human Chained Self Alignments\ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb hg38\ priority 6\ scoreFilter 20000\ shortLabel Self Alignment\ spectrum on\ track chainSelf\ type chain hg38\ visibility hide\ umap36Quantitative Umap M36 bigWig 0.027778 1.0 Multi-read mappability with 36-mers 0 6 80 70 240 167 162 247 0 0 0 map 0 bigDataUrl /gbdb/hg38/hoffmanMappability/k36.Umap.MultiTrackMappability.bw\ color 80,70,240\ longLabel Multi-read mappability with 36-mers\ parent umapBigWig off\ priority 6\ shortLabel Umap M36\ subGroups view=MR\ track umap36Quantitative\ type bigWig 0.027778 1.0\ visibility hide\ iscaLikelyPathogenic Uncert Path gvf ClinGen CNVs: Uncertain: Likely Pathogenic 3 6 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/?term=$$ phenDis 1 longLabel ClinGen CNVs: Uncertain: Likely Pathogenic\ parent iscaViewDetail off\ shortLabel Uncert Path\ subGroups view=cnv class=likP level=sub\ track iscaLikelyPathogenic\ tgpHG02024_VN049_KHV VN049 KHV Trio vcfPhasedTrio 1000 Genomes Kinh in Ho Chi Minh City, Vietnam Trio 2 6 0 0 0 127 127 127 0 0 23 chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX, varRep 0 longLabel 1000 Genomes Kinh in Ho Chi Minh City, Vietnam Trio\ parent tgpTrios\ shortLabel VN049 KHV Trio\ track tgpHG02024_VN049_KHV\ type vcfPhasedTrio\ vcfChildSample HG02024|child\ vcfParentSamples HG02025|mother,HG02026|father\ visibility full\ chainAquChr2 aquChr2 Chain chain aquChr2 Golden eagle (Oct. 2014 (aquChr-1.0.2/aquChr2)) Chained Alignments 3 7 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Golden eagle (Oct. 2014 (aquChr-1.0.2/aquChr2)) Chained Alignments\ otherDb aquChr2\ parent vertebrateChainNetViewchain off\ shortLabel aquChr2 Chain\ subGroups view=chain species=s016 clade=c01\ track chainAquChr2\ type chain aquChr2\ chainPonAbe3 Orangutan Chain chain ponAbe3 Orangutan (Jan. 2018 (Susie_PABv2/ponAbe3)) Chained Alignments 3 7 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Orangutan (Jan. 2018 (Susie_PABv2/ponAbe3)) Chained Alignments\ otherDb ponAbe3\ parent primateChainNetViewchain off\ shortLabel Orangutan Chain\ subGroups view=chain species=s013a clade=c00\ track chainPonAbe3\ type chain ponAbe3\ netMm39 Mouse Net netAlign mm39 chainMm39 Mouse (Jun. 2020 (GRCm39/mm39)) Alignment Net 1 7 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Alignment Net\ otherDb mm39\ parent placentalChainNetViewnet on\ shortLabel Mouse Net\ subGroups view=net species=s012a clade=c00\ track netMm39\ type netAlign mm39 chainMm39\ encTfChipPkENCFF576PUH A549 CREB1 1 narrowPeak Transcription Factor ChIP-seq Peaks of CREB1 in A549 from ENCODE 3 (ENCFF576PUH) 0 7 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of CREB1 in A549 from ENCODE 3 (ENCFF576PUH)\ parent encTfChipPk off\ shortLabel A549 CREB1 1\ subGroups cellType=A549 factor=CREB1\ track encTfChipPkENCFF576PUH\ cloneEndABC18 ABC18 bed 12 Agencourt fosmid library 18 0 7 0 0 0 127 127 127 0 0 0 map 1 colorByStrand 0,0,128 0,128,0\ longLabel Agencourt fosmid library 18\ parent cloneEndSuper off\ priority 7\ shortLabel ABC18\ subGroups source=agencourt\ track cloneEndABC18\ type bed 12\ visibility hide\ affyCytoScanHD Affy CytoScan HD bigBed 12 Affymetrix Cytoscan HD GeneChip Array 3 7 0 0 0 127 127 127 0 0 0

Description

Agilent Arrays

\ The arrays listed in this track are probes from the\ Agilent Catalog Oligonucleotide Microarrays.\

\ Agilent GenetiSure Cyto\

\ \

Illumina 450k and 850k Methylation Arrays

Credits

\ Thanks to the Aliglent and Illumina support teams for sharing the data and the UCSC Genome Browser\ engineers for configuring the data.

\ varRep 1 bigDataUrl /gbdb/hg38/genotypeArrays/affyCytoScanHD.bb\ html genotypeArrays\ itemRgb on\ longLabel Affymetrix Cytoscan HD GeneChip Array\ parent genotypeArrays on\ priority 7\ shortLabel Affy CytoScan HD\ track affyCytoScanHD\ type bigBed 12\ visibility pack\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_tpm_fwd AorticSmsToFgf2_00hr15minBr2+ bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_forward 1 7 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12741-135I5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep2%20%28LK5%29.CNhs13359.12741-135I5.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12741-135I5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_00hr15minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12741-135I5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_ctss_fwd AorticSmsToFgf2_00hr15minBr2+ bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_forward 0 7 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12741-135I5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep2%20%28LK5%29.CNhs13359.12741-135I5.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12741-135I5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_00hr15minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12741-135I5\ urlLabel FANTOM5 Details:\ bismap100Neg Bismap S100 - bigBed 6 Single-read mappability with 100-mers after bisulfite conversion (reverse strand) 0 7 240 170 80 247 212 167 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k100.G2A-Converted.bb\ color 240,170,80\ longLabel Single-read mappability with 100-mers after bisulfite conversion (reverse strand)\ parent bismapBigBed off\ priority 7\ shortLabel Bismap S100 -\ subGroups view=SR\ track bismap100Neg\ visibility hide\ bismap50Neg Bismap S50 - bigBed 6 Single-read mappability with 50-mers after bisulfite conversion (reverse strand) 0 7 240 120 80 247 187 167 0 0 0 map 1 bigDataUrl /gbdb/hg38/hoffmanMappability/k50.G2A-Converted.bb\ color 240,120,80\ longLabel Single-read mappability with 50-mers after bisulfite conversion (reverse strand)\ parent bismapBigBed off\ priority 7\ shortLabel Bismap S50 -\ subGroups view=SR\ track bismap50Neg\ visibility hide\ gtexCovBladder Bladder bigWig Bladder 0 7 205 183 158 230 219 206 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-S3XE-1226-SM-4AD4L.Bladder.RNAseq.bw\ color 205,183,158\ longLabel Bladder\ parent gtexCov\ shortLabel Bladder\ track gtexCovBladder\ unipChain Chains bigBed 12 + UniProt Mature Protein Products (Polypeptide Chains) 1 7 0 0 0 127 127 127 0 0 0 genes 1 bigDataUrl /gbdb/hg38/uniprot/unipChain.bb\ filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)\ longLabel UniProt Mature Protein Products (Polypeptide Chains)\ parent uniprot\ priority 7\ shortLabel Chains\ track unipChain\ type bigBed 12 +\ urls uniProtId="http://www.uniprot.org/uniprot/$$#ptm_processing" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"\ visibility dense\ primateChainNetViewchain Chains bed 3 Primate Genomes, Chain and Net Alignments 3 7 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Primate Genomes, Chain and Net Alignments\ parent primateChainNet\ shortLabel Chains\ spectrum on\ track primateChainNetViewchain\ view chain\ visibility pack\ COAD COAD bigLolly 12 + Colon adenocarcinoma 0 7 0 0 0 127 127 127 0 0 0 phenDis 1 autoScale on\ bigDataUrl /gbdb/hg38/gdcCancer/COAD.bb\ configurable off\ group phenDis\ lollyField 13\ longLabel Colon adenocarcinoma\ parent gdcCancer off\ priority 7\ shortLabel COAD\ track COAD\ type bigLolly 12 +\ urls case_id=https://portal.gdc.cancer.gov/cases/193294\ iscaCuratedPathogenic Curated Path gvf ClinGen CNVs: Curated Pathogenic 3 7 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/?term=$$ phenDis 1 longLabel ClinGen CNVs: Curated Pathogenic\ parent iscaViewDetail off\ shortLabel Curated Path\ subGroups view=cnv class=path level=cur\ track iscaCuratedPathogenic\ lincRNAsCTForeskin_R Foreskin_R bed 5 + lincRNAs from foreskin_r 1 7 0 60 120 127 157 187 1 0 0 genes 1 longLabel lincRNAs from foreskin_r\ origAssembly hg19\ parent lincRNAsAllCellType on\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel Foreskin_R\ subGroups view=lincRNAsRefseqExp tissueType=foreskin_r\ track lincRNAsCTForeskin_R\ knownGeneV38 GENCODE V38 bigGenePred GENCODE V38 0 7 0 0 0 127 127 127 0 0 0

Description

\ The GENCODE Genes track (version 38, May 2021) shows high-quality manual\ annotations merged with evidence-based automated annotations across the entire\ human genome generated by the\ GENCODE project.\ By default, only the basic gene set is\ displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts\ that GENCODE believes will be useful to the majority of users.

\ \

\ The following table provides statistics for the v38 release derived from the GTF file that contains\ annotations only on the main chromosomes. More information on how they were generated can be found\ in the GENCODE site.

\ \

\ \ \ \ \ \ \ \
GENCODE v38 Release Stats
Genes Observed Transcripts Observed
Protein-coding genes 19,955 Protein-coding transcripts 86,757
Long non-coding RNA genes 17,944 - full length protein-coding 61,015
Small non-coding RNA genes 7,567 - partial length protein-coding 25,742
Pseudogenes 14,773 Nonsense mediated decay transcripts 18,881
Immunoglobulin/T-cell receptor gene segments 409 Long non-coding RNA loci transcripts 48,752

\

GENCODE v38 Release Stats
Genes	Observed	Transcripts	Observed
Protein-coding genes	19,955	Protein-coding transcripts	86,757
Long non-coding RNA genes	17,944	- full length protein-coding	61,015
Small non-coding RNA genes	7,567	- partial length protein-coding	25,742
Pseudogenes	14,773	Nonsense mediated decay transcripts	18,881
Immunoglobulin/T-cell receptor gene segments	409	Long non-coding RNA loci transcripts	48,752

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ \

Coloring for the gene annotations is based on the annotation type:

coding\
non-coding\
pseudogene\
problem\

\ \ \ \

\ \

Methods

\ The GENCODE v38 track was built from the GENCODE downloads file \ gencode.v38.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources \ were correlated with the GENCODE data to build association tables.

\ \

Related Data

\ The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a\ downloadable\ file.\ \

\ One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list\ is then available on the table menu.\ \ \

Data access

\ \

Credits

\ The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a\ computational pipeline developed by Jim Kent and Brian Raney.

\ \

References

\ \

A full list of GENCODE publications is available\ at The GENCODE\ Project web site.\

\ \

Data Release Policy

GENCODE data are available for use without restrictions.

\ genes 1 baseColorDefault genomicCodons\ bigDataUrl /gbdb/hg38/gencode/gencodeV38.bb\ defaultLabelFields geneName\ defaultLinkedTables kgXref\ directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s\ externalDb knownGeneV38\ group genes\ html knownGeneV38\ idXref kgAlias kgID alias\ intronGap 12\ isGencode3 on\ itemRgb on\ labelFields geneName,name,geneName2,name2\ longLabel GENCODE V38\ maxItems 50000\ parent knownGeneArchive\ priority 7\ searchIndex name\ shortLabel GENCODE V38\ track knownGeneV38\ type bigGenePred\ visibility hide\ geneHancerInteractions GH Interactions bigInteract Interactions between GeneHancer regulatory elements and genes 2 7 0 0 0 127 127 127 0 0 0 https://www.genecards.org/cgi-bin/carddisp.pl?gene=$&keywords=$&prefilter=enhancers#enhancers regulation 1 bigDataUrl /gbdb/hg38/geneHancer/geneHancerInteractionsAll.v2.hg38.bb\ longLabel Interactions between GeneHancer regulatory elements and genes\ parent ghInteraction off\ shortLabel GH Interactions\ subGroups set=b_ALL view=c_I\ track geneHancerInteractions\ urlLabel Interaction in GeneCards\ wgEncodeRegDnaseUwHct116Peak HCT-116 Pk narrowPeak HCT-116 colorectal carcinoma cell line DNaseI Peaks from ENCODE 1 7 255 150 85 255 202 170 1 0 0 regulation 1 color 255,150,85\ longLabel HCT-116 colorectal carcinoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HCT-116 Pk\ subGroups view=a_Peaks cellType=HCT-116 treatment=n_a tissue=colon cancer=cancer\ track wgEncodeRegDnaseUwHct116Peak\ wgEncodeRegDnaseUwHct116Wig HCT-116 Sg bigWig 0 27405.3 HCT-116 colorectal carcinoma cell line DNaseI Signal from ENCODE 0 7 255 150 85 255 202 170 0 0 0 regulation 1 color 255,150,85\ longLabel HCT-116 colorectal carcinoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.06881\ shortLabel HCT-116 Sg\ subGroups cellType=HCT-116 treatment=n_a tissue=colon cancer=cancer\ table wgEncodeRegDnaseUwHct116Signal\ track wgEncodeRegDnaseUwHct116Wig\ type bigWig 0 27405.3\ chainHprcGCA_018467155v1 HG01891.mat chain GCA_018467155.1 HG01891.mat HG01891.pri.mat.f1_v2 (May 2021 GCA_018467155.1_HG01891.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 7 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01891.mat HG01891.pri.mat.f1_v2 (May 2021 GCA_018467155.1_HG01891.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018467155.1\ parent hprcChainNetViewchain off\ priority 23\ shortLabel HG01891.mat\ subGroups view=chain sample=s023 population=afr subpop=acb hap=mat\ track chainHprcGCA_018467155v1\ type chain GCA_018467155.1\ hr_na12249Vcf HR_NA12249 Variants vcfTabix HR_NA12249 Variants 0 7 0 0 0 127 127 127 0 0 0 map 1 bigDataUrl /gbdb/hg38/problematic/highRepro/HR_NA12249.sort.vcf.gz\ longLabel HR_NA12249 Variants\ parent highReproVcfs\ shortLabel HR_NA12249 Variants\ subGroups view=vcfs\ track hr_na12249Vcf\ type vcfTabix\ wgEncodeRegTxnCaltechRnaSeqK562R2x75Il200SigPooled K562 bigWig 0 65535 Transcription of K562 cells from ENCODE 0 7 149 128 255 202 191 255 0 0 0 regulation 1 color 149,128,255\ longLabel Transcription of K562 cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegTxn\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ priority 7\ shortLabel K562\ track wgEncodeRegTxnCaltechRnaSeqK562R2x75Il200SigPooled\ type bigWig 0 65535\ primateChainNetViewnet Nets bed 3 Primate Genomes, Chain and Net Alignments 1 7 0 0 0 255 255 0 0 0 0 compGeno 1 longLabel Primate Genomes, Chain and Net Alignments\ parent primateChainNet\ shortLabel Nets\ track primateChainNetViewnet\ view net\ visibility dense\ wgEncodeRegMarkH3k4me1Nhlf NHLF bigWig 0 6866 H3K4Me1 Mark (Often Found Near Regulatory Elements) on NHLF Cells from ENCODE 0 7 255 128 212 255 191 233 0 0 0 regulation 1 color 255,128,212\ longLabel H3K4Me1 Mark (Often Found Near Regulatory Elements) on NHLF Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k4me1\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel NHLF\ table wgEncodeBroadHistoneNhlfH3k4me1StdSig\ track wgEncodeRegMarkH3k4me1Nhlf\ type bigWig 0 6866\ wgEncodeRegMarkH3k4me3Nhlf NHLF bigWig 0 19229 H3K4Me3 Mark (Often Found Near Promoters) on NHLF Cells from ENCODE 0 7 255 128 212 255 191 233 0 0 0 regulation 1 color 255,128,212\ longLabel H3K4Me3 Mark (Often Found Near Promoters) on NHLF Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k4me3\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel NHLF\ table wgEncodeBroadHistoneNhlfH3k4me3StdSig\ track wgEncodeRegMarkH3k4me3Nhlf\ type bigWig 0 19229\ wgEncodeRegMarkH3k27acNhlf NHLF bigWig 0 3851 H3K27Ac Mark (Often Found Near Regulatory Elements) on NHLF Cells from ENCODE 2 7 255 128 212 255 191 233 0 0 0 regulation 1 color 255,128,212\ longLabel H3K27Ac Mark (Often Found Near Regulatory Elements) on NHLF Cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegMarkH3k27ac\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel NHLF\ table wgEncodeBroadHistoneNhlfH3k27acStdSig\ track wgEncodeRegMarkH3k27acNhlf\ type bigWig 0 3851\ primateChainNet Primate Chain/Net bed 3 Primate Genomes, Chain and Net Alignments 0 7 0 0 0 255 255 0 0 0 0

Description

Chain Track

\ The chain track shows alignments of human (Dec. 2013 (GRCh38/hg38)) to\ other genomes using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ human and the other genome simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \

\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ other assembly or an insertion in the human assembly.\ Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the other genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.

\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.

\ \

Net Track

\ The net track shows only the alignments from the highest-scoring chain\ for each region of the human genome assembly. It is useful for finding\ orthologous regions and for studying genome rearrangement. The human\ sequence used in this annotation is from the Dec. 2013 (GRCh38/hg38) assembly.

\ \

Display Conventions and Configuration

Chain Track

By default, the chains to chromosome-based assemblies are colored\ based on which chromosome they map to in the aligning organism. To turn\ off the coloring, check the "off" button next to: Color\ track based on chromosome.

\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.

\ \

Net Track

\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.

\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.

\ Individual items in the display are categorized as one of four types\ (other than gap):

Top - the best, longest match. Displayed on level 1.\
Syn - line-ups on the same chromosome as the gap in the level above\ it.\
Inv - a line-up on the same chromosome as the gap above it, but in \ the opposite orientation.\
NonSyn - a match to a chromosome different from the gap in the \ level above.\

\ \

Methods

Chain track

\ The assemblies were examined for any transposons that had been inserted\ since the divergence of the two species. Any such transposons were\ removed before running the alignment. The abbreviated genomes were\ aligned with lastz, and the removed transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single human chromosome and a single\ chromosome from the other genome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks.\

\ The lastz matrices used for these alignments can be found in our\ download directory\ for the Dec. 2013 (GRCh38/hg38) assembly. See the README.txt file within the relevant\ vsAssembly directory for details (e.g., parameters for the alignment with\ tarSyr2 can be found in the vsTarSyr2/ subdirectory).\

\ For the alignments to Chimp and Rhesus, chains scoring below a minimum\ score of '5000' were discarded; the remaining chains\ are displayed in this track. The linear gap matrix used with axtChain:
\

-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\

\ \ For the alignments to Tarsier and Bonobo, chains scoring\ below a minimum score of '3000' were discarded; the remaining chains\ are displayed in this track. The same linear gap matrix shown above\ was used with axtChain.\

Chains for low-coverage assemblies for which no browser has been built \ are not available as browser tracks, but only from our\ downloads page.\

\ \ See also: lastz parameters and other details (e.g., update time) \ and chain minimum score and gap parameters used in these alignments.\ \

Net track

\ Chains were derived from lastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.

\ \

Credits

\ Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, \ The Pennsylvania State University.

\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.

\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.

\ The browser display and database storage of the chains and nets were created\ by Robert Baertsch and Jim Kent.

Description

\ \

\ The RefSeq Genes track shows known human protein-coding and\ non-protein-coding genes taken from the NCBI RNA reference sequences\ collection (RefSeq). The data underlying this track are updated weekly.

\ \

\ Please visit the Feedback for Gene and Reference Sequences (RefSeq) page to\ make suggestions, submit additions and corrections, or ask for help concerning\ RefSeq records.\

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ \

\ This track follows the display conventions for\ \ gene prediction tracks.\ The color shading indicates the level of review the RefSeq record has\ undergone: predicted (light), provisional (medium), reviewed (dark).\

\ \

\ The item labels and display colors of features within this track can be\ configured through the controls at the top of the track description page.\

Label: By default, items are labeled by gene name. Click the\ appropriate Label option to display the accession name instead of the gene\ name, show both the gene and accession names, or turn off the label\ completely.
Codon coloring: This track contains an optional codon coloring\ feature that allows users to quickly validate and compare gene predictions.\ To display codon colors, select the genomic codons option from the\ Color track by codons pull-down menu. For more information about this\ feature, go to the\ \ Coloring Gene Predictions and Annotations by Codon page.
Hide non-coding genes: By default, both the protein-coding and\ non-protein-coding genes are displayed. If you wish to see only the coding\ genes, click this box.

\ \

Methods

\ \

\ RefSeq RNAs were aligned against the human genome using BLAT. Those\ with an alignment of less than 15% were discarded. When a single RNA\ aligned in multiple places, the alignment having the highest base identity\ was identified. Only alignments having a base identity level within 0.1% of\ the best and at least 96% base identity with the genomic sequence were kept.\

\ \

Credits

\ \

\ This track was produced at UCSC from RNA sequence data generated by scientists\ worldwide and curated by the NCBI\ RefSeq project.\

\ \

References

\ \

\ Kent WJ.\ \ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.\ PMID: 11932250; PMC: PMC187518\

\ \

\ Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\ Landrum MJ, McGarvey KM et al.\ \ RefSeq: an update on mammalian reference sequences.\ Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63.\ PMID: 24259432; PMC: PMC3965018\

\ \

\ Pruitt KD, Tatusova T, Maglott DR.\ \ NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.\ Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.\ PMID: 15608248; PMC: PMC539979\

\ genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ color 12,12,120\ group genes\ idXref hgFixed.refLink mrnaAcc name\ longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*)\ parent refSeqComposite off\ priority 7\ shortLabel UCSC RefSeq\ track refGene\ type genePred refPep refMrna\ visibility dense\ umap50Quantitative Umap M50 bigWig 0.02 1.0 Multi-read mappability with 50-mers 0 7 80 120 240 167 187 247 0 0 0 map 0 bigDataUrl /gbdb/hg38/hoffmanMappability/k50.Umap.MultiTrackMappability.bw\ color 80,120,240\ longLabel Multi-read mappability with 50-mers\ parent umapBigWig off\ priority 7\ shortLabel Umap M50\ subGroups view=MR\ track umap50Quantitative\ type bigWig 0.02 1.0\ visibility hide\ tgpNA19240_Y117_YRI Y117 YRI Trio vcfPhasedTrio 1000 Genomes Yoruban in Ibadan, Nigeria Trio 2 7 0 0 0 127 127 127 0 0 23 chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX, varRep 0 longLabel 1000 Genomes Yoruban in Ibadan, Nigeria Trio\ parent tgpTrios\ shortLabel Y117 YRI Trio\ track tgpNA19240_Y117_YRI\ type vcfPhasedTrio\ vcfChildSample NA19240|child\ vcfParentSamples NA19238|mother,NA19239|father\ visibility full\ netAquChr2 aquChr2 Net netAlign aquChr2 chainAquChr2 Golden eagle (Oct. 2014 (aquChr-1.0.2/aquChr2)) Alignment Net 1 8 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Golden eagle (Oct. 2014 (aquChr-1.0.2/aquChr2)) Alignment Net\ otherDb aquChr2\ parent vertebrateChainNetViewnet off\ shortLabel aquChr2 Net\ subGroups view=net species=s016 clade=c01\ track netAquChr2\ type netAlign aquChr2 chainAquChr2\ netPonAbe3 Orangutan Net netAlign ponAbe3 chainPonAbe3 Orangutan (Jan. 2018 (Susie_PABv2/ponAbe3)) Alignment Net 1 8 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Orangutan (Jan. 2018 (Susie_PABv2/ponAbe3)) Alignment Net\ otherDb ponAbe3\ parent primateChainNetViewnet off\ shortLabel Orangutan Net\ subGroups view=net species=s013a clade=c00\ track netPonAbe3\ type netAlign ponAbe3 chainPonAbe3\ netMm10 Mouse Net netAlign mm10 chainMm10 Mouse (Dec. 2011 (GRCm38/mm10)) Alignment Net 1 8 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Mouse (Dec. 2011 (GRCm38/mm10)) Alignment Net\ otherDb mm10\ parent placentalChainNetViewnet on\ shortLabel Mouse Net\ subGroups view=net species=s012a clade=c00\ track netMm10\ type netAlign mm10 chainMm10\ encTfChipPkENCFF186ZET A549 CREB1 2 narrowPeak Transcription Factor ChIP-seq Peaks of CREB1 in A549 from ENCODE 3 (ENCFF186ZET) 0 8 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of CREB1 in A549 from ENCODE 3 (ENCFF186ZET)\ parent encTfChipPk off\ shortLabel A549 CREB1 2\ subGroups cellType=A549 factor=CREB1\ track encTfChipPkENCFF186ZET\ cloneEndABC20 ABC20 bed 12 Agencourt fosmid library 20 0 8 0 0 0 127 127 127 0 0 0 map 1 colorByStrand 0,0,128 0,128,0\ longLabel Agencourt fosmid library 20\ parent cloneEndSuper off\ priority 8\ shortLabel ABC20\ subGroups source=agencourt\ track cloneEndABC20\ type bed 12\ visibility hide\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_tpm_rev AorticSmsToFgf2_00hr15minBr2- bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_reverse 1 8 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12741-135I5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep2%20%28LK5%29.CNhs13359.12741-135I5.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12741-135I5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_00hr15minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12741-135I5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_ctss_rev AorticSmsToFgf2_00hr15minBr2- bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_reverse 0 8 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12741-135I5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep2%20%28LK5%29.CNhs13359.12741-135I5.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12741-135I5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_00hr15minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12741-135I5\ urlLabel FANTOM5 Details:\ gtexCovBrainAmygdala Brain Amygd bigWig Brain Amygdala 0 8 238 238 0 246 246 127 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-T5JC-0011-R4A-SM-32PLT.Brain_Amygdala.RNAseq.bw\ color 238,238,0\ longLabel Brain Amygdala\ parent gtexCov\ shortLabel Brain Amygd\ track gtexCovBrainAmygdala\ placentalChainNetViewchain Chains bed 3 Non-primate Placental Mammal Genomes, Chain and Net Alignments 3 8 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Non-primate Placental Mammal Genomes, Chain and Net Alignments\ parent placentalChainNet\ shortLabel Chains\ spectrum on\ track placentalChainNetViewchain\ view chain\ visibility pack\ phastCons470way Cons 470 Mammals bigWig 0 1 470 mammals conservation by PhastCons 0 8 70 130 70 130 70 70 0 0 0 compGeno 0 altColor 130,70,70\ autoScale off\ bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons470way/hg38.phastCons470way.bw\ color 70,130,70\ configurable on\ longLabel 470 mammals conservation by PhastCons\ maxHeightPixels 100:40:11\ noInherit on\ parent cons470wayViewphastcons off\ priority 8\ shortLabel Cons 470 Mammals\ spanList 1\ subGroups view=phastcons\ track phastCons470way\ type bigWig 0 1\ windowingFunction mean\ unipDisulfBond Disulf. Bonds bigBed 12 + UniProt Disulfide Bonds 1 8 0 0 0 127 127 127 0 0 0 genes 1 bigDataUrl /gbdb/hg38/uniprot/unipDisulfBond.bb\ filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)\ longLabel UniProt Disulfide Bonds\ parent uniprot\ priority 8\ shortLabel Disulf. Bonds\ track unipDisulfBond\ type bigBed 12 +\ visibility dense\ DLBC DLBC bigLolly 12 + Lymphoid Neoplasm Diffuse Large B-cell Lymphoma 0 8 0 0 0 127 127 127 0 0 0 phenDis 1 autoScale on\ bigDataUrl /gbdb/hg38/gdcCancer/DLBC.bb\ configurable off\ group phenDis\ lollyField 13\ longLabel Lymphoid Neoplasm Diffuse Large B-cell Lymphoma\ parent gdcCancer off\ priority 8\ shortLabel DLBC\ track DLBC\ type bigLolly 12 +\ urls case_id=https://portal.gdc.cancer.gov/cases/193294\ unipDomain Domains bigBed 12 + UniProt Domains 1 8 0 0 0 127 127 127 0 0 0 genes 1 bigDataUrl /gbdb/hg38/uniprot/unipDomain.bb\ filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)\ longLabel UniProt Domains\ parent uniprot\ priority 8\ shortLabel Domains\ track unipDomain\ type bigBed 12 +\ urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"\ visibility dense\ knownGeneV36 GENCODE V36 bigGenePred GENCODE V36 0 8 0 0 0 127 127 127 0 0 0

Description

\ The GENCODE Genes track (version 36, Oct 2020) shows high-quality manual\ annotations merged with evidence-based automated annotations across the entire\ human genome generated by the\ GENCODE project.\ By default, only the basic gene set is\ displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts\ that GENCODE believes will be useful to the majority of users.

\ \

\ The following table provides statistics for the v36 release derived from the GTF file that contains\ annotations only on the main chromosomes. More information on how they were generated can be found\ in the GENCODE site.

\ \

\ \ \ \ \ \ \ \
GENCODE v36 Release Stats
Genes Observed Transcripts Observed
Protein-coding genes 19,965 Protein-coding transcripts 83,986
Long non-coding RNA genes 17,910 - full length protein-coding 57,935
Small non-coding RNA genes 7,576 - partial length protein-coding 26,051
Pseudogenes 14,749 Nonsense mediated decay transcripts 15,811
Immunoglobulin/T-cell receptor gene segments 645 Long non-coding RNA loci transcripts 48,351

\

GENCODE v36 Release Stats
Genes	Observed	Transcripts	Observed
Protein-coding genes	19,965	Protein-coding transcripts	83,986
Long non-coding RNA genes	17,910	- full length protein-coding	57,935
Small non-coding RNA genes	7,576	- partial length protein-coding	26,051
Pseudogenes	14,749	Nonsense mediated decay transcripts	15,811
Immunoglobulin/T-cell receptor gene segments	645	Long non-coding RNA loci transcripts	48,351

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Display Conventions and Configuration

\ \

Coloring for the gene annotations is based on the annotation type:

coding\
non-coding\
pseudogene\
problem\
all 2-way pseudogenes\
all polyA annotations\

\ \ \ \

\ \

Methods

\ The GENCODE v36 track was built from the GENCODE downloads file \ gencode.v36.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources \ were correlated with the GENCODE data to build association tables.

\ \

Related Data

\ The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a\ downloadable\ file.\ \

\ One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list\ is then available on the table menu.\ \ \

Data access

\ Transposons that have been inserted since the human/other\ split were removed from the assemblies. The abbreviated genomes were\ aligned with lastz, and the transposons were added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single human chromosome and a single\ chromosome from the other genome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks.\ \ \ \ Chains scoring below a minimum score of '5000' were discarded;\ the remaining chains are displayed in this track. The linear gap\ matrix used with axtChain:
\

-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\

\ \ See also: lastz parameters used in these alignments,\ and chain minimum score and gap parameters used in these alignments.\

\ \

Net track

\ \

Credits

\ Lastz (previously known as blastz) was developed at\ Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.

\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.

\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.

\ The browser display and database storage of the chains and nets were created\ by Robert Baertsch and Jim Kent.

\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.

\ \

References

\ Chiaromonte F, Yap VB, Miller W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput. 2002:115-26.\ PMID: 11928468\

\ \

\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\ Haussler D, Miller W.\ Human-mouse alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.\ PMID: 12529312; PMC: PMC430961\

Description

\ \

\ This track depicts masked sequence as determined by\ WindowMasker. The\ WindowMasker tool is included in the NCBI C++ toolkit. The source code\ for the entire toolkit is available from the NCBI\ \ FTP site.\

\ \

Methods

\ \

\ To create this track, WindowMasker was run with the following parameters:\

\
windowmasker -mk_counts true -input hg38.fa -output wm_counts\
windowmasker -ustat wm_counts -sdust true -input hg38.fa -output repeats.bed\

\ The repeats.bed (BED3) file was loaded into the "windowmaskerSdust" table for\ this track.\

\ \

References

\ \

\ Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\ WindowMasker: window-based masker for sequenced genomes.\ Bioinformatics. 2006 Jan 15;22(2):134-41.\ PMID: 16287941\

\ rep 1 group rep\ longLabel Genomic Intervals Masked by WindowMasker + SDust\ priority 8\ shortLabel WM + SDust\ track windowmaskerSdust\ type bed 3\ visibility hide\ chainThaSir1 thaSir1 Chain chain thaSir1 Garter snake (Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1)) Chained Alignments 3 9 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Garter snake (Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1)) Chained Alignments\ otherDb thaSir1\ parent vertebrateChainNetViewchain off\ shortLabel thaSir1 Chain\ subGroups view=chain species=s028b clade=c02\ track chainThaSir1\ type chain thaSir1\ chainNomLeu3 Gibbon Chain chain nomLeu3 Gibbon (Oct. 2012 (GGSC Nleu3.0/nomLeu3)) Chained Alignments 3 9 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Gibbon (Oct. 2012 (GGSC Nleu3.0/nomLeu3)) Chained Alignments\ otherDb nomLeu3\ parent primateChainNetViewchain off\ shortLabel Gibbon Chain\ subGroups view=chain species=s014 clade=c00\ track chainNomLeu3\ type chain nomLeu3\ chainRn7 Rat Chain chain rn7 Rat (Nov. 2020 (mRatBN7.2/rn7)) Chained Alignments 3 9 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Rat (Nov. 2020 (mRatBN7.2/rn7)) Chained Alignments\ otherDb rn7\ parent placentalChainNetViewchain off\ shortLabel Rat Chain\ subGroups view=chain species=s024a clade=c00\ track chainRn7\ type chain rn7\ phastConsElements470way 470 Mamm. El bigBed 5 . 470 mammals Conserved Elements 0 9 110 10 40 182 132 147 0 0 0 compGeno 1 bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons470way/hg38.phastConsElements470way.bb\ color 110,10,40\ longLabel 470 mammals Conserved Elements\ noInherit on\ parent cons470wayViewelements off\ priority 9\ shortLabel 470 Mamm. El\ subGroups view=elements\ track phastConsElements470way\ type bigBed 5 .\ encTfChipPkENCFF535MZG A549 CTCF 1 narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in A549 from ENCODE 3 (ENCFF535MZG) 0 9 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in A549 from ENCODE 3 (ENCFF535MZG)\ parent encTfChipPk off\ shortLabel A549 CTCF 1\ subGroups cellType=A549 factor=CTCF\ track encTfChipPkENCFF535MZG\ unipModif AA Modifications bigBed 12 + UniProt Amino Acid Modifications 1 9 0 0 0 127 127 127 0 0 0 genes 1 bigDataUrl /gbdb/hg38/uniprot/unipModif.bb\ filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL)\ longLabel UniProt Amino Acid Modifications\ parent uniprot\ priority 9\ shortLabel AA Modifications\ track unipModif\ type bigBed 12 +\ urls uniProtId="http://www.uniprot.org/uniprot/$$#aaMod_section" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$"\ visibility dense\ cloneEndABC21 ABC21 bed 12 Agencourt fosmid library 21 0 9 0 0 0 127 127 127 0 0 0 map 1 colorByStrand 0,0,128 0,128,0\ longLabel Agencourt fosmid library 21\ parent cloneEndSuper off\ priority 9\ shortLabel ABC21\ subGroups source=agencourt\ track cloneEndABC21\ type bed 12\ visibility hide\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep3LK6_CNhs13568_tpm_fwd AorticSmsToFgf2_00hr15minBr3+ bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep3 (LK6)_CNhs13568_12839-137B4_forward 1 9 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12839-137B4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep3%20%28LK6%29.CNhs13568.12839-137B4.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep3 (LK6)_CNhs13568_12839-137B4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12839-137B4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_00hr15minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep3LK6_CNhs13568_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12839-137B4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep3LK6_CNhs13568_ctss_fwd AorticSmsToFgf2_00hr15minBr3+ bigWig Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep3 (LK6)_CNhs13568_12839-137B4_forward 0 9 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12839-137B4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2000hr15min%2c%20biol_rep3%20%28LK6%29.CNhs13568.12839-137B4.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep3 (LK6)_CNhs13568_12839-137B4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12839-137B4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_00hr15minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep3LK6_CNhs13568_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12839-137B4\ urlLabel FANTOM5 Details:\ bismap24Quantitative Bismap M24 bigWig 0.041667 1.0 Multi-read mappability with 24-mers after bisulfite conversion 2 9 240 20 80 247 137 167 0 0 0 map 0 bigDataUrl /gbdb/hg38/hoffmanMappability/k24.Bismap.MultiTrackMappability.bw\ color 240,20,80\ longLabel Multi-read mappability with 24-mers after bisulfite conversion\ parent bismapBigWig on\ priority 9\ shortLabel Bismap M24\ subGroups view=MR\ track bismap24Quantitative\ type bigWig 0.041667 1.0\ visibility full\ gtexCovBrainAnteriorcingulatecortexBA24 Brain Ant cin cort bigWig Brain Anterior cingulate cortex BA24 0 9 238 238 0 246 246 127 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-14PN4-0011-R3b-SM-686ZU.Brain_Anterior_cingulate_cortex_BA24.RNAseq.bw\ color 238,238,0\ longLabel Brain Anterior cingulate cortex BA24\ parent gtexCov\ shortLabel Brain Ant cin cort\ track gtexCovBrainAnteriorcingulatecortexBA24\ vertebrateChainNetViewchain Chains bed 3 Non-placental Vertebrate Genomes, Chain and Net Alignments 3 9 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Non-placental Vertebrate Genomes, Chain and Net Alignments\ parent vertebrateChainNet\ shortLabel Chains\ spectrum on\ track vertebrateChainNetViewchain\ view chain\ visibility pack\ ESCA ESCA bigLolly 12 + Esophageal carcinoma 0 9 0 0 0 127 127 127 0 0 0 phenDis 1 autoScale on\ bigDataUrl /gbdb/hg38/gdcCancer/ESCA.bb\ configurable off\ group phenDis\ lollyField 13\ longLabel Esophageal carcinoma\ parent gdcCancer off\ priority 9\ shortLabel ESCA\ track ESCA\ type bigLolly 12 +\ urls case_id=https://portal.gdc.cancer.gov/cases/193294\ wgEncodeRegDnaseUwHffPeak HFF Pk narrowPeak HFF foreskin fibroblast DNaseI Peaks from ENCODE 1 9 255 163 85 255 209 170 1 0 0 regulation 1 color 255,163,85\ longLabel HFF foreskin fibroblast DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HFF Pk\ subGroups view=a_Peaks cellType=HFF treatment=n_a tissue=skin cancer=normal\ track wgEncodeRegDnaseUwHffPeak\ wgEncodeRegDnaseUwHffWig HFF Sg bigWig 0 17635.9 HFF foreskin fibroblast DNaseI Signal from ENCODE 0 9 255 163 85 255 209 170 0 0 0 regulation 1 color 255,163,85\ longLabel HFF foreskin fibroblast DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.0818\ shortLabel HFF Sg\ subGroups cellType=HFF treatment=n_a tissue=skin cancer=normal\ table wgEncodeRegDnaseUwHffSignal\ track wgEncodeRegDnaseUwHffWig\ type bigWig 0 17635.9\ chainHprcGCA_018505825v1 HG02109.mat chain GCA_018505825.1 HG02109.mat HG02109.pri.mat.f1_v2 (May 2021 GCA_018505825.1_HG02109.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 9 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02109.mat HG02109.pri.mat.f1_v2 (May 2021 GCA_018505825.1_HG02109.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018505825.1\ parent hprcChainNetViewchain off\ priority 25\ shortLabel HG02109.mat\ subGroups view=chain sample=s025 population=afr subpop=acb hap=mat\ track chainHprcGCA_018505825v1\ type chain GCA_018505825.1\ lincRNAsCThLF_r1 hLF_r1 bed 5 + lincRNAs from hlf_r1 1 9 0 60 120 127 157 187 1 0 0 genes 1 longLabel lincRNAs from hlf_r1\ origAssembly hg19\ parent lincRNAsAllCellType on\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel hLF_r1\ subGroups view=lincRNAsRefseqExp tissueType=hlf_r1\ track lincRNAsCThLF_r1\ vertebrateChainNetViewnet Nets bed 3 Non-placental Vertebrate Genomes, Chain and Net Alignments 1 9 0 0 0 255 255 0 0 0 0 compGeno 1 longLabel Non-placental Vertebrate Genomes, Chain and Net Alignments\ parent vertebrateChainNet\ shortLabel Nets\ track vertebrateChainNetViewnet\ view net\ visibility dense\ wgEncodeRegTxnCaltechRnaSeqNhlfR2x75Il200SigPooled NHLF bigWig 0 65535 Transcription of NHLF cells from ENCODE 0 9 255 128 212 255 191 233 0 0 0 regulation 1 color 255,128,212\ longLabel Transcription of NHLF cells from ENCODE\ origAssembly hg19\ parent wgEncodeRegTxn\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ priority 9\ shortLabel NHLF\ track wgEncodeRegTxnCaltechRnaSeqNhlfR2x75Il200SigPooled\ type bigWig 0 65535\ iscaPathGainCum Path Gain bedGraph 4 ClinGen CNVs: Pathogenic Gain Coverage 2 9 0 0 200 127 127 227 0 0 0 phenDis 0 color 0,0,200\ longLabel ClinGen CNVs: Pathogenic Gain Coverage\ parent iscaViewTotal\ shortLabel Path Gain\ subGroups view=cov class=path level=sub\ track iscaPathGainCum\ ncbiRefSeqHgmd RefSeq HGMD genePred NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD 1 9 20 20 160 137 137 207 0 0 0 genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ color 20,20,160\ idXref ncbiRefSeqLink mrnaAcc name\ longLabel NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD\ parent refSeqComposite off\ priority 9\ shortLabel RefSeq HGMD\ track ncbiRefSeqHgmd\ trackHandler ncbiRefSeq\ type genePred\ SeqCap-EZ_MedExomePlusMito_hg19_capture_targets SeqCap EZ Med+Mito P bigBed Roche - SeqCap EZ MedExome + Mito Capture Probe Footprint 0 9 100 143 255 177 199 255 0 0 0 map 1 bigDataUrl /gbdb/hg38/exomeProbesets/SeqCap_EZ_MedExomePlusMito_hg38_capture_targets.bb\ color 100,143,255\ longLabel Roche - SeqCap EZ MedExome + Mito Capture Probe Footprint\ parent exomeProbesets on\ shortLabel SeqCap EZ Med+Mito P\ track SeqCap-EZ_MedExomePlusMito_hg19_capture_targets\ type bigBed\ vertebrateChainNet Vertebrate Chain/Net bed 3 Non-placental Vertebrate Genomes, Chain and Net Alignments 0 9 0 0 0 255 255 0 0 0 0

Description

Chain Track

\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.

\ \

Net Track

\ \

Display Conventions and Configuration

Chain Track

\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.

\ \

Net Track

\ Individual items in the display are categorized as one of four types\ (other than gap):

Top - the best, longest match. Displayed on level 1.\
Syn - line-ups on the same chromosome as the gap in the level above\ it.\
Inv - a line-up on the same chromosome as the gap above it, but in \ the opposite orientation.\
NonSyn - a match to a chromosome different from the gap in the \ level above.\

\ \

Methods

Chain track

\
\
\
\ The following lastz matrix was used
for the alignments to: Wallaby, Tasmanian Devil\
\ \ \ \ \ \ \ \
A C G T
A 91 -114 -31 -123
C -114 100 -125 -31
G -31 -125 100 -114
T -123 -31 -114 91
\ \ \
\
\ The following lastz matrix was used
for the alignments to: American Alligator, Medium Ground Finch,
\ Opossum, Platypus, Chicken, Zebra Finch, Lizard, X. tropicalis,
\ Stickleback, Fugu, Zebrafish, Tetraodon, Medaka, Lamprey\
\ \ \ \ \ \ \
A C G T
A 91 -90 -25 -100
C -90 100 -100 -25
G -25 -100 100 -90
T -100 -25 -90 91
\

\ \ For the Wallaby alignment, chains scoring below a minimum score\ of '3000' were discarded; the remaining chains are displayed in this track.\ The linear gap matrix used with axtChain:
\ \

-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\

\ \ For the alignments to: American Alligator, Medium Ground Finch, Tasmanian Devil, Opossum, Platypus, Chicken,\ Zebra Finch, Lizard, X. tropicalis, Stickleback, Fugu, Zebrafish, Tetraodon,\ Medaka and Lamprey, chains scoring below a minimum score\ of '5000' were discarded; the remaining chains are displayed\ in this track. The linear gap matrix used with axtChain:
\ \

-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\

\ More details on the Variant type(s) can be found on the Sequence Ontology page.

\ \

Display Conventions and Configuration

gnomAD v4.1

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

\ \

gnomAD v3.1.1

\ The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,\ except as noted below.

\ \

There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).\
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one\ variant, with additional information available on the details page, which has roughly halved the\ number of items in the bigBed.\
The bigBed has been split into two files, one with the information necessary for the track\ display, and one with the information necessary for the details page. For more information on\ this data format, please see the Data Access section below.\
The VEP annotation is shown as a table instead of spread across multiple fields.\
Intergenic variants have not been pre-filtered.\

\ \

gnomAD v3.1

\ By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters\ described below), before the track switches to dense display mode.\

\ \

\ Mouse hover on an item will display many details about each variant, including the affected gene(s),\ the variant type, and annotation (missense, synonymous, etc).\

\ \

\ Clicking on an item will display additional details on the variant, including a population frequency\ table showing allele count in each sub-population.\

\ \

\ Following the conventions on the gnomAD browser, items are shaded according to their Annotation\ type:\ \ \ \ \ \
pLoF
Missense
Synonymous
Other
\

\ Four filters are available for these tracks, the same as the underlying VCF:\

AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))\
InbreedingCoeff: Inbreeding Coefficient < -0.3\
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)\
Pass: Variant passes all 3 filters\

\ \

\ There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.\

\ \ \

UCSC Methods

\ The gnomAD v3.1.1 and v4.1 data is unfiltered.

\ For the v3.1 update only, in order to cut \ down on the amount of displayed data, the following variant\ types have been filtered out, but are still viewable in the gnomAD browser:\

Regulatory Region Variants\
Downstream/Upstream Gene Variants\
Transcription Factor Binding Site Variants\

\ \

\ For the full steps used to create the gnomAD tracks at UCSC, please see the\ hg38 gnomad makedoc.\

\ \ \

Data Access

\ \

\
# find item of interest:\
bigBedToBed genomes.bb stdout | head -4 | tail -1\
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted for brevity..]    chr1-12417-G-A    67293    902\
\
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:\
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz\
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant",  [..omitted for brevity..]\

\ \

\ The data can also be found directly from the gnomAD downloads page. Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.\

\ \

\ Please note that some annotations within the provided files may have restrictions on usage. See here for more information. \

\ \

\ \

Source transcript alignments were obtained from vertebrate organisms\ in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank \ mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,\ were used as available.\
For all vertebrate assemblies that had BLASTZ alignment chains and\ nets to the human (hg38) genome, a subset of the alignment chains were\ selected as follows:\
- For organisms whose branch distance was no more than 0.5\ (as computed by phyloFit, see Conservation track description for details),\ syntenic filtering was used. Reciprocal best nets were used if available;\ otherwise, nets were selected with the netfilter -syn command.\ The chains corresponding to the selected nets were used for mapping.\
- For more distant species, where the determination of synteny is difficult,\ the full set of chains was used for mapping. This allows for more genes to\ map at the expense of some mapping to paralogous regions. The\ post-alignment filtering step removes some of the duplications.\
\
The pslMap program was used to do a base-level projection of\ the source transcript alignments via the selected chains\ to the human genome, resulting in pairwise alignments of the source transcripts to\ the genome.\
The resulting alignments were filtered with pslCDnaFilter\ with a global near-best criteria of 0.5% in finished genomes\ (human and mouse) and 1.0% in other genomes. Alignments\ where less than 20% of the transcript mapped were discarded.\

\ \

\ To ensure unique identifiers for each alignment, cDNA and gene accessions were\ made unique by appending a suffix for each location in the source genome and\ again for each mapped location in the destination genome. The format is:\

\
   accession.version-srcUniq.destUniq\

\ \ Where srcUniq is a number added to make each source alignment unique, and\ destUniq is added to give the subsequent TransMap alignments unique\ identifiers.\

\ For example, in the cow genome, there are two alignments of mRNA BC149621.1.\ These are assigned the identifiers BC149621.1-1 and BC149621.1-2.\ When these are mapped to the human genome, BC149621.1-1 maps to a single\ location and is given the identifier BC149621.1-1.1. However, BC149621.1-2\ maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note\ that multiple TransMap mappings are usually the result of tandem duplications, where both\ chains are identified as syntenic.\

\ \

Data Access

\ \

\ The raw data for these tracks can be accessed interactively through the\ Table Browser or the\ Data Integrator.\ For automated analysis, the annotations are stored in\ bigPsl files (containing a\ number of extra columns) and can be downloaded from our\ download server, \ or queried using our API. For more \ information on accessing track data see our \ Track Data Access FAQ.\ The files are associated with these tracks in the following way:\

TransMap Ensembl - hg38.ensembl.transMapV4.bigPsl
TransMap RefGene - hg38.refseq.transMapV4.bigPsl
TransMap RNA - hg38.rna.transMapV4.bigPsl
TransMap ESTs - hg38.est.transMapV4.bigPsl

\ Individual regions or the whole genome annotation can be obtained using our tool\ bigBedToBed which can be compiled from the source code or downloaded as\ a precompiled binary for your system. Instructions for downloading source code and\ binaries can be found\ here.\ The tool can also be used to obtain only features within a given range, for example:\

\ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/transMap/V4/hg38.refseq.transMapV4.bigPsl\ -chrom=chr6 -start=0 -end=1000000 stdout\\ \

Credits

\ \

\ This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide and annotations produced by the RefSeq,\ Ensembl, and GENCODE annotations projects.

\ \

References

\ Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S,\ Lau C et al.\ \ Targeted discovery of novel human exons by comparative genomics.\ Genome Res. 2007 Dec;17(12):1763-73.\ PMID: 17989246; PMC: PMC2099585\

\ \

\ Stanke M, Diekhans M, Baertsch R, Haussler D.\ \ Using native and syntenically mapped cDNA alignments to improve de novo gene finding.\ Bioinformatics. 2008 Mar 1;24(5):637-44.\ PMID: 18218656\

\ \

\ Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D.\ \ Comparative genomics search for losses of long-established genes on the human lineage.\ PLoS Comput Biol. 2007 Dec;3(12):e247.\ PMID: 18085818; PMC: PMC2134963\

\ \ genes 1 baseColorDefault diffCodons\ baseColorUseCds given\ baseColorUseSequence lfExtra\ bigDataUrl /gbdb/hg38/transMap/V5/hg38.ensembl.transMapV5.bigPsl\ canPack on\ color 0,100,0\ defaultLabelFields orgAbbrev,geneName\ group genes\ html transMapEnsembl\ indelDoubleInsert on\ indelQueryInsert on\ labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId,geneType,transcriptType\ labelSeparator " "\ longLabel TransMap Ensembl and GENCODE Mappings Version 5\ priority 10.001\ searchIndex name,srcTransId,geneName,geneId\ shortLabel TransMap Ensembl\ showCdsAllScales .\ showCdsMaxZoom 10000.0\ showDiffBasesAllScales .\ showDiffBasesMaxZoom 10000.0\ superTrack transMapV5 pack\ track transMapEnsemblV5\ transMapSrcSet ensembl\ type bigPsl\ visibility pack\ transMapRefSeqV5 TransMap RefGene bigPsl TransMap RefSeq Gene Mappings Version 5 3 10.003 0 100 0 127 177 127 0 0 0

Description

\ \

\ This track contains RefSeq Gene alignments produced by\ the TransMap cross-species alignment algorithm\ from other vertebrate species in the UCSC Genome Browser.\ For closer evolutionary distances, the alignments are created using\ syntenically filtered BLASTZ alignment chains, resulting in a prediction of the\ orthologous genes in human.\

\ \ \

Display Conventions and Configuration

\ \

\ This track follows the display conventions for \ PSL alignment tracks.

Methods

\ \

Source transcript alignments were obtained from vertebrate organisms\ in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank \ mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,\ were used as available.\
For all vertebrate assemblies that had BLASTZ alignment chains and\ nets to the human (hg38) genome, a subset of the alignment chains were\ selected as follows:\
- For organisms whose branch distance was no more than 0.5\ (as computed by phyloFit, see Conservation track description for details),\ syntenic filtering was used. Reciprocal best nets were used if available;\ otherwise, nets were selected with the netfilter -syn command.\ The chains corresponding to the selected nets were used for mapping.\
- For more distant species, where the determination of synteny is difficult,\ the full set of chains was used for mapping. This allows for more genes to\ map at the expense of some mapping to paralogous regions. The\ post-alignment filtering step removes some of the duplications.\
\
The pslMap program was used to do a base-level projection of\ the source transcript alignments via the selected chains\ to the human genome, resulting in pairwise alignments of the source transcripts to\ the genome.\
The resulting alignments were filtered with pslCDnaFilter\ with a global near-best criteria of 0.5% in finished genomes\ (human and mouse) and 1.0% in other genomes. Alignments\ where less than 20% of the transcript mapped were discarded.\

\ \

\
   accession.version-srcUniq.destUniq\

\ \ Where srcUniq is a number added to make each source alignment unique, and\ destUniq is added to give the subsequent TransMap alignments unique\ identifiers.\

\ \

Data Access

\ \

TransMap Ensembl - hg38.ensembl.transMapV4.bigPsl
TransMap RefGene - hg38.refseq.transMapV4.bigPsl
TransMap RNA - hg38.rna.transMapV4.bigPsl
TransMap ESTs - hg38.est.transMapV4.bigPsl

\ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/transMap/V4/hg38.refseq.transMapV4.bigPsl\ -chrom=chr6 -start=0 -end=1000000 stdout\\ \

Credits

\ \

References

\ \

\ Stanke M, Diekhans M, Baertsch R, Haussler D.\ \ Using native and syntenically mapped cDNA alignments to improve de novo gene finding.\ Bioinformatics. 2008 Mar 1;24(5):637-44.\ PMID: 18218656\

\ \

\ \ genes 1 baseColorDefault diffCodons\ baseColorUseCds given\ baseColorUseSequence lfExtra\ bigDataUrl /gbdb/hg38/transMap/V5/hg38.refseq.transMapV5.bigPsl\ canPack on\ color 0,100,0\ defaultLabelFields orgAbbrev,geneName\ group genes\ html transMapRefSeq\ indelDoubleInsert on\ indelQueryInsert on\ labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId\ labelSeparator " "\ longLabel TransMap RefSeq Gene Mappings Version 5\ priority 10.003\ searchIndex name,srcTransId,geneName,geneId\ shortLabel TransMap RefGene\ showCdsAllScales .\ showCdsMaxZoom 10000.0\ showDiffBasesAllScales .\ showDiffBasesMaxZoom 10000.0\ superTrack transMapV5 pack\ track transMapRefSeqV5\ transMapSrcSet refseq\ type bigPsl\ visibility pack\ transMapRnaV5 TransMap RNA bigPsl TransMap GenBank RNA Mappings Version 5 0 10.004 0 100 0 127 177 127 0 0 0

Description

\ \

\ This track contains GenBank mRNA alignments produced by\ the TransMap cross-species alignment algorithm\ from other vertebrate species in the UCSC Genome Browser.\ For closer evolutionary distances, the alignments are created using\ syntenically filtered BLASTZ alignment chains, resulting in a prediction of the\ orthologous genes in human.\

\ \ \

Display Conventions and Configuration

\ \

\ This track follows the display conventions for \ PSL alignment tracks.

Methods

\ \

Source transcript alignments were obtained from vertebrate organisms\ in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank \ mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,\ were used as available.\
For all vertebrate assemblies that had BLASTZ alignment chains and\ nets to the human (hg38) genome, a subset of the alignment chains were\ selected as follows:\
- For organisms whose branch distance was no more than 0.5\ (as computed by phyloFit, see Conservation track description for details),\ syntenic filtering was used. Reciprocal best nets were used if available;\ otherwise, nets were selected with the netfilter -syn command.\ The chains corresponding to the selected nets were used for mapping.\
- For more distant species, where the determination of synteny is difficult,\ the full set of chains was used for mapping. This allows for more genes to\ map at the expense of some mapping to paralogous regions. The\ post-alignment filtering step removes some of the duplications.\
\
The pslMap program was used to do a base-level projection of\ the source transcript alignments via the selected chains\ to the human genome, resulting in pairwise alignments of the source transcripts to\ the genome.\
The resulting alignments were filtered with pslCDnaFilter\ with a global near-best criteria of 0.5% in finished genomes\ (human and mouse) and 1.0% in other genomes. Alignments\ where less than 20% of the transcript mapped were discarded.\

\ \

\
   accession.version-srcUniq.destUniq\

\ \ Where srcUniq is a number added to make each source alignment unique, and\ destUniq is added to give the subsequent TransMap alignments unique\ identifiers.\

\ \

Data Access

\ \

TransMap Ensembl - hg38.ensembl.transMapV4.bigPsl
TransMap RefGene - hg38.refseq.transMapV4.bigPsl
TransMap RNA - hg38.rna.transMapV4.bigPsl
TransMap ESTs - hg38.est.transMapV4.bigPsl

\ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/transMap/V4/hg38.refseq.transMapV4.bigPsl\ -chrom=chr6 -start=0 -end=1000000 stdout\\ \

Credits

\ \

References

\ \

\ Stanke M, Diekhans M, Baertsch R, Haussler D.\ \ Using native and syntenically mapped cDNA alignments to improve de novo gene finding.\ Bioinformatics. 2008 Mar 1;24(5):637-44.\ PMID: 18218656\

\ \

\ \ genes 1 baseColorDefault diffCodons\ baseColorUseCds given\ baseColorUseSequence lfExtra\ bigDataUrl /gbdb/hg38/transMap/V5/hg38.rna.transMapV5.bigPsl\ canPack on\ color 0,100,0\ defaultLabelFields orgAbbrev,srcTransId\ group genes\ html transMapRna\ indelDoubleInsert on\ indelQueryInsert on\ labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName\ labelSeparator " "\ longLabel TransMap GenBank RNA Mappings Version 5\ priority 10.004\ searchIndex name,srcTransId,geneName\ shortLabel TransMap RNA\ showCdsAllScales .\ showCdsMaxZoom 10000.0\ showDiffBasesAllScales .\ showDiffBasesMaxZoom 10000.0\ superTrack transMapV5 hide\ track transMapRnaV5\ transMapSrcSet rna\ type bigPsl\ visibility hide\ transMapEstV5 TransMap ESTs bigPsl TransMap EST Mappings Version 5 0 10.005 0 100 0 127 177 127 0 0 0

Description

\ \

\ This track contains GenBank spliced EST alignments produced by\ the TransMap cross-species alignment algorithm\ from other vertebrate species in the UCSC Genome Browser.\ For closer evolutionary distances, the alignments are created using\ syntenically filtered BLASTZ alignment chains, resulting in a prediction of the\ orthologous genes in human.\

\ \ \

Display Conventions and Configuration

\ \

\ This track follows the display conventions for \ PSL alignment tracks.

Methods

\ \

Source transcript alignments were obtained from vertebrate organisms\ in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank \ mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,\ were used as available.\
For all vertebrate assemblies that had BLASTZ alignment chains and\ nets to the human (hg38) genome, a subset of the alignment chains were\ selected as follows:\
- For organisms whose branch distance was no more than 0.5\ (as computed by phyloFit, see Conservation track description for details),\ syntenic filtering was used. Reciprocal best nets were used if available;\ otherwise, nets were selected with the netfilter -syn command.\ The chains corresponding to the selected nets were used for mapping.\
- For more distant species, where the determination of synteny is difficult,\ the full set of chains was used for mapping. This allows for more genes to\ map at the expense of some mapping to paralogous regions. The\ post-alignment filtering step removes some of the duplications.\
\
The pslMap program was used to do a base-level projection of\ the source transcript alignments via the selected chains\ to the human genome, resulting in pairwise alignments of the source transcripts to\ the genome.\
The resulting alignments were filtered with pslCDnaFilter\ with a global near-best criteria of 0.5% in finished genomes\ (human and mouse) and 1.0% in other genomes. Alignments\ where less than 20% of the transcript mapped were discarded.\

\ \

\
   accession.version-srcUniq.destUniq\

\ \ Where srcUniq is a number added to make each source alignment unique, and\ destUniq is added to give the subsequent TransMap alignments unique\ identifiers.\

\ \

Data Access

\ \

TransMap Ensembl - hg38.ensembl.transMapV4.bigPsl
TransMap RefGene - hg38.refseq.transMapV4.bigPsl
TransMap RNA - hg38.rna.transMapV4.bigPsl
TransMap ESTs - hg38.est.transMapV4.bigPsl

\ \

\ To obtain read coverage, the GTEx Laboratory, Data Analysis and Coordinating\ Center (LDACC) at the Broad Institute decided to select a single, high-quality\ representative sample for each tissue type, since aggregated tracks may\ obscure certain features or even introduce some artifacts (e.g. intronic\ coverage). For each tissue, the selected sample has the highest RIN value with\ a high coverage (>80M reads) and exonic rate (>85%). \ The alignment-to-coverage pipeline is available from Github:\ Python script,\ Docker file and \ Pipeline WDL description. \

To show the exact GTEx sample that was used for each tissue,\ click the "Schema" link on the track configuration page (above), the filename\ under "bigDataUrl" includes the identifier.

\ \

Subject and Sample Characteristics

\ \

Data Access

\ The raw data for the GTEx Read Coverage track can be accessed interactively through the \ Table Browser.\

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gtex/gtexGeneV8.bb -chrom=chr21\
-start=0 -end=100000000 stdout

\ Data can also be obtained directly from GTEx at the following link:\ \ https://gtexportal.org/home/datasets

\ \

Credits

\ Statistical analysis and data interpretation was performed by The GTEx Consortium Analysis \ Working Group. \ Data was provided by the GTEx LDACC at The Broad Institute of MIT and Harvard.

\ \

References

\ GTEx Consortium.\ \ The GTEx Consortium atlas of genetic regulatory effects across human tissues.\ Science. 2020 Sep 11;369(6509):1318-1330.\ PMID: 32913098;\ PMC: PMC7737656

\ \

\ GTEx Consortium.\ \ The Genotype-Tissue Expression (GTEx) project.\ Nat Genet. 2013 Jun;45(6):580-5.\ PMID: 23715323; \ PMC: PMC4010069

\ \

\ expression 0 autoScale group\ compositeTrack on\ group expression\ longLabel GTEx V8 RNA-Seq Read Coverage by Tissue\ maxHeightPixels 100:50:8\ priority 10.20\ shortLabel GTEx RNA-Seq Coverage\ track gtexCov\ type bigWig\ ukbDepletion UKB Depl. Rank Score bigWig 0.0 1.0 UK Biobank / deCODE Genetics Depletion Rank Score 1 10.5 0 0 0 127 127 127 0 0 0

Description

\ \

Note that another important constraint score, gnomAD\ constraint, is not part of this container track but can be found in the hg38 gnomAD\ track.\

\ \ The algorithms included in this track are:\

\ JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: \ JARVIS scores were created by first scanning the entire genome with a\ sliding-window approach (using a 1-nucleotide step), recording the number of\ all TOPMED variants and common variants, irrespective of their predicted effect,\ within each window, to eventually calculate a single-nucleotide resolution\ genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS\ was then combined with primary genomic sequence context, and additional genomic\ annotations with a multi-module deep learning framework to infer\ pathogenicity of noncoding regions that still remains naive to existing\ phylogenetic conservation metrics. The higher the score, the more deleterious\ the prediction. This score covers the entire genome, except the gaps.\ \
\ HMC - Homologous Missense Constraint:\ Homologous Missense Constraint (HMC) is a amino acid level measure\ of genetic intolerance of missense variants within human populations.\ For all assessable amino-acid positions in Pfam domains, the number of\ missense substitutions directly observed in gnomAD (Observed) was counted\ and compared to the expected value under a neutral evolution\ model (Expected). The upper limit of a 95% confidence interval for the\ Observed/Expected ratio is defined as the HMC score. Missense variants\ disrupting the amino-acid positions with HMC<0.8 are predicted to be\ likely deleterious. This score only covers PFAM domains within coding regions.\ \
\ MetaDome - Tolerance Landscape Score (hg19 only):\ MetaDome Tolerance Landscape scores are computed as a missense over synonymous \ variant count ratio, which is calculated in a sliding window (with a size of 21 \ codons/residues) to provide \ a per-position indication of regional tolerance to missense variation. The \ variant database was gnomAD and the score corrected for codon composition. Scores \ <0.7 are considered intolerant. This score covers only coding regions.\ \
\ MTR - Missense Tolerance Ratio (hg19 only):\ Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying \ selection acting specifically on missense variants in a given window of \ protein-coding sequence. It is estimated across sliding windows of 31 codons \ (default) and uses observed standing variation data from the WES component of \ gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores\ were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here\ is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), \ but this score only covers coding regions.\ \
\ UK Biobank depletion rank score (hg38 only):\ Halldorsson et al. tabulated the number of UK Biobank variants in each\ 500bp window of the genome and compared this number to an expected number\ given the heptamer nucleotide composition of the window and the fraction of\ heptamers with a sequence variant across the genome and their mutational\ classes. A variant depletion score was computed for every overlapping set\ of 500-bp windows in the genome with a 50-bp step size. They then assigned\ a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least\ depletion) for each 500-bp window. Since the windows are overlapping, we\ plot the value only in the central 50bp of the 500bp window, following\ advice from the author of the score,\ Hakon Jonsson, deCODE Genetics. He suggested that the value of the central\ window, rather than the worst possible score of all overlapping windows, is\ the most informative for a position. This score covers almost the entire genome,\ only very few regions were excluded, where the genome sequence had too many gap characters.

\ \

Display Conventions and Configuration

\ \

JARVIS

\ See hg19 makeDoc and\ hg38 makeDoc.

\ \

\ \ \ \ \ \ \ \ \ \
Percentile JARVIS score threshold
99th 0.9998
95th 0.9826
90th 0.7338
\

Percentile	JARVIS score threshold
99th	0.9998
95th	0.9826
90th	0.7338

\ \

HMC

\ \

MetaDome

\ \

\ \ \ \ \ \ \ \ \ \
Classification MetaDome Tolerance Score
Highly intolerant ≤ 0.175
Intolerant ≤ 0.525
Slightly intolerant ≤ 0.7
\

Classification	MetaDome Tolerance Score
Highly intolerant	≤ 0.175
Intolerant	≤ 0.525
Slightly intolerant	≤ 0.7

\ \

MTR

\ \

Green items MTR percentiles over 75\
Black items MTR percentiles between 25 and 75\
Red items MTR percentiles below 25\
Blue items No MTR score\

\ \

Methods

\ \

JARVIS

\ Scores were downloaded and converted to a single bigWig file. See the\ hg19 makeDoc and the\ hg38 makeDoc for more info.\

\ \

HMC

\ Scores were downloaded and converted to .bedGraph files with a custom Python \ script. The bedGraph files were then converted to bigWig files, as documented in our \ makeDoc hg19 build log.

\ \

\ \

Display Conventions and Configuration

\ This track is a multi-view composite track that contains differing data sets\ (views). Instructions for configuring multi-view tracks are\ here.\ To show only selected subtracks, uncheck the boxes next to the tracks that\ you wish to hide.

\ Views available on this track are:\

Genes: The gene annotations in this view are divided into three subtracks:

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

\ Maximum number of transcripts to display\ is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks.\ Starting with the GENCODE human V42 and mouse VM31 releases, \ transcripts are assigned rank within the gene. The ranks may be used to filter the number of transcripts\ displayed in a principled manner. Transcript ranking is not available in the lift37 releases.\ See Methods for details of rank assignment.\

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

\ The GENCODE project aims to annotate all evidence-based gene features on the \ human and mouse reference sequence with high accuracy by integrating \ computational approaches (including comparative methods), manual\ annotation and targeted experimental verification. This goal includes identifying \ all protein-coding loci with associated alternative variants, non-coding\ loci which have transcript evidence, and pseudogenes. \ For a detailed description of the methods and references used, see\ Harrow et al. (2006).\

\ \

\ GENCODE Basic Set selection:\ The GENCODE Basic Set is intended to provide a simplified subset of\ the GENCODE transcript annotations that will be useful to the majority of\ users. The goal was to have a high-quality basic set that also covered all loci. \ Selection of GENCODE annotations for inclusion in the basic set\ was determined independently for the coding and non-coding transcripts at each\ gene locus.\

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

\ Transcription Support Level (TSL):\ It is important that users understand how to assess transcript annotations\ that they see in GENCODE. While some transcript models have a high level of\ support through the full length of their exon structure, there are also\ transcripts that are poorly supported and that should be considered\ speculative. The Transcription Support Level (TSL) is a method to highlight the\ well-supported and poorly-supported transcript models for users. The method\ relies on the primary data that can support full-length transcript\ structure: mRNA and EST alignments supplied by UCSC and Ensembl.

\ \

The mRNA and EST alignments are compared to the GENCODE transcripts and the\ transcripts are scored according to how well the alignment matches over its\ full length. \ The GENCODE TSL provides a consistent method of evaluating the\ level of support that a GENCODE transcript annotation is\ actually expressed in mouse. Mouse transcript sequences from the \ International Nucleotide\ Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as\ the evidence for this analysis.\ \ Exonerate RNA alignments from Ensembl,\ BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in\ the analysis. Erroneous transcripts and libraries identified in lists\ maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as\ suspect. GENCODE annotations for protein-coding and non-protein-coding\ transcripts are compared with the evidence alignments.

\ \

Annotations in the MHC region and other immunological genes are not\ evaluated, as automatic alignments tend to be very problematic. \ Methods for evaluating single-exon genes are still being developed and \ they are not included\ in the current analysis. Multi-exon GENCODE annotations are evaluated using\ the criteria that all introns are supported by an evidence alignment and the\ evidence alignment does not indicate that there are unannotated exons. Small\ insertions and deletions in evidence alignments are assumed to be due to\ polymorphisms and not considered as differing from the annotations. All\ intron boundaries must match exactly. The transcript start and end locations\ are allowed to differ.

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

APPRIS\ is a system to annotate alternatively spliced transcripts based on a range of computational\ methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes.\ APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal\ isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable.

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 47 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 47 corresponds to Ensembl 113.

See also: The GENCODE Project\

\ \

Credits

The GENCODE project is an international collaboration funded by NIH/NHGRI\ grant U41HG007234. More information is available\ at www.gencodegenes.org,\ Participating GENCODE institutions and personnel can be found\ \ here.\

\ \

References

\ Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong\ J, Barnes I et al.\ \ GENCODE 2021.\ Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923.\ PMID: 33270111;\ PMC: PMC7778937;\ DOI: 10.1093/nar/gkaa1087\

\ \ \

A full list of GENCODE publications are available\ at The GENCODE\ Project web site.\

\ \

Data Release Policy

GENCODE data are available for use without restrictions.

\ \ genes 1 allButtonPair on\ compositeTrack on\ configurable off\ dragAndDrop subTracks\ fileSortOrder labVersion=Contents dccAccession=UCSC_Accession\ group genes\ longLabel All GENCODE annotations from V47 (Ensembl 113)\ maxTransEnabled on\ pennantIcon New red ../goldenPath/newsarch.html#110824 "Updated Nov. 8, 2024"\ priority 34.158\ shortLabel All GENCODE V47\ sortOrder name=+ view=+\ subGroup1 view View aGenes=Genes bPolya=PolyA\ subGroup2 name Name Basic=Basic Comprehensive=Comprehensive Pseudogenes=Pseudogenes zPolyA=PolyA\ superTrack wgEncodeGencodeSuper pack\ track wgEncodeGencodeV47\ type genePred\ visibility pack\ wgEncodeGencodeVersion 47\ wgEncodeGencodeV47ViewGenes Genes genePred All GENCODE annotations from V47 (Ensembl 113) 3 34.158 0 0 0 127 127 127 0 0 0 genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ cdsDrawDefault genomic\\ codons\ configurable on\ filterBy attrs.transcriptClass:Transcript_Class=coding,nonCoding,pseudo,problem transcriptMethod:Transcript_Annotation_Method=manual,automatic,manual_only,automatic_only attrs.transcriptType:Transcript_Biotype=artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lncRNA,miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,nonsense_mediated_decay,non_stop_decay,processed_pseudogene,processed_transcript,protein_coding,protein_coding_CDS_not_defined,protein_coding_LoF,pseudogene,retained_intron,ribozyme,rRNA,rRNA_pseudogene,scaRNA,scRNA,snoRNA,snRNA,sRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene,vault_RNA tag:Tag=3_nested_supported_extension,3_standard_supported_extension,454_RNA_Seq_supported,5_nested_supported_extension,5_standard_supported_extension,alternative_3_UTR,alternative_5_UTR,annotation_in_progress,appris_alternative_1,appris_alternative_2,appris_principal_1,appris_principal_2,appris_principal_3,appris_principal_4,appris_principal_5,artifactual_duplication,basic,bicistronic,CAGE_supported_TSS,CCDS,cds_end_NF,cds_start_NF,confirm_experimentally,dotter_confirmed,downstream_ATG,Ensembl_canonical,EnsEMBL_merge_exception,exp_conf,fragmented_locus,fragmented_mixed_strand_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,MANE_Plus_Clinical,MANE_Select,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,nested_454_RNA_Seq_supported,NMD_exception,NMD_likely_if_extended,non_ATG_start,non_canonical_conserved,non_canonical_genome_sequence_error,non_canonical_other,non_canonical_polymorphism,non_canonical_TEC,non_canonical_U12,non_submitted_evidence,not_best_in_genome_evidence,not_organism_supported,overlapping_locus,overlapping_uORF,overlaps_pseudogene,polymorphic_pseudogene_no_stop,precursor_RNA,pseudo_consens,readthrough_gene,readthrough_transcript,reference_genome_error,retained_intron_CDS,retained_intron_final,retained_intron_first,retrogene,RNA_Seq_supported_only,RNA_Seq_supported_partial,RP_supported_TIS,seleno,Selenoprotein,semi_processed,sequence_error,stop_codon_readthrough,TAGENE,upstream_ATG,upstream_uORF supportLevel:Support_Level=tsl1,tsl2,tsl3,tsl4,tsl5,tslNA\ gClass_coding 12,12,120\ gClass_nonCoding 0,153,0\ gClass_problem 254,0,0\ gClass_pseudo 255,51,255\ geneClasses coding nonCoding pseudo problem\ highlightBy transcriptMethod:Transcript_Annotation_Method=manual,automatic,manual_only,automatic_only attrs.transcriptType:Transcript_Biotype=artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lncRNA,miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,nonsense_mediated_decay,non_stop_decay,processed_pseudogene,processed_transcript,protein_coding,protein_coding_CDS_not_defined,protein_coding_LoF,pseudogene,retained_intron,ribozyme,rRNA,rRNA_pseudogene,scaRNA,scRNA,snoRNA,snRNA,sRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene,vault_RNA tag:Tag=3_nested_supported_extension,3_standard_supported_extension,454_RNA_Seq_supported,5_nested_supported_extension,5_standard_supported_extension,alternative_3_UTR,alternative_5_UTR,annotation_in_progress,appris_alternative_1,appris_alternative_2,appris_principal_1,appris_principal_2,appris_principal_3,appris_principal_4,appris_principal_5,artifactual_duplication,basic,bicistronic,CAGE_supported_TSS,CCDS,cds_end_NF,cds_start_NF,confirm_experimentally,dotter_confirmed,downstream_ATG,Ensembl_canonical,EnsEMBL_merge_exception,exp_conf,fragmented_locus,fragmented_mixed_strand_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,MANE_Plus_Clinical,MANE_Select,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,nested_454_RNA_Seq_supported,NMD_exception,NMD_likely_if_extended,non_ATG_start,non_canonical_conserved,non_canonical_genome_sequence_error,non_canonical_other,non_canonical_polymorphism,non_canonical_TEC,non_canonical_U12,non_submitted_evidence,not_best_in_genome_evidence,not_organism_supported,overlapping_locus,overlapping_uORF,overlaps_pseudogene,polymorphic_pseudogene_no_stop,precursor_RNA,pseudo_consens,readthrough_gene,readthrough_transcript,reference_genome_error,retained_intron_CDS,retained_intron_final,retained_intron_first,retrogene,RNA_Seq_supported_only,RNA_Seq_supported_partial,RP_supported_TIS,seleno,Selenoprotein,semi_processed,sequence_error,stop_codon_readthrough,TAGENE,upstream_ATG,upstream_uORF supportLevel:Support_Level=tsl1,tsl2,tsl3,tsl4,tsl5,tslNA\ highlightColor 255,255,0\ idXref wgEncodeGencodeAttrsV47 transcriptId geneId\ itemClassClassColumn transcriptClass\ itemClassNameColumn transcriptId\ itemClassTbl wgEncodeGencodeAttrsV47\ longLabel All GENCODE annotations from V47 (Ensembl 113)\ parent wgEncodeGencodeV47\ shortLabel Genes\ track wgEncodeGencodeV47ViewGenes\ type genePred\ view aGenes\ visibility pack\ wgEncodeGencodeV47ViewPolya PolyA genePred All GENCODE annotations from V47 (Ensembl 113) 0 34.158 0 0 0 127 127 127 0 0 0 genes 1 configurable off\ longLabel All GENCODE annotations from V47 (Ensembl 113)\ parent wgEncodeGencodeV47\ shortLabel PolyA\ track wgEncodeGencodeV47ViewPolya\ type genePred\ view cPolya\ visibility hide\ wgEncodeGencodeV46 All GENCODE V46 genePred All GENCODE annotations from V46 (Ensembl 112) 0 34.159 0 0 0 127 127 127 0 0 0

Description

\ The GENCODE Genes track (version 46, May 2024) shows high-quality manual\ annotations merged with evidence-based automated annotations across the entire\ human genome generated by the\ GENCODE project.\ The GENCODE gene set presents a full merge\ between HAVANA manual annotation process and Ensembl automatic annotation pipeline.\ Priority is given to the manually curated HAVANA annotation using predicted\ Ensembl annotations when there are no corresponding manual annotations.\ The 46 annotation was carried out on genome assembly GRCh38 (hg38).\

\ The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the\ corresponding release.\

\ \

Display Conventions and Configuration

\ Views available on this track are:\

Genes: The gene annotations in this view are divided into three subtracks:

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 46 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 46 corresponds to Ensembl 112.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 45 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 45 corresponds to Ensembl 111.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 44 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 44 corresponds to Ensembl 110.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 43 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 43 corresponds to Ensembl 109.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 42 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 42 corresponds to Ensembl 108.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 41 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 41 corresponds to Ensembl 107.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 40 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 40 corresponds to Ensembl 106.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 39 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 39 corresponds to Ensembl 105.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 38 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 38 corresponds to Ensembl 104.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 37 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 37 corresponds to Ensembl 103.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 36 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 36 corresponds to Ensembl 102.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 35 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 35 corresponds to Ensembl 101.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 34 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 34 corresponds to Ensembl 100.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 33 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 33 corresponds to Ensembl 99.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

GENCODE GFF3 and GTF files are available from the\ GENCODE release 32 site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 32 corresponds to Ensembl 98.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 31\ site.

\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 31 corresponds to Ensembl 97.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 30 site.\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 30 corresponds to Ensembl 96.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 29 site.\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 29 corresponds to Ensembl 94.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 28 site.\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 28 corresponds to Ensembl 92.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 27 site.\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 27 corresponds to Ensembl 90.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 26 site.\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 26 corresponds to Ensembl 88.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 25 site.\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 25 corresponds to Ensembl 85.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 24 site.\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 24 corresponds to Ensembl 84.

\ \

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Downloads

\ GENCODE GFF3 and GTF files are available from the\ GENCODE release 23 site.\ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 23 corresponds to Ensembl 81 and 82.

\ \

See also: The GENCODE Project\

Display Conventions and Configuration

\ Views available on this track are:\

Genes: The gene annotations in this view are divided into three subtracks:

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 22 corresponds to Ensembl 79.

See also: The GENCODE Project\

GENCODE Basic set is a subset of the Comprehensive set. \ The selection criteria are described in the methods section.
GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations,\ including polymorphic pseudogenes. This includes both manual and\ automatic annotations. This is a super-set of the Basic set.
GENCODE Pseudogenes include all annotations except polymorphic pseudogenes.

\ \

PolyA

GENCODE PolyA contains polyA signals and sites manually annotated on\ the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of\ transcripts containing at least 3 A's not matching the genome.

\ \

Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks\ using the following criteria:

Transcript class: filter by the basic biological function of a transcript\ annotation\
- All - don't filter by transcript class
- coding - display protein coding transcripts, including polymorphic pseudogenes
- nonCoding - display non-protein coding transcripts
- pseudo - display pseudogene transcript annotations
- problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)\
\
Transcript Annotation Method: filter by the method used to create the annotation\
- All - don't filter by transcript class
- manual - display manually created annotations, including those that are \ also created automatically
- automatic - display automatically created annotations, including those that are \ also created manually
- manual_only - display manually created annotations that were\ not annotated by the automatic method
- automatic_only - display automatically created annotations that were\ not annotated by the manual method
\
Transcript Biotype: filter transcripts by\ Biotype
Support Level: filter transcripts by transcription support level

\ \

Coloring for the gene annotations is based on the annotation type:

coding \
non-coding \
pseudogene \
problem\
all polyA annotations\

\ \

Methods

\ \

Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given\ locus:\
- All full-length coding transcripts (except problem transcripts or transcripts that are\ nonsense-mediated decay) were included in the basic set.
- If there were no transcripts meeting the above criteria, then the partial coding\ transcript with the largest CDS was included in the basic set (excluding problem transcripts).
\
Criteria for selection of non-coding transcripts at a given locus:\
- All full-length non-coding transcripts (except problem transcripts)\ with a well characterized Biotype (see below) were included in the\ basic set.
- If there were no transcripts meeting the above criteria, then the largest non-coding\ transcript was included in the basic set (excluding problem transcripts).
\
If no transcripts were included by either of the above criteria, the longest\ problem transcript is included.\

\ \

\ Non-coding transcript categorization: \ Non-coding transcripts are categorized using\ their biotype\ and the following criteria:\

well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA
poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping

\ \

Transcript ranking:\ Within each gene, transcripts have been ranked according to the \ following criteria. The ranking approach is preliminary and will\ change is future releases.\

\ \

Protein_coding genes\
1. MANE or Ensembl canonical
  \ -1st: MANE Select / Ensembl canonical
  \ -2nd: MANE Plus Clinical
  \
2. Coding biotypes
  \ -1st: protein_coding and protein_coding_LoF
  \ -2nd: NMDs and NSDs
  \ -3rd: retained intron and protein_coding_CDS_not_defined
  \
3. Completeness
  \ -1st: full length
  \ -2nd: CDS start/end not found
  \
4. CARS score (only for coding transcripts)
  \
5. Transcript genomic span and length (only for non-coding transcripts)
  \
\
Non-coding genes\
1. Transcript biotype
  \ -1st: transcript biotype identical to gene biotype\
2. Ensembl canonical\
3. GENCODE basic\
4. Transcript genomic span\
5. Transcript length\
\

\ \

The following categories are assigned to each of the evaluated annotations:

\ \

tsl1 - all splice junctions of the transcript are supported by\ at least one non-suspect mRNA\
tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
tsl3 - the only support is from a single EST
tsl4 - the best supporting EST is flagged as suspect
tsl5 - no single transcript supports the model structure
tslNA - the transcript was not analyzed for one of the following reasons:\
- pseudogene annotation, including transcribed pseudogenes\
- immunoglobin gene transcript\
- T-cell receptor transcript\
- single-exon transcript (will be included in a future version)\
\

\ \

PRINCIPAL:1 - Transcript(s) expected to code for the main functional\ isoform based solely on the core modules in the APPRIS. \
PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ database chooses two or more of the CDS variants as "candidates" to be the\ principal variant.\
PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear\ principal variant and more than one of the variants have distinct\ CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier\ as the principal variant. The lower the CCDS identifier, the earlier it\ was annotated.\
PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear\ principal CDS and there is more than one variant with distinct (but\ consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as\ the principal variant.\
PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear\ principal variant and none of the candidate variants are annotated by CCDS,\ APPRIS selects the longest of the candidate isoforms as the principal variant.\ For genes in which the APPRIS core modules are unable to choose a clear\ principal variant (approximately 25% of human protein coding genes), the\ "candidate" variants not chosen as principal are labeled in the following way:\
ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at\ least three tested species.\
ALTERNATIVE:2 - Candidate transcript(s) models that appear to be\ conserved in fewer than three tested species. Non-candidate transcripts are\ not tagged and are considered as "Minor" transcripts. Further information and\ additional web services can be found at the APPRIS website.\

\ \ \ \

Verification

\ \

\ Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.\ Those experiments can be found at GEO:

GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes).
GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009.
GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human.
GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).
GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010).
GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

See Harrow et al. (2006) for information on verification\ techniques.\

\ \

Release Notes

\ GENCODE version 20 corresponds to Ensembl 76 and Vega 56.

\ \

See also: The GENCODE Project\

\ \

Credits

\ \

References

\ \ \

A full list of GENCODE publications are available\ at The GENCODE\ Project web site.\

\ \

Data Release Policy

GENCODE data are available for use without restrictions.

\ \ genes 1 allButtonPair on\ compositeTrack on\ configurable off\ dragAndDrop subTracks\ fileSortOrder labVersion=Contents dccAccession=UCSC_Accession\ group genes\ longLabel Gene Annotations from GENCODE Version 20 (Ensembl 76)\ priority 34.185\ shortLabel GENCODE V20 (Ensembl 76)\ sortOrder name=+ view=+\ subGroup1 view View aGenes=Genes b2-way=2-way cPolya=PolyA\ subGroup2 name Name Basic=Basic Comprehensive=Comprehensive Pseudogenes=Pseudogenes yTwo-way=2-way_Pseudogenes zPolyA=PolyA\ superTrack wgEncodeGencodeSuper hide\ track wgEncodeGencodeV20\ type genePred\ visibility hide\ wgEncodeGencodeAnnotationRemark wgEncodeGencodeAnnotationRemarkV20\ wgEncodeGencodeAttrs wgEncodeGencodeAttrsV20\ wgEncodeGencodeExonSupport wgEncodeGencodeExonSupportV20\ wgEncodeGencodeGeneSource wgEncodeGencodeGeneSourceV20\ wgEncodeGencodePdb wgEncodeGencodePdbV20\ wgEncodeGencodePolyAFeature wgEncodeGencodePolyAFeatureV20\ wgEncodeGencodePubMed wgEncodeGencodePubMedV20\ wgEncodeGencodeRefSeq wgEncodeGencodeRefSeqV20\ wgEncodeGencodeTag wgEncodeGencodeTagV20\ wgEncodeGencodeTranscriptSource wgEncodeGencodeTranscriptSourceV20\ wgEncodeGencodeTranscriptSupport wgEncodeGencodeTranscriptSupportV20\ wgEncodeGencodeTranscriptionSupportLevel wgEncodeGencodeTranscriptionSupportLevelV20\ wgEncodeGencodeUniProt wgEncodeGencodeUniProtV20\ wgEncodeGencodeVersion 20\ wgEncodeGencodeV20ViewGenes Genes genePred Gene Annotations from GENCODE Version 20 (Ensembl 76) 3 34.185 0 0 0 127 127 127 0 0 0 genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ cdsDrawDefault genomic\\ codons\ configurable on\ filterBy attrs.transcriptClass:Transcript_Class=coding,nonCoding,pseudo,problem transcriptMethod:Transcript_Annotation_Method=manual,automatic,manual_only,automatic_only attrs.transcriptType:Transcript_Biotype=3prime_overlapping_ncrna,antisense,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_V_gene,IG_V_pseudogene,lincRNA,miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,nonsense_mediated_decay,non_stop_decay,polymorphic_pseudogene,processed_pseudogene,processed_transcript,protein_coding,pseudogene,retained_intron,rRNA,sense_intronic,sense_overlapping,snoRNA,snRNA,transcribed_processed_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene supportLevel:Support_Level=tsl1,tsl2,tsl3,tsl4,tsl5,tslNA\ gClass_coding 12,12,120\ gClass_nonCoding 0,153,0\ gClass_problem 254,0,0\ gClass_pseudo 255,51,255\ geneClasses coding nonCoding pseudo problem\ highlightBy supportLevel:Support_Level=tsl1,tsl2,tsl3,tsl4,tsl5,tslNA attrs.transcriptType:Transcript_Biotype=3prime_overlapping_ncrna,antisense,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_V_gene,IG_V_pseudogene,lincRNA,miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,nonsense_mediated_decay,non_stop_decay,polymorphic_pseudogene,processed_pseudogene,processed_transcript,protein_coding,pseudogene,retained_intron,rRNA,sense_intronic,sense_overlapping,snoRNA,snRNA,transcribed_processed_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene\ highlightColor 255,255,0\ idXref wgEncodeGencodeAttrsV20 transcriptId geneId\ itemClassClassColumn transcriptClass\ itemClassNameColumn transcriptId\ itemClassTbl wgEncodeGencodeAttrsV20\ longLabel Gene Annotations from GENCODE Version 20 (Ensembl 76)\ parent wgEncodeGencodeV20\ shortLabel Genes\ track wgEncodeGencodeV20ViewGenes\ type genePred\ view aGenes\ visibility pack\ wgEncodeGencodeV20ViewPolya PolyA genePred Gene Annotations from GENCODE Version 20 (Ensembl 76) 0 34.185 0 0 0 127 127 127 0 0 0 genes 1 configurable off\ longLabel Gene Annotations from GENCODE Version 20 (Ensembl 76)\ parent wgEncodeGencodeV20\ shortLabel PolyA\ track wgEncodeGencodeV20ViewPolya\ type genePred\ view cPolya\ visibility hide\ encTfChipPkENCFF915LKZ A549 POLR2A 1 narrowPeak Transcription Factor ChIP-seq Peaks of POLR2A in A549 from ENCODE 3 (ENCFF915LKZ) 0 35 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of POLR2A in A549 from ENCODE 3 (ENCFF915LKZ)\ parent encTfChipPk off\ shortLabel A549 POLR2A 1\ subGroups cellType=A549 factor=POLR2A\ track encTfChipPkENCFF915LKZ\ AorticSmoothMuscleCellResponseToFGF203hrBiolRep2LK20_CNhs13364_tpm_fwd AorticSmsToFgf2_03hrBr2+ bigWig Aortic smooth muscle cell response to FGF2, 03hr, biol_rep2 (LK20)_CNhs13364_12746-136A1_forward 1 35 255 0 0 255 127 127 0 0 0 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regulation 1 color 204,255,85\ longLabel HGF gingival fibroblast DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.29794\ shortLabel HGF Sg\ subGroups cellType=HGF treatment=n_a tissue=periodontium cancer=normal\ table wgEncodeRegDnaseUwHgfSignal\ track wgEncodeRegDnaseUwHgfWig\ type bigWig 0 3410.39\ gtexCovLiver Liver bigWig Liver 0 36 205 183 158 230 219 206 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-Y5LM-0426-SM-4VBRO.Liver.RNAseq.bw\ color 205,183,158\ longLabel Liver\ parent gtexCov\ shortLabel Liver\ track gtexCovLiver\ encTfChipPkENCFF897QCA A549 RAD21 narrowPeak Transcription Factor ChIP-seq Peaks of RAD21 in A549 from ENCODE 3 (ENCFF897QCA) 0 37 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of RAD21 in A549 from ENCODE 3 (ENCFF897QCA)\ parent encTfChipPk off\ shortLabel A549 RAD21\ subGroups cellType=A549 factor=RAD21\ track encTfChipPkENCFF897QCA\ 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AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_ctss_fwd AorticSmsToFgf2_03hrBr3+ bigWig Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_forward 0 37 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12844-137B9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2003hr%2c%20biol_rep3%20%28LK21%29.CNhs13573.12844-137B9.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12844-137B9 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_03hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12844-137B9\ urlLabel FANTOM5 Details:\ chainHprcGCA_018472605v1 HG00621.mat chain GCA_018472605.1 HG00621.mat HG00621.pri.mat.f1_v2 (May 2021 GCA_018472605.1_HG00621.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 37 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG00621.mat HG00621.pri.mat.f1_v2 (May 2021 GCA_018472605.1_HG00621.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018472605.1\ parent hprcChainNetViewchain off\ priority 82\ shortLabel HG00621.mat\ subGroups view=chain sample=s082 population=eas subpop=chs hap=mat\ track chainHprcGCA_018472605v1\ type chain GCA_018472605.1\ gtexCovLung Lung bigWig Lung 0 37 154 205 50 204 230 152 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-Y5V5-0826-SM-4VBQD.Lung.RNAseq.bw\ color 154,205,50\ longLabel Lung\ parent gtexCov\ shortLabel Lung\ track gtexCovLung\ wgEncodeRegDnaseUwNhdfneoPeak NHDF-neo Pk narrowPeak NHDF-neo dermal fibroblast, neonate DNaseI Peaks from ENCODE 1 37 198 255 85 226 255 170 1 0 0 regulation 1 color 198,255,85\ longLabel NHDF-neo dermal fibroblast, neonate DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel NHDF-neo Pk\ subGroups view=a_Peaks cellType=NHDF-neo treatment=n_a tissue=skin cancer=normal\ track wgEncodeRegDnaseUwNhdfneoPeak\ wgEncodeRegDnaseUwNhdfneoWig NHDF-neo Sg bigWig 0 13455.2 NHDF-neo dermal fibroblast, neonate DNaseI Signal from ENCODE 0 37 198 255 85 226 255 170 0 0 0 regulation 1 color 198,255,85\ longLabel NHDF-neo dermal fibroblast, neonate DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.3069\ shortLabel NHDF-neo Sg\ subGroups cellType=NHDF-neo treatment=n_a tissue=skin cancer=normal\ table wgEncodeRegDnaseUwNhdfneoSignal\ track wgEncodeRegDnaseUwNhdfneoWig\ type bigWig 0 13455.2\ encTfChipPkENCFF993WZP A549 RCOR1 narrowPeak Transcription Factor ChIP-seq Peaks of RCOR1 in A549 from ENCODE 3 (ENCFF993WZP) 0 38 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of RCOR1 in A549 from ENCODE 3 (ENCFF993WZP)\ parent encTfChipPk off\ shortLabel A549 RCOR1\ subGroups cellType=A549 factor=RCOR1\ track encTfChipPkENCFF993WZP\ AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_tpm_rev AorticSmsToFgf2_03hrBr3- bigWig Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_reverse 1 38 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12844-137B9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2003hr%2c%20biol_rep3%20%28LK21%29.CNhs13573.12844-137B9.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12844-137B9 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_03hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12844-137B9\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_ctss_rev AorticSmsToFgf2_03hrBr3- bigWig Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_reverse 0 38 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12844-137B9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2003hr%2c%20biol_rep3%20%28LK21%29.CNhs13573.12844-137B9.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12844-137B9 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_03hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12844-137B9\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwHaepicPeak HAEpiC Pk narrowPeak HAEpiC amniotic epithelium (AEC) DNaseI Peaks from ENCODE 1 38 189 255 85 222 255 170 1 0 0 regulation 1 color 189,255,85\ longLabel HAEpiC amniotic epithelium (AEC) DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HAEpiC Pk\ subGroups view=a_Peaks cellType=HAEpiC treatment=n_a tissue=embryo cancer=normal\ track wgEncodeRegDnaseUwHaepicPeak\ wgEncodeRegDnaseUwHaepicWig HAEpiC Sg bigWig 0 10858.1 HAEpiC amniotic epithelium (AEC) DNaseI Signal from ENCODE 0 38 189 255 85 222 255 170 0 0 0 regulation 1 color 189,255,85\ longLabel HAEpiC amniotic epithelium (AEC) DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.32226\ shortLabel HAEpiC Sg\ subGroups cellType=HAEpiC treatment=n_a tissue=embryo cancer=normal\ table wgEncodeRegDnaseUwHaepicSignal\ track wgEncodeRegDnaseUwHaepicWig\ type bigWig 0 10858.1\ netHprcGCA_018472605v1 HG00621.mat netAlign GCA_018472605.1 chainHprcGCA_018472605v1 HG00621.mat HG00621.pri.mat.f1_v2 (May 2021 GCA_018472605.1_HG00621.pri.mat.f1_v2) HPRC project computed Chain Nets 1 38 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG00621.mat HG00621.pri.mat.f1_v2 (May 2021 GCA_018472605.1_HG00621.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018472605.1\ parent hprcChainNetViewnet off\ priority 82\ shortLabel HG00621.mat\ subGroups view=net sample=s082 population=eas subpop=chs hap=mat\ track netHprcGCA_018472605v1\ type netAlign GCA_018472605.1 chainHprcGCA_018472605v1\ gtexCovMinorSalivaryGland Minor Saliv Gland bigWig Minor Salivary Gland 0 38 205 183 158 230 219 206 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-Y5LM-1826-SM-4VDT9.Minor_Salivary_Gland.RNAseq.bw\ color 205,183,158\ longLabel Minor Salivary Gland\ parent gtexCov\ shortLabel Minor Saliv Gland\ track gtexCovMinorSalivaryGland\ encTfChipPkENCFF107EWI A549 REST 1 narrowPeak Transcription Factor ChIP-seq Peaks of REST in A549 from ENCODE 3 (ENCFF107EWI) 0 39 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of REST in A549 from ENCODE 3 (ENCFF107EWI)\ parent encTfChipPk off\ shortLabel A549 REST 1\ subGroups cellType=A549 factor=REST\ track encTfChipPkENCFF107EWI\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_tpm_fwd AorticSmsToFgf2_05hrBr1+ bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_forward 1 39 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12650-134H4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep1%20%28LK25%29.CNhs13347.12650-134H4.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12650-134H4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_05hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12650-134H4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_ctss_fwd AorticSmsToFgf2_05hrBr1+ bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_forward 0 39 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12650-134H4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep1%20%28LK25%29.CNhs13347.12650-134H4.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12650-134H4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_05hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12650-134H4\ urlLabel FANTOM5 Details:\ chainHprcGCA_018472575v1 HG00621.pat chain GCA_018472575.1 HG00621.pat HG00621.alt.pat.f1_v2 (May 2021 GCA_018472575.1_HG00621.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 39 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG00621.pat HG00621.alt.pat.f1_v2 (May 2021 GCA_018472575.1_HG00621.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018472575.1\ parent hprcChainNetViewchain off\ priority 79\ shortLabel HG00621.pat\ subGroups view=chain sample=s079 population=eas subpop=chs hap=pat\ track chainHprcGCA_018472575v1\ type chain GCA_018472575.1\ gtexCovMuscleSkeletal Muscle Skeletal bigWig Muscle Skeletal 0 39 122 103 238 188 179 246 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-NFK9-0626-SM-2HMIV.Muscle_Skeletal.RNAseq.bw\ color 122,103,238\ longLabel Muscle Skeletal\ parent gtexCov\ shortLabel Muscle Skeletal\ track gtexCovMuscleSkeletal\ wgEncodeRegDnaseUwSkmcPeak SKMC Pk narrowPeak SKMC skeletal muscle cell DNaseI Peaks from ENCODE 1 39 182 255 85 218 255 170 1 0 0 regulation 1 color 182,255,85\ longLabel SKMC skeletal muscle cell DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel SKMC Pk\ subGroups view=a_Peaks cellType=SKMC treatment=n_a tissue=muscle cancer=normal\ track wgEncodeRegDnaseUwSkmcPeak\ wgEncodeRegDnaseUwSkmcWig SKMC Sg bigWig 0 2130.04 SKMC skeletal muscle cell DNaseI Signal from ENCODE 0 39 182 255 85 218 255 170 0 0 0 regulation 1 color 182,255,85\ longLabel SKMC skeletal muscle cell DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.3337\ shortLabel SKMC Sg\ subGroups cellType=SKMC treatment=n_a tissue=muscle cancer=normal\ table wgEncodeRegDnaseUwSkmcSignal\ track wgEncodeRegDnaseUwSkmcWig\ type bigWig 0 2130.04\ encTfChipPkENCFF706DRE A549 REST 2 narrowPeak Transcription Factor ChIP-seq Peaks of REST in A549 from ENCODE 3 (ENCFF706DRE) 0 40 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of REST in A549 from ENCODE 3 (ENCFF706DRE)\ parent encTfChipPk off\ shortLabel A549 REST 2\ subGroups cellType=A549 factor=REST\ track encTfChipPkENCFF706DRE\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_tpm_rev AorticSmsToFgf2_05hrBr1- bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_reverse 1 40 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12650-134H4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep1%20%28LK25%29.CNhs13347.12650-134H4.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12650-134H4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_05hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12650-134H4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_ctss_rev AorticSmsToFgf2_05hrBr1- bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_reverse 0 40 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12650-134H4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep1%20%28LK25%29.CNhs13347.12650-134H4.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12650-134H4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_05hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12650-134H4\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwHbvsmcPeak HBVSMC Pk narrowPeak HBVSMC brain vascular smooth muscle DNaseI Peaks from ENCODE 1 40 176 255 85 215 255 170 1 0 0 regulation 1 color 176,255,85\ longLabel HBVSMC brain vascular smooth muscle DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HBVSMC Pk\ subGroups view=a_Peaks cellType=HBVSMC treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHbvsmcPeak\ wgEncodeRegDnaseUwHbvsmcWig HBVSMC Sg bigWig 0 3766.42 HBVSMC brain vascular smooth muscle DNaseI Signal from ENCODE 0 40 176 255 85 215 255 170 0 0 0 regulation 1 color 176,255,85\ longLabel HBVSMC brain vascular smooth muscle DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.34687\ shortLabel HBVSMC Sg\ subGroups cellType=HBVSMC treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHbvsmcSignal\ track wgEncodeRegDnaseUwHbvsmcWig\ type bigWig 0 3766.42\ netHprcGCA_018472575v1 HG00621.pat netAlign GCA_018472575.1 chainHprcGCA_018472575v1 HG00621.pat HG00621.alt.pat.f1_v2 (May 2021 GCA_018472575.1_HG00621.alt.pat.f1_v2) HPRC project computed Chain Nets 1 40 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG00621.pat HG00621.alt.pat.f1_v2 (May 2021 GCA_018472575.1_HG00621.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018472575.1\ parent hprcChainNetViewnet off\ priority 79\ shortLabel HG00621.pat\ subGroups view=net sample=s079 population=eas subpop=chs hap=pat\ track netHprcGCA_018472575v1\ type netAlign GCA_018472575.1 chainHprcGCA_018472575v1\ gtexCovNerveTibial Nerve Tibial bigWig Nerve Tibial 0 40 255 215 0 255 235 127 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-TML8-1626-SM-32QOO.Nerve_Tibial.RNAseq.bw\ color 255,215,0\ longLabel Nerve Tibial\ parent gtexCov\ shortLabel Nerve Tibial\ track gtexCovNerveTibial\ encTfChipPkENCFF179WDI A549 RFX5 narrowPeak Transcription Factor ChIP-seq Peaks of RFX5 in A549 from ENCODE 3 (ENCFF179WDI) 0 41 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of RFX5 in A549 from ENCODE 3 (ENCFF179WDI)\ parent encTfChipPk off\ shortLabel A549 RFX5\ subGroups cellType=A549 factor=RFX5\ track encTfChipPkENCFF179WDI\ wgEncodeRegDnaseUwAg04449Peak AG04449 Pk narrowPeak AG04449 fetal skin fibroblast DNaseI Peaks from ENCODE 1 41 152 255 85 203 255 170 1 0 0 regulation 1 color 152,255,85\ longLabel AG04449 fetal skin fibroblast DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel AG04449 Pk\ subGroups view=a_Peaks cellType=AG04449 treatment=n_a tissue=skin cancer=normal\ track wgEncodeRegDnaseUwAg04449Peak\ wgEncodeRegDnaseUwAg04449Wig AG04449 Sg bigWig 0 20132.8 AG04449 fetal skin fibroblast DNaseI Signal from ENCODE 0 41 152 255 85 203 255 170 0 0 0 regulation 1 color 152,255,85\ longLabel AG04449 fetal skin fibroblast DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.36656\ shortLabel AG04449 Sg\ subGroups cellType=AG04449 treatment=n_a tissue=skin cancer=normal\ table wgEncodeRegDnaseUwAg04449Signal\ track wgEncodeRegDnaseUwAg04449Wig\ type bigWig 0 20132.8\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_tpm_fwd AorticSmsToFgf2_05hrBr2+ bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_forward 1 41 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12748-136A3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep2%20%28LK26%29.CNhs13367.12748-136A3.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12748-136A3 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_05hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12748-136A3\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_ctss_fwd AorticSmsToFgf2_05hrBr2+ bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_forward 0 41 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12748-136A3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep2%20%28LK26%29.CNhs13367.12748-136A3.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12748-136A3 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_05hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12748-136A3\ urlLabel FANTOM5 Details:\ chainHprcGCA_018472585v1 HG00673.pat chain GCA_018472585.1 HG00673.pat HG00673.alt.pat.f1_v2 (May 2021 GCA_018472585.1_HG00673.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 41 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG00673.pat HG00673.alt.pat.f1_v2 (May 2021 GCA_018472585.1_HG00673.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018472585.1\ parent hprcChainNetViewchain off\ priority 80\ shortLabel HG00673.pat\ subGroups view=chain sample=s080 population=eas subpop=chs hap=pat\ track chainHprcGCA_018472585v1\ type chain GCA_018472585.1\ gtexCovOvary Ovary bigWig Ovary 0 41 255 182 193 255 218 224 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-ZVT2-0326-SM-5E44G.Ovary.RNAseq.bw\ color 255,182,193\ longLabel Ovary\ parent gtexCov\ shortLabel Ovary\ track gtexCovOvary\ encTfChipPkENCFF110EOX A549 RNF2 narrowPeak Transcription Factor ChIP-seq Peaks of RNF2 in A549 from ENCODE 3 (ENCFF110EOX) 0 42 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of RNF2 in A549 from ENCODE 3 (ENCFF110EOX)\ parent encTfChipPk off\ shortLabel A549 RNF2\ subGroups cellType=A549 factor=RNF2\ track encTfChipPkENCFF110EOX\ wgEncodeRegDnaseUwAg04450Peak AG04450 Pk narrowPeak AG04450 fetal lung fibroblast DNaseI Peaks from ENCODE 1 42 144 255 85 199 255 170 1 0 0 regulation 1 color 144,255,85\ longLabel AG04450 fetal lung fibroblast DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel AG04450 Pk\ subGroups view=a_Peaks cellType=AG04450 treatment=n_a tissue=lung cancer=normal\ track wgEncodeRegDnaseUwAg04450Peak\ wgEncodeRegDnaseUwAg04450Wig AG04450 Sg bigWig 0 18229.7 AG04450 fetal lung fibroblast DNaseI Signal from ENCODE 0 42 144 255 85 199 255 170 0 0 0 regulation 1 color 144,255,85\ longLabel AG04450 fetal lung fibroblast DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.37094\ shortLabel AG04450 Sg\ subGroups cellType=AG04450 treatment=n_a tissue=lung cancer=normal\ table wgEncodeRegDnaseUwAg04450Signal\ track wgEncodeRegDnaseUwAg04450Wig\ type bigWig 0 18229.7\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_tpm_rev AorticSmsToFgf2_05hrBr2- bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_reverse 1 42 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12748-136A3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep2%20%28LK26%29.CNhs13367.12748-136A3.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12748-136A3 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_05hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12748-136A3\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_ctss_rev AorticSmsToFgf2_05hrBr2- bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_reverse 0 42 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12748-136A3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep2%20%28LK26%29.CNhs13367.12748-136A3.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12748-136A3 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_05hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12748-136A3\ urlLabel FANTOM5 Details:\ netHprcGCA_018472585v1 HG00673.pat netAlign GCA_018472585.1 chainHprcGCA_018472585v1 HG00673.pat HG00673.alt.pat.f1_v2 (May 2021 GCA_018472585.1_HG00673.alt.pat.f1_v2) HPRC project computed Chain Nets 1 42 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG00673.pat HG00673.alt.pat.f1_v2 (May 2021 GCA_018472585.1_HG00673.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018472585.1\ parent hprcChainNetViewnet off\ priority 80\ shortLabel HG00673.pat\ subGroups view=net sample=s080 population=eas subpop=chs hap=pat\ track netHprcGCA_018472585v1\ type netAlign GCA_018472585.1 chainHprcGCA_018472585v1\ gtexCovPancreas Pancreas bigWig Pancreas 0 42 205 155 29 230 205 142 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1H1E6-0826-SM-9WG83.Pancreas.RNAseq.bw\ color 205,155,29\ longLabel Pancreas\ parent gtexCov\ shortLabel Pancreas\ track gtexCovPancreas\ encTfChipPkENCFF567BJI A549 SIN3A 1 narrowPeak Transcription Factor ChIP-seq Peaks of SIN3A in A549 from ENCODE 3 (ENCFF567BJI) 0 43 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of SIN3A in A549 from ENCODE 3 (ENCFF567BJI)\ parent encTfChipPk off\ shortLabel A549 SIN3A 1\ subGroups cellType=A549 factor=SIN3A\ track encTfChipPkENCFF567BJI\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_tpm_fwd AorticSmsToFgf2_05hrBr3+ bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_forward 1 43 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12846-137C2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep3%20%28LK27%29.CNhs13575.12846-137C2.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12846-137C2 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_05hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12846-137C2\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_ctss_fwd AorticSmsToFgf2_05hrBr3+ bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_forward 0 43 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12846-137C2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep3%20%28LK27%29.CNhs13575.12846-137C2.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12846-137C2 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_05hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12846-137C2\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwHahPeak HA-h Pk narrowPeak HA-h hippocampal astrocyte DNaseI Peaks from ENCODE 1 43 122 255 85 188 255 170 1 0 0 regulation 1 color 122,255,85\ longLabel HA-h hippocampal astrocyte DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HA-h Pk\ subGroups view=a_Peaks cellType=HA-h treatment=n_a tissue=brain cancer=normal\ track wgEncodeRegDnaseUwHahPeak\ wgEncodeRegDnaseUwHahWig HA-h Sg bigWig 0 10262.5 HA-h hippocampal astrocyte DNaseI Signal from ENCODE 0 43 122 255 85 188 255 170 0 0 0 regulation 1 color 122,255,85\ longLabel HA-h hippocampal astrocyte DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.38256\ shortLabel HA-h Sg\ subGroups cellType=HA-h treatment=n_a tissue=brain cancer=normal\ table wgEncodeRegDnaseUwHahSignal\ track wgEncodeRegDnaseUwHahWig\ type bigWig 0 10262.5\ chainHprcGCA_018472595v1 HG00438.pat chain GCA_018472595.1 HG00438.pat HG00438.alt.pat.f1_v2 (May 2021 GCA_018472595.1_HG00438.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 43 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG00438.pat HG00438.alt.pat.f1_v2 (May 2021 GCA_018472595.1_HG00438.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018472595.1\ parent hprcChainNetViewchain off\ priority 81\ shortLabel HG00438.pat\ subGroups view=chain sample=s081 population=eas subpop=chs hap=pat\ track chainHprcGCA_018472595v1\ type chain GCA_018472595.1\ gtexCovPituitary Pituitary bigWig Pituitary 0 43 180 238 180 217 246 217 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-Y111-2926-SM-4TT25.Pituitary.RNAseq.bw\ color 180,238,180\ longLabel Pituitary\ parent gtexCov\ shortLabel Pituitary\ track gtexCovPituitary\ encTfChipPkENCFF708HTR A549 SIN3A 2 narrowPeak Transcription Factor ChIP-seq Peaks of SIN3A in A549 from ENCODE 3 (ENCFF708HTR) 0 44 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of SIN3A in A549 from ENCODE 3 (ENCFF708HTR)\ parent encTfChipPk off\ shortLabel A549 SIN3A 2\ subGroups cellType=A549 factor=SIN3A\ track encTfChipPkENCFF708HTR\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_tpm_rev AorticSmsToFgf2_05hrBr3- bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_reverse 1 44 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12846-137C2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep3%20%28LK27%29.CNhs13575.12846-137C2.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12846-137C2 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_05hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12846-137C2\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_ctss_rev AorticSmsToFgf2_05hrBr3- bigWig Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_reverse 0 44 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12846-137C2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2005hr%2c%20biol_rep3%20%28LK27%29.CNhs13575.12846-137C2.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12846-137C2 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_05hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12846-137C2\ urlLabel FANTOM5 Details:\ netHprcGCA_018472595v1 HG00438.pat netAlign GCA_018472595.1 chainHprcGCA_018472595v1 HG00438.pat HG00438.alt.pat.f1_v2 (May 2021 GCA_018472595.1_HG00438.alt.pat.f1_v2) HPRC project computed Chain Nets 1 44 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG00438.pat HG00438.alt.pat.f1_v2 (May 2021 GCA_018472595.1_HG00438.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018472595.1\ parent hprcChainNetViewnet off\ priority 81\ shortLabel HG00438.pat\ subGroups view=net sample=s081 population=eas subpop=chs hap=pat\ track netHprcGCA_018472595v1\ type netAlign GCA_018472595.1 chainHprcGCA_018472595v1\ wgEncodeRegDnaseUwM059jPeak M059J Pk narrowPeak M059J glioblastoma cell line DNaseI Peaks from ENCODE 1 44 96 255 85 175 255 170 1 0 0 regulation 1 color 96,255,85\ longLabel M059J glioblastoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel M059J Pk\ subGroups view=a_Peaks cellType=M059J treatment=n_a tissue=brain cancer=cancer\ track wgEncodeRegDnaseUwM059jPeak\ wgEncodeRegDnaseUwM059jWig M059J Sg bigWig 0 6527.58 M059J glioblastoma cell line DNaseI Signal from ENCODE 0 44 96 255 85 175 255 170 0 0 0 regulation 1 color 96,255,85\ longLabel M059J glioblastoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.39616\ shortLabel M059J Sg\ subGroups cellType=M059J treatment=n_a tissue=brain cancer=cancer\ table wgEncodeRegDnaseUwM059jSignal\ track wgEncodeRegDnaseUwM059jWig\ type bigWig 0 6527.58\ gtexCovProstate Prostate bigWig Prostate 0 44 217 217 217 236 236 236 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-14DAR-1026-SM-73KV3.Prostate.RNAseq.bw\ color 217,217,217\ longLabel Prostate\ parent gtexCov\ shortLabel Prostate\ track gtexCovProstate\ encTfChipPkENCFF189NMX A549 SIX5 narrowPeak Transcription Factor ChIP-seq Peaks of SIX5 in A549 from ENCODE 3 (ENCFF189NMX) 0 45 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of SIX5 in A549 from ENCODE 3 (ENCFF189NMX)\ parent encTfChipPk off\ shortLabel A549 SIX5\ subGroups cellType=A549 factor=SIX5\ track encTfChipPkENCFF189NMX\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_tpm_fwd AorticSmsToFgf2_06hrBr1+ bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_forward 1 45 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12651-134H5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep1%20%28LK28%29.CNhs13348.12651-134H5.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12651-134H5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_06hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12651-134H5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_ctss_fwd AorticSmsToFgf2_06hrBr1+ bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_forward 0 45 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12651-134H5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep1%20%28LK28%29.CNhs13348.12651-134H5.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12651-134H5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_06hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12651-134H5\ urlLabel FANTOM5 Details:\ chainHprcGCA_018469405v1 HG01258.mat chain GCA_018469405.1 HG01258.mat HG01258.pri.mat.f1_v2 (May 2021 GCA_018469405.1_HG01258.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 45 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01258.mat HG01258.pri.mat.f1_v2 (May 2021 GCA_018469405.1_HG01258.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469405.1\ parent hprcChainNetViewchain off\ priority 69\ shortLabel HG01258.mat\ subGroups view=chain sample=s069 population=amr subpop=clm hap=mat\ track chainHprcGCA_018469405v1\ type chain GCA_018469405.1\ wgEncodeRegDnaseUwRpmi7951Peak RPMI-7951 Pk narrowPeak RPMI-7951 melanoma cell line DNaseI Peaks from ENCODE 1 45 85 255 90 170 255 172 1 0 0 regulation 1 color 85,255,90\ longLabel RPMI-7951 melanoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel RPMI-7951 Pk\ subGroups view=a_Peaks cellType=RPMI-7951 treatment=n_a tissue=skin cancer=cancer\ track wgEncodeRegDnaseUwRpmi7951Peak\ wgEncodeRegDnaseUwRpmi7951Wig RPMI-7951 Sg bigWig 0 7339.21 RPMI-7951 melanoma cell line DNaseI Signal from ENCODE 0 45 85 255 90 170 255 172 0 0 0 regulation 1 color 85,255,90\ longLabel RPMI-7951 melanoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.40485\ shortLabel RPMI-7951 Sg\ subGroups cellType=RPMI-7951 treatment=n_a tissue=skin cancer=cancer\ table wgEncodeRegDnaseUwRpmi7951Signal\ track wgEncodeRegDnaseUwRpmi7951Wig\ type bigWig 0 7339.21\ gtexCovSkinNotSunExposedSuprapubic Skin not sun exp bigWig Skin Not Sun Exposed Suprapubic 0 45 58 95 205 156 175 230 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1JN76-0626-SM-CKZOQ.Skin_Not_Sun_Exposed_Suprapubic.RNAseq.bw\ color 58,95,205\ longLabel Skin Not Sun Exposed Suprapubic\ parent gtexCov\ shortLabel Skin not sun exp\ track gtexCovSkinNotSunExposedSuprapubic\ encTfChipPkENCFF256LDD A549 SMC3 narrowPeak Transcription Factor ChIP-seq Peaks of SMC3 in A549 from ENCODE 3 (ENCFF256LDD) 0 46 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of SMC3 in A549 from ENCODE 3 (ENCFF256LDD)\ parent encTfChipPk off\ shortLabel A549 SMC3\ subGroups cellType=A549 factor=SMC3\ track encTfChipPkENCFF256LDD\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_tpm_rev AorticSmsToFgf2_06hrBr1- bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_reverse 1 46 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12651-134H5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep1%20%28LK28%29.CNhs13348.12651-134H5.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12651-134H5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_06hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12651-134H5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_ctss_rev AorticSmsToFgf2_06hrBr1- bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_reverse 0 46 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12651-134H5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep1%20%28LK28%29.CNhs13348.12651-134H5.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12651-134H5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_06hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12651-134H5\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwHaspPeak HA-sp Pk narrowPeak HA-sp spinal cord astrocyte DNaseI Peaks from ENCODE 1 46 85 255 124 170 255 189 1 0 0 regulation 1 color 85,255,124\ longLabel HA-sp spinal cord astrocyte DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HA-sp Pk\ subGroups view=a_Peaks cellType=HA-sp treatment=n_a tissue=spinal_cord cancer=normal\ track wgEncodeRegDnaseUwHaspPeak\ wgEncodeRegDnaseUwHaspWig HA-sp Sg bigWig 0 8189.49 HA-sp spinal cord astrocyte DNaseI Signal from ENCODE 0 46 85 255 124 170 255 189 0 0 0 regulation 1 color 85,255,124\ longLabel HA-sp spinal cord astrocyte DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.42221\ shortLabel HA-sp Sg\ subGroups cellType=HA-sp treatment=n_a tissue=spinal_cord cancer=normal\ table wgEncodeRegDnaseUwHaspSignal\ track wgEncodeRegDnaseUwHaspWig\ type bigWig 0 8189.49\ netHprcGCA_018469405v1 HG01258.mat netAlign GCA_018469405.1 chainHprcGCA_018469405v1 HG01258.mat HG01258.pri.mat.f1_v2 (May 2021 GCA_018469405.1_HG01258.pri.mat.f1_v2) HPRC project computed Chain Nets 1 46 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG01258.mat HG01258.pri.mat.f1_v2 (May 2021 GCA_018469405.1_HG01258.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469405.1\ parent hprcChainNetViewnet off\ priority 69\ shortLabel HG01258.mat\ subGroups view=net sample=s069 population=amr subpop=clm hap=mat\ track netHprcGCA_018469405v1\ type netAlign GCA_018469405.1 chainHprcGCA_018469405v1\ gtexCovSkinSunExposedLowerleg Skin sun exp bigWig Skin Sun Exposed Lower leg 0 46 30 144 255 142 199 255 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1C475-1826-SM-73KWA.Skin_Sun_Exposed_Lower_leg.RNAseq.bw\ color 30,144,255\ longLabel Skin Sun Exposed Lower leg\ parent gtexCov\ shortLabel Skin sun exp\ track gtexCovSkinSunExposedLowerleg\ encTfChipPkENCFF404OSB A549 SP1 narrowPeak Transcription Factor ChIP-seq Peaks of SP1 in A549 from ENCODE 3 (ENCFF404OSB) 0 47 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of SP1 in A549 from ENCODE 3 (ENCFF404OSB)\ parent encTfChipPk off\ shortLabel A549 SP1\ subGroups cellType=A549 factor=SP1\ track encTfChipPkENCFF404OSB\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_tpm_fwd AorticSmsToFgf2_06hrBr2+ bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_forward 1 47 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12749-136A4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep2%20%28LK29%29.CNhs13368.12749-136A4.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12749-136A4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_06hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12749-136A4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_ctss_fwd AorticSmsToFgf2_06hrBr2+ bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_forward 0 47 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12749-136A4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep2%20%28LK29%29.CNhs13368.12749-136A4.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12749-136A4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_06hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12749-136A4\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwHcfaaPeak HCFaa Pk narrowPeak HCFaa cardiac fibroblast DNaseI Peaks from ENCODE 1 47 85 255 150 170 255 202 1 0 0 regulation 1 color 85,255,150\ longLabel HCFaa cardiac fibroblast DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HCFaa Pk\ subGroups view=a_Peaks cellType=HCFaa treatment=n_a tissue=heart cancer=normal\ track wgEncodeRegDnaseUwHcfaaPeak\ wgEncodeRegDnaseUwHcfaaWig HCFaa Sg bigWig 0 3845.33 HCFaa cardiac fibroblast DNaseI Signal from ENCODE 0 47 85 255 150 170 255 202 0 0 0 regulation 1 color 85,255,150\ longLabel HCFaa cardiac fibroblast DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.43568\ shortLabel HCFaa Sg\ subGroups cellType=HCFaa treatment=n_a tissue=heart cancer=normal\ table wgEncodeRegDnaseUwHcfaaSignal\ track wgEncodeRegDnaseUwHcfaaWig\ type bigWig 0 3845.33\ chainHprcGCA_018469665v1 HG01123.mat chain GCA_018469665.1 HG01123.mat HG01123.pri.mat.f1_v2.1 (May 2021 GCA_018469665.1_HG01123.pri.mat.f1_v2.1) HPRC project computed Chained Alignments 3 47 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01123.mat HG01123.pri.mat.f1_v2.1 (May 2021 GCA_018469665.1_HG01123.pri.mat.f1_v2.1) HPRC project computed Chained Alignments\ otherDb GCA_018469665.1\ parent hprcChainNetViewchain off\ priority 70\ shortLabel HG01123.mat\ subGroups view=chain sample=s070 population=amr subpop=clm hap=mat\ track chainHprcGCA_018469665v1\ type chain GCA_018469665.1\ gtexCovSmallIntestineTerminalIleum Small Intestine bigWig Small Intestine Terminal Ileum 0 47 205 183 158 230 219 206 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1PIEJ-1526-SM-E6CP8.Small_Intestine_Terminal_Ileum.RNAseq.bw\ color 205,183,158\ longLabel Small Intestine Terminal Ileum\ parent gtexCov\ shortLabel Small Intestine\ track gtexCovSmallIntestineTerminalIleum\ encTfChipPkENCFF624DDK A549 SREBF1 narrowPeak Transcription Factor ChIP-seq Peaks of SREBF1 in A549 from ENCODE 3 (ENCFF624DDK) 0 48 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of SREBF1 in A549 from ENCODE 3 (ENCFF624DDK)\ parent encTfChipPk off\ shortLabel A549 SREBF1\ subGroups cellType=A549 factor=SREBF1\ track encTfChipPkENCFF624DDK\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_tpm_rev AorticSmsToFgf2_06hrBr2- bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_reverse 1 48 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12749-136A4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep2%20%28LK29%29.CNhs13368.12749-136A4.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12749-136A4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_06hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12749-136A4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_ctss_rev AorticSmsToFgf2_06hrBr2- bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_reverse 0 48 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12749-136A4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep2%20%28LK29%29.CNhs13368.12749-136A4.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12749-136A4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_06hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12749-136A4\ urlLabel FANTOM5 Details:\ netHprcGCA_018469665v1 HG01123.mat netAlign GCA_018469665.1 chainHprcGCA_018469665v1 HG01123.mat HG01123.pri.mat.f1_v2.1 (May 2021 GCA_018469665.1_HG01123.pri.mat.f1_v2.1) HPRC project computed Chain Nets 1 48 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG01123.mat HG01123.pri.mat.f1_v2.1 (May 2021 GCA_018469665.1_HG01123.pri.mat.f1_v2.1) HPRC project computed Chain Nets\ otherDb GCA_018469665.1\ parent hprcChainNetViewnet off\ priority 70\ shortLabel HG01123.mat\ subGroups view=net sample=s070 population=amr subpop=clm hap=mat\ track netHprcGCA_018469665v1\ type netAlign GCA_018469665.1 chainHprcGCA_018469665v1\ gtexCovSpleen Spleen bigWig Spleen 0 48 205 183 158 230 219 206 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-14PKU-0526-SM-6871A.Spleen.RNAseq.bw\ color 205,183,158\ longLabel Spleen\ parent gtexCov\ shortLabel Spleen\ track gtexCovSpleen\ wgEncodeRegDnaseUwWi384ohtam20nm72hrPeak WI-38 40HTAM Pk narrowPeak WI-38 embryonic lung fibroblast cell line (40HTAM) DNaseI Peaks from ENCODE 1 48 85 255 171 170 255 213 1 0 0 regulation 1 color 85,255,171\ longLabel WI-38 embryonic lung fibroblast cell line (40HTAM) DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel WI-38 40HTAM Pk\ subGroups view=a_Peaks cellType=WI-38 treatment=OHTAM_20nM_72hr tissue=lung cancer=normal\ track wgEncodeRegDnaseUwWi384ohtam20nm72hrPeak\ wgEncodeRegDnaseUwWi384ohtam20nm72hrWig WI-38 40HTAM Sg bigWig 0 9068.99 WI-38 embryonic lung fibroblast cell line (40HTAM) DNaseI Signal from ENCODE 0 48 85 255 171 170 255 213 0 0 0 regulation 1 color 85,255,171\ longLabel WI-38 embryonic lung fibroblast cell line (40HTAM) DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.44843\ shortLabel WI-38 40HTAM Sg\ subGroups cellType=WI-38 treatment=OHTAM_20nM_72hr tissue=lung cancer=normal\ table wgEncodeRegDnaseUwWi384ohtam20nm72hrSignal\ track wgEncodeRegDnaseUwWi384ohtam20nm72hrWig\ type bigWig 0 9068.99\ encTfChipPkENCFF483YCC A549 SREBF2 narrowPeak Transcription Factor ChIP-seq Peaks of SREBF2 in A549 from ENCODE 3 (ENCFF483YCC) 0 49 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of SREBF2 in A549 from ENCODE 3 (ENCFF483YCC)\ parent encTfChipPk off\ shortLabel A549 SREBF2\ subGroups cellType=A549 factor=SREBF2\ track encTfChipPkENCFF483YCC\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_tpm_fwd AorticSmsToFgf2_06hrBr3+ bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_forward 1 49 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12847-137C3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep3%20%28LK30%29.CNhs13576.12847-137C3.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12847-137C3 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_06hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12847-137C3\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_ctss_fwd AorticSmsToFgf2_06hrBr3+ bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_forward 0 49 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12847-137C3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep3%20%28LK30%29.CNhs13576.12847-137C3.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12847-137C3 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_06hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=forward\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12847-137C3\ urlLabel FANTOM5 Details:\ chainHprcGCA_018469685v1 HG01361.mat chain GCA_018469685.1 HG01361.mat HG01361.pri.mat.f1_v2 (May 2021 GCA_018469685.1_HG01361.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 49 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01361.mat HG01361.pri.mat.f1_v2 (May 2021 GCA_018469685.1_HG01361.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469685.1\ parent hprcChainNetViewchain off\ priority 72\ shortLabel HG01361.mat\ subGroups view=chain sample=s072 population=amr subpop=clm hap=mat\ track chainHprcGCA_018469685v1\ type chain GCA_018469685.1\ wgEncodeRegDnaseUwNhdfadPeak NHDF-Ad Pk narrowPeak NHDF-Ad dermal fibroblast DNaseI Peaks from ENCODE 1 49 85 255 180 170 255 217 1 0 0 regulation 1 color 85,255,180\ longLabel NHDF-Ad dermal fibroblast DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel NHDF-Ad Pk\ subGroups view=a_Peaks cellType=NHDF-Ad treatment=n_a tissue=skin cancer=normal\ track wgEncodeRegDnaseUwNhdfadPeak\ wgEncodeRegDnaseUwNhdfadWig NHDF-Ad Sg bigWig 0 2200.64 NHDF-Ad dermal fibroblast DNaseI Signal from ENCODE 0 49 85 255 180 170 255 217 0 0 0 regulation 1 color 85,255,180\ longLabel NHDF-Ad dermal fibroblast DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.46595\ shortLabel NHDF-Ad Sg\ subGroups cellType=NHDF-Ad treatment=n_a tissue=skin cancer=normal\ table wgEncodeRegDnaseUwNhdfadSignal\ track wgEncodeRegDnaseUwNhdfadWig\ type bigWig 0 2200.64\ gtexCovStomach Stomach bigWig Stomach 0 49 255 211 155 255 233 205 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-NFK9-1526-SM-3LK7B.Stomach.RNAseq.bw\ color 255,211,155\ longLabel Stomach\ parent gtexCov\ shortLabel Stomach\ track gtexCovStomach\ encTfChipPkENCFF886KDK A549 TAF1 narrowPeak Transcription Factor ChIP-seq Peaks of TAF1 in A549 from ENCODE 3 (ENCFF886KDK) 0 50 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of TAF1 in A549 from ENCODE 3 (ENCFF886KDK)\ parent encTfChipPk off\ shortLabel A549 TAF1\ subGroups cellType=A549 factor=TAF1\ track encTfChipPkENCFF886KDK\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_tpm_rev AorticSmsToFgf2_06hrBr3- bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_reverse 1 50 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12847-137C3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep3%20%28LK30%29.CNhs13576.12847-137C3.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12847-137C3 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToFgf2_06hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12847-137C3\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_ctss_rev AorticSmsToFgf2_06hrBr3- bigWig Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_reverse 0 50 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12847-137C3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20FGF2%2c%2006hr%2c%20biol_rep3%20%28LK30%29.CNhs13576.12847-137C3.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12847-137C3 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToFgf2_06hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_FGF2 strand=reverse\ track AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12847-137C3\ urlLabel FANTOM5 Details:\ netHprcGCA_018469685v1 HG01361.mat netAlign GCA_018469685.1 chainHprcGCA_018469685v1 HG01361.mat HG01361.pri.mat.f1_v2 (May 2021 GCA_018469685.1_HG01361.pri.mat.f1_v2) HPRC project computed Chain Nets 1 50 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG01361.mat HG01361.pri.mat.f1_v2 (May 2021 GCA_018469685.1_HG01361.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469685.1\ parent hprcChainNetViewnet off\ priority 72\ shortLabel HG01361.mat\ subGroups view=net sample=s072 population=amr subpop=clm hap=mat\ track netHprcGCA_018469685v1\ type netAlign GCA_018469685.1 chainHprcGCA_018469685v1\ wgEncodeRegDnaseUwHsmmPeak HSMM Pk narrowPeak HSMM skeletal muscle myoblast DNaseI Peaks from ENCODE 1 50 85 255 190 170 255 222 1 0 0 regulation 1 color 85,255,190\ longLabel HSMM skeletal muscle myoblast DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak on\ shortLabel HSMM Pk\ subGroups view=a_Peaks cellType=HSMM treatment=n_a tissue=muscle cancer=normal\ track wgEncodeRegDnaseUwHsmmPeak\ wgEncodeRegDnaseUwHsmmWig HSMM Sg bigWig 0 14177.3 HSMM skeletal muscle myoblast DNaseI Signal from ENCODE 0 50 85 255 190 170 255 222 0 0 0 regulation 1 color 85,255,190\ longLabel HSMM skeletal muscle myoblast DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig on\ priority 1.48469\ shortLabel HSMM Sg\ subGroups cellType=HSMM treatment=n_a tissue=muscle cancer=normal\ table wgEncodeRegDnaseUwHsmmSignal\ track wgEncodeRegDnaseUwHsmmWig\ type bigWig 0 14177.3\ gtexCovTestis Testis bigWig Testis 0 50 166 166 166 210 210 210 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1JKYN-1026-SM-CGQG4.Testis.RNAseq.bw\ color 166,166,166\ longLabel Testis\ parent gtexCov\ shortLabel Testis\ track gtexCovTestis\ encTfChipPkENCFF228CDD A549 TCF12 narrowPeak Transcription Factor ChIP-seq Peaks of TCF12 in A549 from ENCODE 3 (ENCFF228CDD) 0 51 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of TCF12 in A549 from ENCODE 3 (ENCFF228CDD)\ parent encTfChipPk off\ shortLabel A549 TCF12\ subGroups cellType=A549 factor=TCF12\ track encTfChipPkENCFF228CDD\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_tpm_fwd AorticSmsToIL1b_00hr00minBr1+ bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_forward 1 51 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12652-134H6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep1%20%28LK31%29.CNhs13349.12652-134H6.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12652-134H6 sequence_tech=hCAGE\ parent TSS_activity_TPM on\ shortLabel AorticSmsToIL1b_00hr00minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12652-134H6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_ctss_fwd AorticSmsToIL1b_00hr00minBr1+ bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_forward 0 51 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12652-134H6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep1%20%28LK31%29.CNhs13349.12652-134H6.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12652-134H6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr00minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12652-134H6\ urlLabel FANTOM5 Details:\ chainHprcGCA_018469865v1 HG01358.mat chain GCA_018469865.1 HG01358.mat HG01358.pri.mat.f1_v2.1 (May 2021 GCA_018469865.1_HG01358.pri.mat.f1_v2.1) HPRC project computed Chained Alignments 3 51 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01358.mat HG01358.pri.mat.f1_v2.1 (May 2021 GCA_018469865.1_HG01358.pri.mat.f1_v2.1) HPRC project computed Chained Alignments\ otherDb GCA_018469865.1\ parent hprcChainNetViewchain off\ priority 75\ shortLabel HG01358.mat\ subGroups view=chain sample=s075 population=amr subpop=clm hap=mat\ track chainHprcGCA_018469865v1\ type chain GCA_018469865.1\ wgEncodeRegDnaseUwLhcnm2Peak LHCN-M2 Pk narrowPeak LHCN-M2 skeletal myoblast DNaseI Peaks from ENCODE 1 51 85 255 193 170 255 224 1 0 0 regulation 1 color 85,255,193\ longLabel LHCN-M2 skeletal myoblast DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel LHCN-M2 Pk\ subGroups view=a_Peaks cellType=LHCN-M2 treatment=n_a tissue=muscle cancer=unknown\ track wgEncodeRegDnaseUwLhcnm2Peak\ wgEncodeRegDnaseUwLhcnm2Wig LHCN-M2 Sg bigWig 0 16877.8 LHCN-M2 skeletal myoblast DNaseI Signal from ENCODE 0 51 85 255 193 170 255 224 0 0 0 regulation 1 color 85,255,193\ longLabel LHCN-M2 skeletal myoblast DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.48937\ shortLabel LHCN-M2 Sg\ subGroups cellType=LHCN-M2 treatment=n_a tissue=muscle cancer=unknown\ table wgEncodeRegDnaseUwLhcnm2Signal\ track wgEncodeRegDnaseUwLhcnm2Wig\ type bigWig 0 16877.8\ gtexCovThyroid Thyroid bigWig Thyroid 0 51 0 139 69 127 197 162 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1HSGN-0726-SM-A9G2F.Thyroid.RNAseq.bw\ color 0, 139, 69\ longLabel Thyroid\ parent gtexCov\ shortLabel Thyroid\ track gtexCovThyroid\ encTfChipPkENCFF593EOW A549 USF2 narrowPeak Transcription Factor ChIP-seq Peaks of USF2 in A549 from ENCODE 3 (ENCFF593EOW) 0 52 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of USF2 in A549 from ENCODE 3 (ENCFF593EOW)\ parent encTfChipPk off\ shortLabel A549 USF2\ subGroups cellType=A549 factor=USF2\ track encTfChipPkENCFF593EOW\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_tpm_rev AorticSmsToIL1b_00hr00minBr1- bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_reverse 1 52 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12652-134H6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep1%20%28LK31%29.CNhs13349.12652-134H6.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12652-134H6 sequence_tech=hCAGE\ parent TSS_activity_TPM on\ shortLabel AorticSmsToIL1b_00hr00minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12652-134H6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_ctss_rev AorticSmsToIL1b_00hr00minBr1- bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_reverse 0 52 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12652-134H6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep1%20%28LK31%29.CNhs13349.12652-134H6.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12652-134H6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr00minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12652-134H6\ urlLabel FANTOM5 Details:\ netHprcGCA_018469865v1 HG01358.mat netAlign GCA_018469865.1 chainHprcGCA_018469865v1 HG01358.mat HG01358.pri.mat.f1_v2.1 (May 2021 GCA_018469865.1_HG01358.pri.mat.f1_v2.1) HPRC project computed Chain Nets 1 52 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG01358.mat HG01358.pri.mat.f1_v2.1 (May 2021 GCA_018469865.1_HG01358.pri.mat.f1_v2.1) HPRC project computed Chain Nets\ otherDb GCA_018469865.1\ parent hprcChainNetViewnet off\ priority 75\ shortLabel HG01358.mat\ subGroups view=net sample=s075 population=amr subpop=clm hap=mat\ track netHprcGCA_018469865v1\ type netAlign GCA_018469865.1 chainHprcGCA_018469865v1\ wgEncodeRegDnaseUwLhcnm2Diff4dPeak LHCN-M2 diff4d Pk narrowPeak LHCN-M2 skeletal myoblast (diff 4d) DNaseI Peaks from ENCODE 1 52 85 255 198 170 255 226 1 0 0 regulation 1 color 85,255,198\ longLabel LHCN-M2 skeletal myoblast (diff 4d) DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel LHCN-M2 diff4d Pk\ subGroups view=a_Peaks cellType=LHCN-M2 treatment=DIFF_4d tissue=muscle cancer=unknown\ track wgEncodeRegDnaseUwLhcnm2Diff4dPeak\ wgEncodeRegDnaseUwLhcnm2Diff4dWig LHCN-M2 diff4d Sg bigWig 0 44051.9 LHCN-M2 skeletal myoblast (diff 4d) DNaseI Signal from ENCODE 0 52 85 255 198 170 255 226 0 0 0 regulation 1 color 85,255,198\ longLabel LHCN-M2 skeletal myoblast (diff 4d) DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.49766\ shortLabel LHCN-M2 diff4d Sg\ subGroups cellType=LHCN-M2 treatment=DIFF_4d tissue=muscle cancer=unknown\ table wgEncodeRegDnaseUwLhcnm2Diff4dSignal\ track wgEncodeRegDnaseUwLhcnm2Diff4dWig\ type bigWig 0 44051.9\ gtexCovUterus Uterus bigWig Uterus 0 52 238 213 210 246 234 232 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1MA7W-1526-SM-DHXKS.Uterus.RNAseq.bw\ color 238,213,210\ longLabel Uterus\ parent gtexCov\ shortLabel Uterus\ track gtexCovUterus\ encTfChipPkENCFF613DTQ A549 YY1 narrowPeak Transcription Factor ChIP-seq Peaks of YY1 in A549 from ENCODE 3 (ENCFF613DTQ) 0 53 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of YY1 in A549 from ENCODE 3 (ENCFF613DTQ)\ parent encTfChipPk off\ shortLabel A549 YY1\ subGroups cellType=A549 factor=YY1\ track encTfChipPkENCFF613DTQ\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_tpm_fwd AorticSmsToIL1b_00hr00minBr2+ bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_forward 1 53 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12750-136A5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep2%20%28LK32%29.CNhs13369.12750-136A5.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12750-136A5 sequence_tech=hCAGE\ parent TSS_activity_TPM on\ shortLabel AorticSmsToIL1b_00hr00minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12750-136A5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_ctss_fwd AorticSmsToIL1b_00hr00minBr2+ bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_forward 0 53 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12750-136A5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep2%20%28LK32%29.CNhs13369.12750-136A5.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12750-136A5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr00minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12750-136A5\ urlLabel FANTOM5 Details:\ chainHprcGCA_018469675v1 HG01258.pat chain GCA_018469675.1 HG01258.pat HG01258.alt.pat.f1_v2 (May 2021 GCA_018469675.1_HG01258.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 53 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01258.pat HG01258.alt.pat.f1_v2 (May 2021 GCA_018469675.1_HG01258.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469675.1\ parent hprcChainNetViewchain off\ priority 71\ shortLabel HG01258.pat\ subGroups view=chain sample=s071 population=amr subpop=clm hap=pat\ track chainHprcGCA_018469675v1\ type chain GCA_018469675.1\ wgEncodeRegDnaseUwHsmmtubePeak HSMMtube Pk narrowPeak HSMMtube skeletal muscle myotube DNaseI Peaks from ENCODE 1 53 85 255 204 170 255 229 1 0 0 regulation 1 color 85,255,204\ longLabel HSMMtube skeletal muscle myotube DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HSMMtube Pk\ subGroups view=a_Peaks cellType=HSMMtube treatment=n_a tissue=muscle cancer=normal\ track wgEncodeRegDnaseUwHsmmtubePeak\ wgEncodeRegDnaseUwHsmmtubeWig HSMMtube Sg bigWig 0 14719.7 HSMMtube skeletal muscle myotube DNaseI Signal from ENCODE 0 53 85 255 204 170 255 229 0 0 0 regulation 1 color 85,255,204\ longLabel HSMMtube skeletal muscle myotube DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.50509\ shortLabel HSMMtube Sg\ subGroups cellType=HSMMtube treatment=n_a tissue=muscle cancer=normal\ table wgEncodeRegDnaseUwHsmmtubeSignal\ track wgEncodeRegDnaseUwHsmmtubeWig\ type bigWig 0 14719.7\ gtexCovVagina Vagina bigWig Vagina 0 53 238 213 210 246 234 232 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1IDJU-1026-SM-AHZ2U.Vagina.RNAseq.bw\ color 238,213,210\ longLabel Vagina\ parent gtexCov\ shortLabel Vagina\ track gtexCovVagina\ encTfChipPkENCFF593ZJA A549 ZBTB33 narrowPeak Transcription Factor ChIP-seq Peaks of ZBTB33 in A549 from ENCODE 3 (ENCFF593ZJA) 0 54 254 93 85 254 174 170 0 0 0 regulation 1 color 254,93,85\ longLabel Transcription Factor ChIP-seq Peaks of ZBTB33 in A549 from ENCODE 3 (ENCFF593ZJA)\ parent encTfChipPk off\ shortLabel A549 ZBTB33\ subGroups cellType=A549 factor=ZBTB33\ track encTfChipPkENCFF593ZJA\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_tpm_rev AorticSmsToIL1b_00hr00minBr2- bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_reverse 1 54 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12750-136A5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep2%20%28LK32%29.CNhs13369.12750-136A5.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12750-136A5 sequence_tech=hCAGE\ parent TSS_activity_TPM on\ shortLabel AorticSmsToIL1b_00hr00minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12750-136A5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_ctss_rev AorticSmsToIL1b_00hr00minBr2- bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_reverse 0 54 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12750-136A5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep2%20%28LK32%29.CNhs13369.12750-136A5.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12750-136A5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr00minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12750-136A5\ urlLabel FANTOM5 Details:\ netHprcGCA_018469675v1 HG01258.pat netAlign GCA_018469675.1 chainHprcGCA_018469675v1 HG01258.pat HG01258.alt.pat.f1_v2 (May 2021 GCA_018469675.1_HG01258.alt.pat.f1_v2) HPRC project computed Chain Nets 1 54 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG01258.pat HG01258.alt.pat.f1_v2 (May 2021 GCA_018469675.1_HG01258.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469675.1\ parent hprcChainNetViewnet off\ priority 71\ shortLabel HG01258.pat\ subGroups view=net sample=s071 population=amr subpop=clm hap=pat\ track netHprcGCA_018469675v1\ type netAlign GCA_018469675.1 chainHprcGCA_018469675v1\ wgEncodeRegDnaseUwHuvecPeak HUVEC Pk narrowPeak HUVEC umbilical vein endothelial cell DNaseI Peaks from ENCODE 1 54 85 255 215 170 255 235 1 0 0 regulation 1 color 85,255,215\ longLabel HUVEC umbilical vein endothelial cell DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak on\ shortLabel HUVEC Pk\ subGroups view=a_Peaks cellType=HUVEC treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHuvecPeak\ wgEncodeRegDnaseUwHuvecWig HUVEC Sg bigWig 0 6744.03 HUVEC umbilical vein endothelial cell DNaseI Signal from ENCODE 0 54 85 255 215 170 255 235 0 0 0 regulation 1 color 85,255,215\ longLabel HUVEC umbilical vein endothelial cell DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig on\ priority 1.52185\ shortLabel HUVEC Sg\ subGroups cellType=HUVEC treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHuvecSignal\ track wgEncodeRegDnaseUwHuvecWig\ type bigWig 0 6744.03\ gtexCovWholeBlood Whole Blood bigWig Whole Blood 0 54 255 0 255 255 127 255 0 0 0 expression 0 bigDataUrl /gbdb/hg38/gtex/cov/GTEX-1LG7Z-0005-SM-DKPQ6.Whole_Blood.RNAseq.bw\ color 255,0,255\ longLabel Whole Blood\ parent gtexCov\ shortLabel Whole Blood\ track gtexCovWholeBlood\ encTfChipPkENCFF695QMG A673 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in A673 from ENCODE 3 (ENCFF695QMG) 0 55 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in A673 from ENCODE 3 (ENCFF695QMG)\ parent encTfChipPk off\ shortLabel A673 CTCF\ subGroups cellType=A673 factor=CTCF\ track encTfChipPkENCFF695QMG\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_tpm_fwd AorticSmsToIL1b_00hr00minBr3+ bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_forward 1 55 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12848-137C4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep3%20%28LK33%29.CNhs13577.12848-137C4.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12848-137C4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr00minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12848-137C4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_ctss_fwd AorticSmsToIL1b_00hr00minBr3+ bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_forward 0 55 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12848-137C4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep3%20%28LK33%29.CNhs13577.12848-137C4.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12848-137C4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr00minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12848-137C4\ urlLabel FANTOM5 Details:\ chainHprcGCA_018469695v1 HG01123.pat chain GCA_018469695.1 HG01123.pat HG01123.alt.pat.f1_v2.1 (May 2021 GCA_018469695.1_HG01123.alt.pat.f1_v2.1) HPRC project computed Chained Alignments 3 55 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01123.pat HG01123.alt.pat.f1_v2.1 (May 2021 GCA_018469695.1_HG01123.alt.pat.f1_v2.1) HPRC project computed Chained Alignments\ otherDb GCA_018469695.1\ parent hprcChainNetViewchain off\ priority 73\ shortLabel HG01123.pat\ subGroups view=chain sample=s073 population=amr subpop=clm hap=pat\ track chainHprcGCA_018469695v1\ type chain GCA_018469695.1\ wgEncodeRegDnaseUwHmveclblPeak HMVEC-LBl Pk narrowPeak HMVEC-LBl lung microvascular epithelium. blood DNaseI Peaks from ENCODE 1 55 85 255 220 170 255 237 1 0 0 regulation 1 color 85,255,220\ longLabel HMVEC-LBl lung microvascular epithelium. blood DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMVEC-LBl Pk\ subGroups view=a_Peaks cellType=HMVEC-LBl treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHmveclblPeak\ wgEncodeRegDnaseUwHmveclblWig HMVEC-LBl Sg bigWig 0 2898.86 HMVEC-LBl lung microvascular epithelium. blood DNaseI Signal from ENCODE 0 55 85 255 220 170 255 237 0 0 0 regulation 1 color 85,255,220\ longLabel HMVEC-LBl lung microvascular epithelium. blood DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.52972\ shortLabel HMVEC-LBl Sg\ subGroups cellType=HMVEC-LBl treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHmveclblSignal\ track wgEncodeRegDnaseUwHmveclblWig\ type bigWig 0 2898.86\ encTfChipPkENCFF807XMX A673 EZH2 narrowPeak Transcription Factor ChIP-seq Peaks of EZH2 in A673 from ENCODE 3 (ENCFF807XMX) 0 56 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of EZH2 in A673 from ENCODE 3 (ENCFF807XMX)\ parent encTfChipPk off\ shortLabel A673 EZH2\ subGroups cellType=A673 factor=EZH2\ track encTfChipPkENCFF807XMX\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_tpm_rev AorticSmsToIL1b_00hr00minBr3- bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_reverse 1 56 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12848-137C4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep3%20%28LK33%29.CNhs13577.12848-137C4.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12848-137C4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr00minBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12848-137C4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_ctss_rev AorticSmsToIL1b_00hr00minBr3- bigWig Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_reverse 0 56 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12848-137C4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr00min%2c%20biol_rep3%20%28LK33%29.CNhs13577.12848-137C4.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12848-137C4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr00minBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12848-137C4\ urlLabel FANTOM5 Details:\ netHprcGCA_018469695v1 HG01123.pat netAlign GCA_018469695.1 chainHprcGCA_018469695v1 HG01123.pat HG01123.alt.pat.f1_v2.1 (May 2021 GCA_018469695.1_HG01123.alt.pat.f1_v2.1) HPRC project computed Chain Nets 1 56 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG01123.pat HG01123.alt.pat.f1_v2.1 (May 2021 GCA_018469695.1_HG01123.alt.pat.f1_v2.1) HPRC project computed Chain Nets\ otherDb GCA_018469695.1\ parent hprcChainNetViewnet off\ priority 73\ shortLabel HG01123.pat\ subGroups view=net sample=s073 population=amr subpop=clm hap=pat\ track netHprcGCA_018469695v1\ type netAlign GCA_018469695.1 chainHprcGCA_018469695v1\ wgEncodeRegDnaseUwHmvecdbladPeak HMVEC-dBl-Ad Pk narrowPeak HMVEC-dBl-Ad dermal MV endothelial cell, blood DNaseI Peaks from ENCODE 1 56 85 255 224 170 255 239 1 0 0 regulation 1 color 85,255,224\ longLabel HMVEC-dBl-Ad dermal MV endothelial cell, blood DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMVEC-dBl-Ad Pk\ subGroups view=a_Peaks cellType=HMVEC-dBl-Ad treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHmvecdbladPeak\ wgEncodeRegDnaseUwHmvecdbladWig HMVEC-dBl-Ad Sg bigWig 0 6571.28 HMVEC-dBl-Ad dermal MV endothelial cell, blood DNaseI Signal from ENCODE 0 56 85 255 224 170 255 239 0 0 0 regulation 1 color 85,255,224\ longLabel HMVEC-dBl-Ad dermal MV endothelial cell, blood DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.53388\ shortLabel HMVEC-dBl-Ad Sg\ subGroups cellType=HMVEC-dBl-Ad treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHmvecdbladSignal\ track wgEncodeRegDnaseUwHmvecdbladWig\ type bigWig 0 6571.28\ encTfChipPkENCFF652LEH AG04449 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in AG04449 from ENCODE 3 (ENCFF652LEH) 0 57 152 255 85 203 255 170 0 0 0 regulation 1 color 152,255,85\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in AG04449 from ENCODE 3 (ENCFF652LEH)\ parent encTfChipPk off\ shortLabel AG04449 CTCF\ subGroups cellType=AG04449 factor=CTCF\ track encTfChipPkENCFF652LEH\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_tpm_fwd AorticSmsToIL1b_00hr15minBr1+ bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_forward 1 57 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12653-134H7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep1%20%28LK34%29.CNhs13350.12653-134H7.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12653-134H7 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr15minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12653-134H7\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_ctss_fwd AorticSmsToIL1b_00hr15minBr1+ bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_forward 0 57 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12653-134H7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep1%20%28LK34%29.CNhs13350.12653-134H7.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12653-134H7 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr15minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12653-134H7\ urlLabel FANTOM5 Details:\ chainHprcGCA_018469705v1 HG01361.pat chain GCA_018469705.1 HG01361.pat HG01361.alt.pat.f1_v2 (May 2021 GCA_018469705.1_HG01361.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 57 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01361.pat HG01361.alt.pat.f1_v2 (May 2021 GCA_018469705.1_HG01361.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469705.1\ parent hprcChainNetViewchain off\ priority 74\ shortLabel HG01361.pat\ subGroups view=chain sample=s074 population=amr subpop=clm hap=pat\ track chainHprcGCA_018469705v1\ type chain GCA_018469705.1\ wgEncodeRegDnaseUwHmvecdlyneoPeak HMVEC-dLy-Neo Pk narrowPeak HMVEC-dLy-Neo dermal MV endothelial cell, neonate lymph DNaseI Peaks from ENCODE 1 57 85 255 226 170 255 240 1 0 0 regulation 1 color 85,255,226\ longLabel HMVEC-dLy-Neo dermal MV endothelial cell, neonate lymph DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMVEC-dLy-Neo Pk\ subGroups view=a_Peaks cellType=HMVEC-dLy-Neo treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHmvecdlyneoPeak\ wgEncodeRegDnaseUwHmvecdlyneoWig HMVEC-dLy-Neo Sg bigWig 0 9237.62 HMVEC-dLy-Neo dermal MV endo cell, neonate lymph DNaseI Signal from ENCODE 0 57 85 255 226 170 255 240 0 0 0 regulation 1 color 85,255,226\ longLabel HMVEC-dLy-Neo dermal MV endo cell, neonate lymph DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.53734\ shortLabel HMVEC-dLy-Neo Sg\ subGroups cellType=HMVEC-dLy-Neo treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHmvecdlyneoSignal\ track wgEncodeRegDnaseUwHmvecdlyneoWig\ type bigWig 0 9237.62\ encTfChipPkENCFF788LNG AG04450 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in AG04450 from ENCODE 3 (ENCFF788LNG) 0 58 144 255 85 199 255 170 0 0 0 regulation 1 color 144,255,85\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in AG04450 from ENCODE 3 (ENCFF788LNG)\ parent encTfChipPk off\ shortLabel AG04450 CTCF\ subGroups cellType=AG04450 factor=CTCF\ track encTfChipPkENCFF788LNG\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_tpm_rev AorticSmsToIL1b_00hr15minBr1- bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_reverse 1 58 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12653-134H7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep1%20%28LK34%29.CNhs13350.12653-134H7.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12653-134H7 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr15minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12653-134H7\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_ctss_rev AorticSmsToIL1b_00hr15minBr1- bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_reverse 0 58 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12653-134H7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep1%20%28LK34%29.CNhs13350.12653-134H7.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12653-134H7 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr15minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12653-134H7\ urlLabel FANTOM5 Details:\ netHprcGCA_018469705v1 HG01361.pat netAlign GCA_018469705.1 chainHprcGCA_018469705v1 HG01361.pat HG01361.alt.pat.f1_v2 (May 2021 GCA_018469705.1_HG01361.alt.pat.f1_v2) HPRC project computed Chain Nets 1 58 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG01361.pat HG01361.alt.pat.f1_v2 (May 2021 GCA_018469705.1_HG01361.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469705.1\ parent hprcChainNetViewnet off\ priority 74\ shortLabel HG01361.pat\ subGroups view=net sample=s074 population=amr subpop=clm hap=pat\ track netHprcGCA_018469705v1\ type netAlign GCA_018469705.1 chainHprcGCA_018469705v1\ wgEncodeRegDnaseUwHmvecdblneoPeak HMVEC-dBl-Neo Pk narrowPeak HMVEC-dBl-Neo dermal MV endothelial cell, neonate blood DNaseI Peaks from ENCODE 1 58 85 255 229 170 255 242 1 0 0 regulation 1 color 85,255,229\ longLabel HMVEC-dBl-Neo dermal MV endothelial cell, neonate blood DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMVEC-dBl-Neo Pk\ subGroups view=a_Peaks cellType=HMVEC-dBl-Neo treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHmvecdblneoPeak\ wgEncodeRegDnaseUwHmvecdblneoWig HMVEC-dBl-Neo Sg bigWig 0 6275.08 HMVEC-dBl-Neo dermal MV endo cell, neonate blood DNaseI Signal from ENCODE 0 58 85 255 229 170 255 242 0 0 0 regulation 1 color 85,255,229\ longLabel HMVEC-dBl-Neo dermal MV endo cell, neonate blood DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.54191\ shortLabel HMVEC-dBl-Neo Sg\ subGroups cellType=HMVEC-dBl-Neo treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHmvecdblneoSignal\ track wgEncodeRegDnaseUwHmvecdblneoWig\ type bigWig 0 6275.08\ encTfChipPkENCFF826NCK AG09309 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in AG09309 from ENCODE 3 (ENCFF826NCK) 0 59 255 186 85 255 220 170 0 0 0 regulation 1 color 255,186,85\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in AG09309 from ENCODE 3 (ENCFF826NCK)\ parent encTfChipPk off\ shortLabel AG09309 CTCF\ subGroups cellType=AG09309 factor=CTCF\ track encTfChipPkENCFF826NCK\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_tpm_fwd AorticSmsToIL1b_00hr15minBr2+ bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_forward 1 59 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12751-136A6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep2%20%28LK35%29.CNhs13370.12751-136A6.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12751-136A6 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr15minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12751-136A6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_ctss_fwd AorticSmsToIL1b_00hr15minBr2+ bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_forward 0 59 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12751-136A6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep2%20%28LK35%29.CNhs13370.12751-136A6.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12751-136A6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr15minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12751-136A6\ urlLabel FANTOM5 Details:\ chainHprcGCA_018469965v1 HG01358.pat chain GCA_018469965.1 HG01358.pat HG01358.alt.pat.f1_v2.1 (May 2021 GCA_018469965.1_HG01358.alt.pat.f1_v2.1) HPRC project computed Chained Alignments 3 59 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG01358.pat HG01358.alt.pat.f1_v2.1 (May 2021 GCA_018469965.1_HG01358.alt.pat.f1_v2.1) HPRC project computed Chained Alignments\ otherDb GCA_018469965.1\ parent hprcChainNetViewchain off\ priority 76\ shortLabel HG01358.pat\ subGroups view=chain sample=s076 population=amr subpop=clm hap=pat\ track chainHprcGCA_018469965v1\ type chain GCA_018469965.1\ wgEncodeRegDnaseUwHrgecPeak HRGEC Pk narrowPeak HRGEC renal glomerular endothelial cell DNaseI Peaks from ENCODE 1 59 85 255 232 170 255 243 1 0 0 regulation 1 color 85,255,232\ longLabel HRGEC renal glomerular endothelial cell DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HRGEC Pk\ subGroups view=a_Peaks cellType=HRGEC treatment=n_a tissue=kidney cancer=normal\ track wgEncodeRegDnaseUwHrgecPeak\ wgEncodeRegDnaseUwHrgecWig HRGEC Sg bigWig 0 7095.64 HRGEC renal glomerular endothelial cell DNaseI Signal from ENCODE 0 59 85 255 232 170 255 243 0 0 0 regulation 1 color 85,255,232\ longLabel HRGEC renal glomerular endothelial cell DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.54737\ shortLabel HRGEC Sg\ subGroups cellType=HRGEC treatment=n_a tissue=kidney cancer=normal\ table wgEncodeRegDnaseUwHrgecSignal\ track wgEncodeRegDnaseUwHrgecWig\ type bigWig 0 7095.64\ encTfChipPkENCFF119XBW AG09319 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in AG09319 from ENCODE 3 (ENCFF119XBW) 0 60 255 221 85 255 238 170 0 0 0 regulation 1 color 255,221,85\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in AG09319 from ENCODE 3 (ENCFF119XBW)\ parent encTfChipPk off\ shortLabel AG09319 CTCF\ subGroups cellType=AG09319 factor=CTCF\ track encTfChipPkENCFF119XBW\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_tpm_rev AorticSmsToIL1b_00hr15minBr2- bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_reverse 1 60 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12751-136A6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep2%20%28LK35%29.CNhs13370.12751-136A6.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12751-136A6 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr15minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12751-136A6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_ctss_rev AorticSmsToIL1b_00hr15minBr2- bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_reverse 0 60 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12751-136A6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep2%20%28LK35%29.CNhs13370.12751-136A6.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12751-136A6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr15minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12751-136A6\ urlLabel FANTOM5 Details:\ netHprcGCA_018469965v1 HG01358.pat netAlign GCA_018469965.1 chainHprcGCA_018469965v1 HG01358.pat HG01358.alt.pat.f1_v2.1 (May 2021 GCA_018469965.1_HG01358.alt.pat.f1_v2.1) HPRC project computed Chain Nets 1 60 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG01358.pat HG01358.alt.pat.f1_v2.1 (May 2021 GCA_018469965.1_HG01358.alt.pat.f1_v2.1) HPRC project computed Chain Nets\ otherDb GCA_018469965.1\ parent hprcChainNetViewnet off\ priority 76\ shortLabel HG01358.pat\ subGroups view=net sample=s076 population=amr subpop=clm hap=pat\ track netHprcGCA_018469965v1\ type netAlign GCA_018469965.1 chainHprcGCA_018469965v1\ wgEncodeRegDnaseUwHmvecllyPeak HMVEC-LLy Pk narrowPeak HMVEC-LLy lung microvascular endothelial cell, lymph DNaseI Peaks from ENCODE 1 60 85 255 243 170 255 249 1 0 0 regulation 1 color 85,255,243\ longLabel HMVEC-LLy lung microvascular endothelial cell, lymph DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMVEC-LLy Pk\ subGroups view=a_Peaks cellType=HMVEC-LLy treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHmvecllyPeak\ wgEncodeRegDnaseUwHmvecllyWig HMVEC-LLy Sg bigWig 0 21274 HMVEC-LLy lung microvascular endothelial cell, lymph DNaseI Signal from ENCODE 0 60 85 255 243 170 255 249 0 0 0 regulation 1 color 85,255,243\ longLabel HMVEC-LLy lung microvascular endothelial cell, lymph DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.56304\ shortLabel HMVEC-LLy Sg\ subGroups cellType=HMVEC-LLy treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHmvecllySignal\ track wgEncodeRegDnaseUwHmvecllyWig\ type bigWig 0 21274\ encTfChipPkENCFF100IYW AG10803 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in AG10803 from ENCODE 3 (ENCFF100IYW) 0 61 220 255 85 237 255 170 0 0 0 regulation 1 color 220,255,85\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in AG10803 from ENCODE 3 (ENCFF100IYW)\ parent encTfChipPk off\ shortLabel AG10803 CTCF\ subGroups cellType=AG10803 factor=CTCF\ track encTfChipPkENCFF100IYW\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_tpm_fwd AorticSmsToIL1b_00hr15minBr3+ bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_forward 1 61 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12849-137C5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep3%20%28LK36%29.CNhs13578.12849-137C5.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12849-137C5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr15minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12849-137C5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_ctss_fwd AorticSmsToIL1b_00hr15minBr3+ bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_forward 0 61 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12849-137C5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep3%20%28LK36%29.CNhs13578.12849-137C5.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12849-137C5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr15minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12849-137C5\ urlLabel FANTOM5 Details:\ chainHprcGCA_018469425v1 HG03516.mat chain GCA_018469425.1 HG03516.mat HG03516.pri.mat.f1_v2 (May 2021 GCA_018469425.1_HG03516.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 61 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG03516.mat HG03516.pri.mat.f1_v2 (May 2021 GCA_018469425.1_HG03516.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469425.1\ parent hprcChainNetViewchain off\ priority 44\ shortLabel HG03516.mat\ subGroups view=chain sample=s044 population=afr subpop=esn hap=mat\ track chainHprcGCA_018469425v1\ type chain GCA_018469425.1\ wgEncodeRegDnaseUwHmvecdneoPeak HMVEC-dNeo Pk narrowPeak HMVEC-dNeo dermal MV endothelial cell, neonate DNaseI Peaks from ENCODE 1 61 85 255 244 170 255 249 1 0 0 regulation 1 color 85,255,244\ longLabel HMVEC-dNeo dermal MV endothelial cell, neonate DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMVEC-dNeo Pk\ subGroups view=a_Peaks cellType=HMVEC-dNeo treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHmvecdneoPeak\ wgEncodeRegDnaseUwHmvecdneoWig HMVEC-dNeo Sg bigWig 0 16586 HMVEC-dNeo dermal MV endothelial cell, neonate DNaseI Signal from ENCODE 0 61 85 255 244 170 255 249 0 0 0 regulation 1 color 85,255,244\ longLabel HMVEC-dNeo dermal MV endothelial cell, neonate DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.56474\ shortLabel HMVEC-dNeo Sg\ subGroups cellType=HMVEC-dNeo treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHmvecdneoSignal\ track wgEncodeRegDnaseUwHmvecdneoWig\ type bigWig 0 16586\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_tpm_rev AorticSmsToIL1b_00hr15minBr3- bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_reverse 1 62 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12849-137C5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep3%20%28LK36%29.CNhs13578.12849-137C5.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12849-137C5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr15minBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12849-137C5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_ctss_rev AorticSmsToIL1b_00hr15minBr3- bigWig Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_reverse 0 62 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12849-137C5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr15min%2c%20biol_rep3%20%28LK36%29.CNhs13578.12849-137C5.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12849-137C5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr15minBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12849-137C5\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF594OZI BE2C CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in BE2C from ENCODE 3 (ENCFF594OZI) 0 62 237 85 255 246 170 255 0 0 0 regulation 1 color 237,85,255\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in BE2C from ENCODE 3 (ENCFF594OZI)\ parent encTfChipPk off\ shortLabel BE2C CTCF\ subGroups cellType=BE2C factor=CTCF\ track encTfChipPkENCFF594OZI\ netHprcGCA_018469425v1 HG03516.mat netAlign GCA_018469425.1 chainHprcGCA_018469425v1 HG03516.mat HG03516.pri.mat.f1_v2 (May 2021 GCA_018469425.1_HG03516.pri.mat.f1_v2) HPRC project computed Chain Nets 1 62 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG03516.mat HG03516.pri.mat.f1_v2 (May 2021 GCA_018469425.1_HG03516.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469425.1\ parent hprcChainNetViewnet off\ priority 44\ shortLabel HG03516.mat\ subGroups view=net sample=s044 population=afr subpop=esn hap=mat\ track netHprcGCA_018469425v1\ type netAlign GCA_018469425.1 chainHprcGCA_018469425v1\ wgEncodeRegDnaseUwHmvecdadPeak HMVEC-dAd Pk narrowPeak HMVEC-dAd dermal microvascular endothelial cell DNaseI Peaks from ENCODE 1 62 85 255 246 170 255 250 1 0 0 regulation 1 color 85,255,246\ longLabel HMVEC-dAd dermal microvascular endothelial cell DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMVEC-dAd Pk\ subGroups view=a_Peaks cellType=HMVEC-dAd treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHmvecdadPeak\ wgEncodeRegDnaseUwHmvecdadWig HMVEC-dAd Sg bigWig 0 7923.4 HMVEC-dAd dermal microvascular endothelial cell DNaseI Signal from ENCODE 0 62 85 255 246 170 255 250 0 0 0 regulation 1 color 85,255,246\ longLabel HMVEC-dAd dermal microvascular endothelial cell DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.56686\ shortLabel HMVEC-dAd Sg\ subGroups cellType=HMVEC-dAd treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHmvecdadSignal\ track wgEncodeRegDnaseUwHmvecdadWig\ type bigWig 0 7923.4\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_tpm_fwd AorticSmsToIL1b_00hr30minBr1+ bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_forward 1 63 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12654-134H8 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep1%20%28LK37%29.CNhs13351.12654-134H8.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12654-134H8 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr30minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12654-134H8\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_ctss_fwd AorticSmsToIL1b_00hr30minBr1+ bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_forward 0 63 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12654-134H8 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep1%20%28LK37%29.CNhs13351.12654-134H8.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12654-134H8 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr30minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12654-134H8\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF704JHR BJ CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in BJ from ENCODE 3 (ENCFF704JHR) 0 63 255 184 85 255 219 170 0 0 0 regulation 1 color 255,184,85\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in BJ from ENCODE 3 (ENCFF704JHR)\ parent encTfChipPk off\ shortLabel BJ CTCF\ subGroups cellType=BJ factor=CTCF\ track encTfChipPkENCFF704JHR\ chainHprcGCA_018469415v1 HG03516.pat chain GCA_018469415.1 HG03516.pat HG03516.alt.pat.f1_v2 (May 2021 GCA_018469415.1_HG03516.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 63 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG03516.pat HG03516.alt.pat.f1_v2 (May 2021 GCA_018469415.1_HG03516.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469415.1\ parent hprcChainNetViewchain off\ priority 43\ shortLabel HG03516.pat\ subGroups view=chain sample=s043 population=afr subpop=esn hap=pat\ track chainHprcGCA_018469415v1\ type chain GCA_018469415.1\ wgEncodeRegDnaseUwHrcepicPeak HRCEpiC Pk narrowPeak HRCEpiC renal cortical epithelium DNaseI Peaks from ENCODE 1 63 85 251 255 170 253 255 1 0 0 regulation 1 color 85,251,255\ longLabel HRCEpiC renal cortical epithelium DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HRCEpiC Pk\ subGroups view=a_Peaks cellType=HRCEpiC treatment=n_a tissue=kidney cancer=normal\ track wgEncodeRegDnaseUwHrcepicPeak\ wgEncodeRegDnaseUwHrcepicWig HRCEpiC Sg bigWig 0 4920.93 HRCEpiC renal cortical epithelium DNaseI Signal from ENCODE 0 63 85 251 255 170 253 255 0 0 0 regulation 1 color 85,251,255\ longLabel HRCEpiC renal cortical epithelium DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.58591\ shortLabel HRCEpiC Sg\ subGroups cellType=HRCEpiC treatment=n_a tissue=kidney cancer=normal\ table wgEncodeRegDnaseUwHrcepicSignal\ track wgEncodeRegDnaseUwHrcepicWig\ type bigWig 0 4920.93\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_tpm_rev AorticSmsToIL1b_00hr30minBr1- bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_reverse 1 64 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12654-134H8 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep1%20%28LK37%29.CNhs13351.12654-134H8.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12654-134H8 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr30minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12654-134H8\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_ctss_rev AorticSmsToIL1b_00hr30minBr1- bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_reverse 0 64 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12654-134H8 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep1%20%28LK37%29.CNhs13351.12654-134H8.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12654-134H8 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr30minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12654-134H8\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF910TER B_cell CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in B_cell from ENCODE 3 (ENCFF910TER) 0 64 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in B_cell from ENCODE 3 (ENCFF910TER)\ parent encTfChipPk off\ shortLabel B_cell CTCF\ subGroups cellType=B_cell factor=CTCF\ track encTfChipPkENCFF910TER\ netHprcGCA_018469415v1 HG03516.pat netAlign GCA_018469415.1 chainHprcGCA_018469415v1 HG03516.pat HG03516.alt.pat.f1_v2 (May 2021 GCA_018469415.1_HG03516.alt.pat.f1_v2) HPRC project computed Chain Nets 1 64 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG03516.pat HG03516.alt.pat.f1_v2 (May 2021 GCA_018469415.1_HG03516.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469415.1\ parent hprcChainNetViewnet off\ priority 43\ shortLabel HG03516.pat\ subGroups view=net sample=s043 population=afr subpop=esn hap=pat\ track netHprcGCA_018469415v1\ type netAlign GCA_018469415.1 chainHprcGCA_018469415v1\ wgEncodeRegDnaseUwHrePeak HRE Pk narrowPeak HRE renal epithelium DNaseI Peaks from ENCODE 1 64 85 248 255 170 251 255 1 0 0 regulation 1 color 85,248,255\ longLabel HRE renal epithelium DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HRE Pk\ subGroups view=a_Peaks cellType=HRE treatment=n_a tissue=kidney cancer=normal\ track wgEncodeRegDnaseUwHrePeak\ wgEncodeRegDnaseUwHreWig HRE Sg bigWig 0 6938.49 HRE renal epithelium DNaseI Signal from ENCODE 0 64 85 248 255 170 251 255 0 0 0 regulation 1 color 85,248,255\ longLabel HRE renal epithelium DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.59019\ shortLabel HRE Sg\ subGroups cellType=HRE treatment=n_a tissue=kidney cancer=normal\ table wgEncodeRegDnaseUwHreSignal\ track wgEncodeRegDnaseUwHreWig\ type bigWig 0 6938.49\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_tpm_fwd AorticSmsToIL1b_00hr30minBr2+ bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_forward 1 65 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12752-136A7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep2%20%28LK38%29.CNhs13371.12752-136A7.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12752-136A7 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr30minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12752-136A7\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_ctss_fwd AorticSmsToIL1b_00hr30minBr2+ bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_forward 0 65 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12752-136A7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep2%20%28LK38%29.CNhs13371.12752-136A7.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12752-136A7 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr30minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12752-136A7\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF675JFN C4-2B CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in C4-2B from ENCODE 3 (ENCFF675JFN) 0 65 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in C4-2B from ENCODE 3 (ENCFF675JFN)\ parent encTfChipPk off\ shortLabel C4-2B CTCF\ subGroups cellType=C4-2B factor=CTCF\ track encTfChipPkENCFF675JFN\ chainHprcGCA_018469875v1 HG02622.mat chain GCA_018469875.1 HG02622.mat HG02622.pri.mat.f1_v2 (May 2021 GCA_018469875.1_HG02622.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 65 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02622.mat HG02622.pri.mat.f1_v2 (May 2021 GCA_018469875.1_HG02622.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469875.1\ parent hprcChainNetViewchain\ priority 1\ shortLabel HG02622.mat\ subGroups view=chain sample=s001 population=afr subpop=gwd hap=mat\ track chainHprcGCA_018469875v1\ type chain GCA_018469875.1\ wgEncodeRegDnaseUwNhekPeak NHEK Pk narrowPeak NHEK epidermal keratinocyte DNaseI Peaks from ENCODE 1 65 85 238 255 170 246 255 1 0 0 regulation 1 color 85,238,255\ longLabel NHEK epidermal keratinocyte DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak on\ shortLabel NHEK Pk\ subGroups view=a_Peaks cellType=NHEK treatment=n_a tissue=skin cancer=normal\ track wgEncodeRegDnaseUwNhekPeak\ wgEncodeRegDnaseUwNhekWig NHEK Sg bigWig 0 9597.75 NHEK epidermal keratinocyte DNaseI Signal from ENCODE 0 65 85 238 255 170 246 255 0 0 0 regulation 1 color 85,238,255\ longLabel NHEK epidermal keratinocyte DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig on\ priority 1.60559\ shortLabel NHEK Sg\ subGroups cellType=NHEK treatment=n_a tissue=skin cancer=normal\ table wgEncodeRegDnaseUwNhekSignal\ track wgEncodeRegDnaseUwNhekWig\ type bigWig 0 9597.75\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_tpm_rev AorticSmsToIL1b_00hr30minBr2- bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_reverse 1 66 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12752-136A7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep2%20%28LK38%29.CNhs13371.12752-136A7.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12752-136A7 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr30minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12752-136A7\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_ctss_rev AorticSmsToIL1b_00hr30minBr2- bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_reverse 0 66 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12752-136A7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep2%20%28LK38%29.CNhs13371.12752-136A7.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12752-136A7 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr30minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12752-136A7\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF856AUX C4-2B ZFX narrowPeak Transcription Factor ChIP-seq Peaks of ZFX in C4-2B from ENCODE 3 (ENCFF856AUX) 0 66 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of ZFX in C4-2B from ENCODE 3 (ENCFF856AUX)\ parent encTfChipPk off\ shortLabel C4-2B ZFX\ subGroups cellType=C4-2B factor=ZFX\ track encTfChipPkENCFF856AUX\ netHprcGCA_018469875v1 HG02622.mat netAlign GCA_018469875.1 chainHprcGCA_018469875v1 HG02622.mat HG02622.pri.mat.f1_v2 (May 2021 GCA_018469875.1_HG02622.pri.mat.f1_v2) HPRC project computed Chain Nets 1 66 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02622.mat HG02622.pri.mat.f1_v2 (May 2021 GCA_018469875.1_HG02622.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469875.1\ parent hprcChainNetViewnet\ priority 1\ shortLabel HG02622.mat\ subGroups view=net sample=s001 population=afr subpop=gwd hap=mat\ track netHprcGCA_018469875v1\ type netAlign GCA_018469875.1 chainHprcGCA_018469875v1\ wgEncodeRegDnaseUwSaecPeak SAEC Pk narrowPeak SAEC small airway epithelium DNaseI Peaks from ENCODE 1 66 85 231 255 170 243 255 1 0 0 regulation 1 color 85,231,255\ longLabel SAEC small airway epithelium DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel SAEC Pk\ subGroups view=a_Peaks cellType=SAEC treatment=n_a tissue=lung cancer=normal\ track wgEncodeRegDnaseUwSaecPeak\ wgEncodeRegDnaseUwSaecWig SAEC Sg bigWig 0 4884.78 SAEC small airway epithelium DNaseI Signal from ENCODE 0 66 85 231 255 170 243 255 0 0 0 regulation 1 color 85,231,255\ longLabel SAEC small airway epithelium DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.61604\ shortLabel SAEC Sg\ subGroups cellType=SAEC treatment=n_a tissue=lung cancer=normal\ table wgEncodeRegDnaseUwSaecSignal\ track wgEncodeRegDnaseUwSaecWig\ type bigWig 0 4884.78\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_tpm_fwd AorticSmsToIL1b_00hr30minBr3+ bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_forward 1 67 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12850-137C6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep3%20%28LK39%29.CNhs13579.12850-137C6.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12850-137C6 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr30minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12850-137C6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_ctss_fwd AorticSmsToIL1b_00hr30minBr3+ bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_forward 0 67 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12850-137C6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep3%20%28LK39%29.CNhs13579.12850-137C6.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12850-137C6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr30minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12850-137C6\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF300XXC CD14+monocyte CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in CD14-positive_monocyte from ENCODE 3 (ENCFF300XXC) 0 67 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in CD14-positive_monocyte from ENCODE 3 (ENCFF300XXC)\ parent encTfChipPk off\ shortLabel CD14+monocyte CTCF\ subGroups cellType=CD14-positive_monocyte factor=CTCF\ track encTfChipPkENCFF300XXC\ chainHprcGCA_018469935v1 HG02717.mat chain GCA_018469935.1 HG02717.mat HG02717.pri.mat.f1_v2 (May 2021 GCA_018469935.1_HG02717.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 67 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02717.mat HG02717.pri.mat.f1_v2 (May 2021 GCA_018469935.1_HG02717.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469935.1\ parent hprcChainNetViewchain off\ priority 3\ shortLabel HG02717.mat\ subGroups view=chain sample=s003 population=afr subpop=gwd hap=mat\ track chainHprcGCA_018469935v1\ type chain GCA_018469935.1\ wgEncodeRegDnaseUwPrecPeak PrEC Pk narrowPeak PrEC prostate epithelium DNaseI Peaks from ENCODE 1 67 85 226 255 170 240 255 1 0 0 regulation 1 color 85,226,255\ longLabel PrEC prostate epithelium DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel PrEC Pk\ subGroups view=a_Peaks cellType=PrEC treatment=n_a tissue=prostate cancer=normal\ track wgEncodeRegDnaseUwPrecPeak\ wgEncodeRegDnaseUwPrecWig PrEC Sg bigWig 0 4302.39 PrEC prostate epithelium DNaseI Signal from ENCODE 0 67 85 226 255 170 240 255 0 0 0 regulation 1 color 85,226,255\ longLabel PrEC prostate epithelium DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.62238\ shortLabel PrEC Sg\ subGroups cellType=PrEC treatment=n_a tissue=prostate cancer=normal\ table wgEncodeRegDnaseUwPrecSignal\ track wgEncodeRegDnaseUwPrecWig\ type bigWig 0 4302.39\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_tpm_rev AorticSmsToIL1b_00hr30minBr3- bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_reverse 1 68 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12850-137C6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep3%20%28LK39%29.CNhs13579.12850-137C6.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12850-137C6 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr30minBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12850-137C6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_ctss_rev AorticSmsToIL1b_00hr30minBr3- bigWig Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_reverse 0 68 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12850-137C6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr30min%2c%20biol_rep3%20%28LK39%29.CNhs13579.12850-137C6.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12850-137C6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr30minBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12850-137C6\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF990ZZT Caco-2 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in Caco-2 from ENCODE 3 (ENCFF990ZZT) 0 68 85 193 255 170 224 255 0 0 0 regulation 1 color 85,193,255\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in Caco-2 from ENCODE 3 (ENCFF990ZZT)\ parent encTfChipPk off\ shortLabel Caco-2 CTCF\ subGroups cellType=Caco-2 factor=CTCF\ track encTfChipPkENCFF990ZZT\ wgEncodeRegDnaseUwHeepicPeak HEEpiC Pk narrowPeak HEEpiC esophageal epithelium DNaseI Peaks from ENCODE 1 68 85 220 255 170 237 255 1 0 0 regulation 1 color 85,220,255\ longLabel HEEpiC esophageal epithelium DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HEEpiC Pk\ subGroups view=a_Peaks cellType=HEEpiC treatment=n_a tissue=esophagus cancer=normal\ track wgEncodeRegDnaseUwHeepicPeak\ wgEncodeRegDnaseUwHeepicWig HEEpiC Sg bigWig 0 20601.1 HEEpiC esophageal epithelium DNaseI Signal from ENCODE 0 68 85 220 255 170 237 255 0 0 0 regulation 1 color 85,220,255\ longLabel HEEpiC esophageal epithelium DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.632\ shortLabel HEEpiC Sg\ subGroups cellType=HEEpiC treatment=n_a tissue=esophagus cancer=normal\ table wgEncodeRegDnaseUwHeepicSignal\ track wgEncodeRegDnaseUwHeepicWig\ type bigWig 0 20601.1\ netHprcGCA_018469935v1 HG02717.mat netAlign GCA_018469935.1 chainHprcGCA_018469935v1 HG02717.mat HG02717.pri.mat.f1_v2 (May 2021 GCA_018469935.1_HG02717.pri.mat.f1_v2) HPRC project computed Chain Nets 1 68 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02717.mat HG02717.pri.mat.f1_v2 (May 2021 GCA_018469935.1_HG02717.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469935.1\ parent hprcChainNetViewnet off\ priority 3\ shortLabel HG02717.mat\ subGroups view=net sample=s003 population=afr subpop=gwd hap=mat\ track netHprcGCA_018469935v1\ type netAlign GCA_018469935.1 chainHprcGCA_018469935v1\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_tpm_fwd AorticSmsToIL1b_00hr45minBr1+ bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_forward 1 69 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12655-134H9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep1%20%28LK40%29.CNhs13352.12655-134H9.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12655-134H9 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr45minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12655-134H9\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_ctss_fwd AorticSmsToIL1b_00hr45minBr1+ bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_forward 0 69 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12655-134H9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep1%20%28LK40%29.CNhs13352.12655-134H9.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12655-134H9 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr45minBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12655-134H9\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF837RIT DOHH2 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in DOHH2 from ENCODE 3 (ENCFF837RIT) 0 69 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in DOHH2 from ENCODE 3 (ENCFF837RIT)\ parent encTfChipPk off\ shortLabel DOHH2 CTCF\ subGroups cellType=DOHH2 factor=CTCF\ track encTfChipPkENCFF837RIT\ wgEncodeRegDnaseUwGm06990Peak GM06990 Pk narrowPeak GM06990 B-lymphocyte, lymphoblastoid cell line DNaseI Peaks from ENCODE 1 69 85 205 255 170 230 255 1 0 0 regulation 1 color 85,205,255\ longLabel GM06990 B-lymphocyte, lymphoblastoid cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel GM06990 Pk\ subGroups view=a_Peaks cellType=GM06990 treatment=n_a tissue=blood cancer=unknown\ track wgEncodeRegDnaseUwGm06990Peak\ wgEncodeRegDnaseUwGm06990Wig GM06990 Sg bigWig 0 14706.5 GM06990 B-lymphocyte, lymphoblastoid cell line DNaseI Signal from ENCODE 0 69 85 205 255 170 230 255 0 0 0 regulation 1 color 85,205,255\ longLabel GM06990 B-lymphocyte, lymphoblastoid cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.65365\ shortLabel GM06990 Sg\ subGroups cellType=GM06990 treatment=n_a tissue=blood cancer=unknown\ table wgEncodeRegDnaseUwGm06990Signal\ track wgEncodeRegDnaseUwGm06990Wig\ type bigWig 0 14706.5\ chainHprcGCA_018469955v1 HG02630.mat chain GCA_018469955.1 HG02630.mat HG02630.pri.mat.f1_v2 (May 2021 GCA_018469955.1_HG02630.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 69 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02630.mat HG02630.pri.mat.f1_v2 (May 2021 GCA_018469955.1_HG02630.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469955.1\ parent hprcChainNetViewchain off\ priority 5\ shortLabel HG02630.mat\ subGroups view=chain sample=s005 population=afr subpop=gwd hap=mat\ track chainHprcGCA_018469955v1\ type chain GCA_018469955.1\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_tpm_rev AorticSmsToIL1b_00hr45minBr1- bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_reverse 1 70 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12655-134H9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep1%20%28LK40%29.CNhs13352.12655-134H9.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12655-134H9 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr45minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12655-134H9\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_ctss_rev AorticSmsToIL1b_00hr45minBr1- bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_reverse 0 70 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12655-134H9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep1%20%28LK40%29.CNhs13352.12655-134H9.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12655-134H9 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr45minBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12655-134H9\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF897RQN GM06990 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in GM06990 from ENCODE 3 (ENCFF897RQN) 0 70 85 205 255 170 230 255 0 0 0 regulation 1 color 85,205,255\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in GM06990 from ENCODE 3 (ENCFF897RQN)\ parent encTfChipPk off\ shortLabel GM06990 CTCF\ subGroups cellType=GM06990 factor=CTCF\ track encTfChipPkENCFF897RQN\ wgEncodeRegDnaseUwHepg2Peak HepG2 Pk narrowPeak HepG2 hepatocellular carcinoma cell line DNaseI Peaks from ENCODE 1 70 85 198 255 170 226 255 1 0 0 regulation 1 color 85,198,255\ longLabel HepG2 hepatocellular carcinoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak on\ shortLabel HepG2 Pk\ subGroups view=a_Peaks cellType=HepG2 treatment=n_a tissue=liver cancer=cancer\ track wgEncodeRegDnaseUwHepg2Peak\ wgEncodeRegDnaseUwHepg2Wig HepG2 Sg bigWig 0 4511.03 HepG2 hepatocellular carcinoma cell line DNaseI Signal from ENCODE 0 70 85 198 255 170 226 255 0 0 0 regulation 1 color 85,198,255\ longLabel HepG2 hepatocellular carcinoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig on\ priority 1.66426\ shortLabel HepG2 Sg\ subGroups cellType=HepG2 treatment=n_a tissue=liver cancer=cancer\ table wgEncodeRegDnaseUwHepg2Signal\ track wgEncodeRegDnaseUwHepg2Wig\ type bigWig 0 4511.03\ netHprcGCA_018469955v1 HG02630.mat netAlign GCA_018469955.1 chainHprcGCA_018469955v1 HG02630.mat HG02630.pri.mat.f1_v2 (May 2021 GCA_018469955.1_HG02630.pri.mat.f1_v2) HPRC project computed Chain Nets 1 70 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02630.mat HG02630.pri.mat.f1_v2 (May 2021 GCA_018469955.1_HG02630.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469955.1\ parent hprcChainNetViewnet off\ priority 5\ shortLabel HG02630.mat\ subGroups view=net sample=s005 population=afr subpop=gwd hap=mat\ track netHprcGCA_018469955v1\ type netAlign GCA_018469955.1 chainHprcGCA_018469955v1\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_tpm_fwd AorticSmsToIL1b_00hr45minBr2+ bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_forward 1 71 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12753-136A8 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep2%20%28LK41%29.CNhs13372.12753-136A8.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12753-136A8 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr45minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12753-136A8\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_ctss_fwd AorticSmsToIL1b_00hr45minBr2+ bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_forward 0 71 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12753-136A8 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep2%20%28LK41%29.CNhs13372.12753-136A8.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12753-136A8 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr45minBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12753-136A8\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwCaco2Peak Caco-2 Pk narrowPeak Caco-2 colon adenocarcinoma cell line DNaseI Peaks from ENCODE 1 71 85 193 255 170 224 255 1 0 0 regulation 1 color 85,193,255\ longLabel Caco-2 colon adenocarcinoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel Caco-2 Pk\ subGroups view=a_Peaks cellType=Caco-2 treatment=n_a tissue=colon cancer=cancer\ track wgEncodeRegDnaseUwCaco2Peak\ wgEncodeRegDnaseUwCaco2Wig Caco-2 Sg bigWig 0 4903.16 Caco-2 colon adenocarcinoma cell line DNaseI Signal from ENCODE 0 71 85 193 255 170 224 255 0 0 0 regulation 1 color 85,193,255\ longLabel Caco-2 colon adenocarcinoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.67125\ shortLabel Caco-2 Sg\ subGroups cellType=Caco-2 treatment=n_a tissue=colon cancer=cancer\ table wgEncodeRegDnaseUwCaco2Signal\ track wgEncodeRegDnaseUwCaco2Wig\ type bigWig 0 4903.16\ encTfChipPkENCFF329TZO GM08714 ZNF274 narrowPeak Transcription Factor ChIP-seq Peaks of ZNF274 in GM08714 from ENCODE 3 (ENCFF329TZO) 0 71 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of ZNF274 in GM08714 from ENCODE 3 (ENCFF329TZO)\ parent encTfChipPk off\ shortLabel GM08714 ZNF274\ subGroups cellType=GM08714 factor=ZNF274\ track encTfChipPkENCFF329TZO\ chainHprcGCA_018470445v1 HG02572.mat chain GCA_018470445.1 HG02572.mat HG02572.pri.mat.f1_v2 (May 2021 GCA_018470445.1_HG02572.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 71 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02572.mat HG02572.pri.mat.f1_v2 (May 2021 GCA_018470445.1_HG02572.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018470445.1\ parent hprcChainNetViewchain off\ priority 8\ shortLabel HG02572.mat\ subGroups view=chain sample=s008 population=afr subpop=gwd hap=mat\ track chainHprcGCA_018470445v1\ type chain GCA_018470445.1\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_tpm_rev AorticSmsToIL1b_00hr45minBr2- bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_reverse 1 72 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12753-136A8 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep2%20%28LK41%29.CNhs13372.12753-136A8.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12753-136A8 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr45minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12753-136A8\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_ctss_rev AorticSmsToIL1b_00hr45minBr2- bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_reverse 0 72 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12753-136A8 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep2%20%28LK41%29.CNhs13372.12753-136A8.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12753-136A8 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr45minBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12753-136A8\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF178PUI GM10266 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in GM10266 from ENCODE 3 (ENCFF178PUI) 0 72 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in GM10266 from ENCODE 3 (ENCFF178PUI)\ parent encTfChipPk off\ shortLabel GM10266 CTCF\ subGroups cellType=GM10266 factor=CTCF\ track encTfChipPkENCFF178PUI\ netHprcGCA_018470445v1 HG02572.mat netAlign GCA_018470445.1 chainHprcGCA_018470445v1 HG02572.mat HG02572.pri.mat.f1_v2 (May 2021 GCA_018470445.1_HG02572.pri.mat.f1_v2) HPRC project computed Chain Nets 1 72 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02572.mat HG02572.pri.mat.f1_v2 (May 2021 GCA_018470445.1_HG02572.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018470445.1\ parent hprcChainNetViewnet off\ priority 8\ shortLabel HG02572.mat\ subGroups view=net sample=s008 population=afr subpop=gwd hap=mat\ track netHprcGCA_018470445v1\ type netAlign GCA_018470445.1 chainHprcGCA_018470445v1\ wgEncodeRegDnaseUwSknshraPeak SK-N-SH_RA Pk narrowPeak SK-N-SH_RA neuroblastoma cell line, RA treated DNaseI Peaks from ENCODE 1 72 85 189 255 170 222 255 1 0 0 regulation 1 color 85,189,255\ longLabel SK-N-SH_RA neuroblastoma cell line, RA treated DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel SK-N-SH_RA Pk\ subGroups view=a_Peaks cellType=SK-N-SH_RA treatment=n_a tissue=brain cancer=cancer\ track wgEncodeRegDnaseUwSknshraPeak\ wgEncodeRegDnaseUwSknshraWig SK-N-SH_RA Sg bigWig 0 4488.56 SK-N-SH_RA neuroblastoma cell line, RA treated DNaseI Signal from ENCODE 0 72 85 189 255 170 222 255 0 0 0 regulation 1 color 85,189,255\ longLabel SK-N-SH_RA neuroblastoma cell line, RA treated DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.679\ shortLabel SK-N-SH_RA Sg\ subGroups cellType=SK-N-SH_RA treatment=n_a tissue=brain cancer=cancer\ table wgEncodeRegDnaseUwSknshraSignal\ track wgEncodeRegDnaseUwSknshraWig\ type bigWig 0 4488.56\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_tpm_fwd AorticSmsToIL1b_00hr45minBr3+ bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_forward 1 73 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12851-137C7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep3%20%28LK42%29.CNhs13580.12851-137C7.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12851-137C7 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr45minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12851-137C7\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_ctss_fwd AorticSmsToIL1b_00hr45minBr3+ bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_forward 0 73 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12851-137C7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep3%20%28LK42%29.CNhs13580.12851-137C7.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12851-137C7 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr45minBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12851-137C7\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwCd20ro01778Peak CD20+_RO01778 Pk narrowPeak CD20+_RO01778 B-lymphocyte, CD20+ DNaseI Peaks from ENCODE 1 73 85 183 255 170 219 255 1 0 0 regulation 1 color 85,183,255\ longLabel CD20+_RO01778 B-lymphocyte, CD20+ DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel CD20+_RO01778 Pk\ subGroups view=a_Peaks cellType=CD20_RO01778 treatment=n_a tissue=blood cancer=normal\ track wgEncodeRegDnaseUwCd20ro01778Peak\ wgEncodeRegDnaseUwCd20ro01778Wig CD20+_RO01778 Sg bigWig 0 1572.73 CD20+_RO01778 B-lymphocyte, CD20+ DNaseI Signal from ENCODE 0 73 85 183 255 170 219 255 0 0 0 regulation 1 color 85,183,255\ longLabel CD20+_RO01778 B-lymphocyte, CD20+ DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.68971\ shortLabel CD20+_RO01778 Sg\ subGroups cellType=CD20_RO01778 treatment=n_a tissue=blood cancer=normal\ table wgEncodeRegDnaseUwCd20ro01778Signal\ track wgEncodeRegDnaseUwCd20ro01778Wig\ type bigWig 0 1572.73\ encTfChipPkENCFF751IKT GM12864 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in GM12864 from ENCODE 3 (ENCFF751IKT) 0 73 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in GM12864 from ENCODE 3 (ENCFF751IKT)\ parent encTfChipPk off\ shortLabel GM12864 CTCF\ subGroups cellType=GM12864 factor=CTCF\ track encTfChipPkENCFF751IKT\ chainHprcGCA_018470455v1 HG02886.mat chain GCA_018470455.1 HG02886.mat HG02886.pri.mat.f1_v2 (May 2021 GCA_018470455.1_HG02886.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 73 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02886.mat HG02886.pri.mat.f1_v2 (May 2021 GCA_018470455.1_HG02886.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018470455.1\ parent hprcChainNetViewchain off\ priority 9\ shortLabel HG02886.mat\ subGroups view=chain sample=s009 population=afr subpop=gwd hap=mat\ track chainHprcGCA_018470455v1\ type chain GCA_018470455.1\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_tpm_rev AorticSmsToIL1b_00hr45minBr3- bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_reverse 1 74 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12851-137C7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep3%20%28LK42%29.CNhs13580.12851-137C7.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12851-137C7 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_00hr45minBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12851-137C7\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_ctss_rev AorticSmsToIL1b_00hr45minBr3- bigWig Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_reverse 0 74 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12851-137C7 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2000hr45min%2c%20biol_rep3%20%28LK42%29.CNhs13580.12851-137C7.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12851-137C7 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_00hr45minBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12851-137C7\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF965YZI GM12865 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in GM12865 from ENCODE 3 (ENCFF965YZI) 0 74 85 147 255 170 201 255 0 0 0 regulation 1 color 85,147,255\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in GM12865 from ENCODE 3 (ENCFF965YZI)\ parent encTfChipPk off\ shortLabel GM12865 CTCF\ subGroups cellType=GM12865 factor=CTCF\ track encTfChipPkENCFF965YZI\ netHprcGCA_018470455v1 HG02886.mat netAlign GCA_018470455.1 chainHprcGCA_018470455v1 HG02886.mat HG02886.pri.mat.f1_v2 (May 2021 GCA_018470455.1_HG02886.pri.mat.f1_v2) HPRC project computed Chain Nets 1 74 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02886.mat HG02886.pri.mat.f1_v2 (May 2021 GCA_018470455.1_HG02886.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018470455.1\ parent hprcChainNetViewnet off\ priority 9\ shortLabel HG02886.mat\ subGroups view=net sample=s009 population=afr subpop=gwd hap=mat\ track netHprcGCA_018470455v1\ type netAlign GCA_018470455.1 chainHprcGCA_018470455v1\ wgEncodeRegDnaseUwTh1Peak Th1 Pk narrowPeak Th1 T-lymphocyte, helper type 1 DNaseI Peaks from ENCODE 1 74 85 178 255 170 216 255 1 0 0 regulation 1 color 85,178,255\ longLabel Th1 T-lymphocyte, helper type 1 DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel Th1 Pk\ subGroups view=a_Peaks cellType=Th1 treatment=n_a tissue=blood cancer=unknown\ track wgEncodeRegDnaseUwTh1Peak\ wgEncodeRegDnaseUwTh1Wig Th1 Sg bigWig 0 2056.65 Th1 T-lymphocyte, helper type 1 DNaseI Signal from ENCODE 0 74 85 178 255 170 216 255 0 0 0 regulation 1 color 85,178,255\ longLabel Th1 T-lymphocyte, helper type 1 DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.69959\ shortLabel Th1 Sg\ subGroups cellType=Th1 treatment=n_a tissue=blood cancer=unknown\ table wgEncodeRegDnaseUwTh1Signal\ track wgEncodeRegDnaseUwTh1Wig\ type bigWig 0 2056.65\ AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_tpm_fwd AorticSmsToIL1b_01hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_forward 1 75 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12656-134I1 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2001hr%2c%20biol_rep1%20%28LK43%29.CNhs13353.12656-134I1.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12656-134I1 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_01hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12656-134I1\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_ctss_fwd AorticSmsToIL1b_01hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_forward 0 75 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12656-134I1 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2001hr%2c%20biol_rep1%20%28LK43%29.CNhs13353.12656-134I1.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12656-134I1 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_01hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12656-134I1\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF913EEI GM12873 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in GM12873 from ENCODE 3 (ENCFF913EEI) 0 75 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in GM12873 from ENCODE 3 (ENCFF913EEI)\ parent encTfChipPk off\ shortLabel GM12873 CTCF\ subGroups cellType=GM12873 factor=CTCF\ track encTfChipPkENCFF913EEI\ chainHprcGCA_018473295v1 HG03540.mat chain GCA_018473295.1 HG03540.mat HG03540.pri.mat.f1_v2 (May 2021 GCA_018473295.1_HG03540.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 75 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG03540.mat HG03540.pri.mat.f1_v2 (May 2021 GCA_018473295.1_HG03540.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018473295.1\ parent hprcChainNetViewchain off\ priority 11\ shortLabel HG03540.mat\ subGroups view=chain sample=s011 population=afr subpop=gwd hap=mat\ track chainHprcGCA_018473295v1\ type chain GCA_018473295.1\ wgEncodeRegDnaseUwTh2Peak Th2 Pk narrowPeak Th2 T-lymphocyte, helper type 2 DNaseI Peaks from ENCODE 1 75 85 176 255 170 215 255 1 0 0 regulation 1 color 85,176,255\ longLabel Th2 T-lymphocyte, helper type 2 DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel Th2 Pk\ subGroups view=a_Peaks cellType=Th2 treatment=n_a tissue=blood cancer=unknown\ track wgEncodeRegDnaseUwTh2Peak\ wgEncodeRegDnaseUwTh2Wig Th2 Sg bigWig 0 1526.14 Th2 T-lymphocyte, helper type 2 DNaseI Signal from ENCODE 0 75 85 176 255 170 215 255 0 0 0 regulation 1 color 85,176,255\ longLabel Th2 T-lymphocyte, helper type 2 DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.70375\ shortLabel Th2 Sg\ subGroups cellType=Th2 treatment=n_a tissue=blood cancer=unknown\ table wgEncodeRegDnaseUwTh2Signal\ track wgEncodeRegDnaseUwTh2Wig\ type bigWig 0 1526.14\ AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_tpm_rev AorticSmsToIL1b_01hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_reverse 1 76 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12656-134I1 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2001hr%2c%20biol_rep1%20%28LK43%29.CNhs13353.12656-134I1.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12656-134I1 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_01hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12656-134I1\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_ctss_rev AorticSmsToIL1b_01hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_reverse 0 76 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12656-134I1 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2001hr%2c%20biol_rep1%20%28LK43%29.CNhs13353.12656-134I1.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12656-134I1 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_01hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12656-134I1\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF834WWA GM12874 CTCF narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in GM12874 from ENCODE 3 (ENCFF834WWA) 0 76 0 0 0 127 127 127 0 0 0 regulation 1 longLabel Transcription Factor ChIP-seq Peaks of CTCF in GM12874 from ENCODE 3 (ENCFF834WWA)\ parent encTfChipPk off\ shortLabel GM12874 CTCF\ subGroups cellType=GM12874 factor=CTCF\ track encTfChipPkENCFF834WWA\ netHprcGCA_018473295v1 HG03540.mat netAlign GCA_018473295.1 chainHprcGCA_018473295v1 HG03540.mat HG03540.pri.mat.f1_v2 (May 2021 GCA_018473295.1_HG03540.pri.mat.f1_v2) HPRC project computed Chain Nets 1 76 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG03540.mat HG03540.pri.mat.f1_v2 (May 2021 GCA_018473295.1_HG03540.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018473295.1\ parent hprcChainNetViewnet off\ priority 11\ shortLabel HG03540.mat\ subGroups view=net sample=s011 population=afr subpop=gwd hap=mat\ track netHprcGCA_018473295v1\ type netAlign GCA_018473295.1 chainHprcGCA_018473295v1\ wgEncodeRegDnaseUwTh1wb54553204Peak Th1_Wb54553204 Pk narrowPeak Th1_Wb54553204 T-lymphocyte, helper type 1 DNaseI Peaks from ENCODE 1 76 85 173 255 170 214 255 1 0 0 regulation 1 color 85,173,255\ longLabel Th1_Wb54553204 T-lymphocyte, helper type 1 DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel Th1_Wb54553204 Pk\ subGroups view=a_Peaks cellType=Th1_Wb54553204 treatment=n_a tissue=blood cancer=normal\ track wgEncodeRegDnaseUwTh1wb54553204Peak\ wgEncodeRegDnaseUwTh1wb54553204Wig Th1_Wb54553204 Sg bigWig 0 593.107 Th1_Wb54553204 T-lymphocyte, helper type 1 DNaseI Signal from ENCODE 0 76 85 173 255 170 214 255 0 0 0 regulation 1 color 85,173,255\ longLabel Th1_Wb54553204 T-lymphocyte, helper type 1 DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.70849\ shortLabel Th1_Wb54553204 Sg\ subGroups cellType=Th1_Wb54553204 treatment=n_a tissue=blood cancer=normal\ table wgEncodeRegDnaseUwTh1wb54553204Signal\ track wgEncodeRegDnaseUwTh1wb54553204Wig\ type bigWig 0 593.107\ AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_tpm_fwd AorticSmsToIL1b_01hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_forward 1 77 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12754-136A9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2001hr%2c%20biol_rep2%20%28LK44%29.CNhs13373.12754-136A9.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12754-136A9 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_01hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12754-136A9\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_ctss_fwd AorticSmsToIL1b_01hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_forward 0 77 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12754-136A9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2001hr%2c%20biol_rep2%20%28LK44%29.CNhs13373.12754-136A9.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12754-136A9 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_01hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12754-136A9\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF003VDB GM12878 ARID3A narrowPeak Transcription Factor ChIP-seq Peaks of ARID3A in GM12878 from ENCODE 3 (ENCFF003VDB) 0 77 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of ARID3A in GM12878 from ENCODE 3 (ENCFF003VDB)\ parent encTfChipPk off\ shortLabel GM12878 ARID3A\ subGroups cellType=GM12878 factor=ARID3A\ track encTfChipPkENCFF003VDB\ chainHprcGCA_018503585v1 HG02818.mat chain GCA_018503585.1 HG02818.mat HG02818.pri.mat.f1_v2 (May 2021 GCA_018503585.1_HG02818.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 77 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02818.mat HG02818.pri.mat.f1_v2 (May 2021 GCA_018503585.1_HG02818.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018503585.1\ parent hprcChainNetViewchain off\ priority 14\ shortLabel HG02818.mat\ subGroups view=chain sample=s014 population=afr subpop=gwd hap=mat\ track chainHprcGCA_018503585v1\ type chain GCA_018503585.1\ wgEncodeRegDnaseUwJurkatPeak Jurkat Pk narrowPeak Jurkat T-lymphocyte acute leukemia cell line DNaseI Peaks from ENCODE 1 77 85 165 255 170 210 255 1 0 0 regulation 1 color 85,165,255\ longLabel Jurkat T-lymphocyte acute leukemia cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel Jurkat Pk\ subGroups view=a_Peaks cellType=Jurkat treatment=n_a tissue=blood cancer=cancer\ track wgEncodeRegDnaseUwJurkatPeak\ wgEncodeRegDnaseUwJurkatWig Jurkat Sg bigWig 0 5823.31 Jurkat T-lymphocyte acute leukemia cell line DNaseI Signal from ENCODE 0 77 85 165 255 170 210 255 0 0 0 regulation 1 color 85,165,255\ longLabel Jurkat T-lymphocyte acute leukemia cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.71966\ shortLabel Jurkat Sg\ subGroups cellType=Jurkat treatment=n_a tissue=blood cancer=cancer\ table wgEncodeRegDnaseUwJurkatSignal\ track wgEncodeRegDnaseUwJurkatWig\ type bigWig 0 5823.31\ AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_tpm_rev AorticSmsToIL1b_01hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_reverse 1 78 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12754-136A9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2001hr%2c%20biol_rep2%20%28LK44%29.CNhs13373.12754-136A9.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12754-136A9 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_01hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12754-136A9\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_ctss_rev AorticSmsToIL1b_01hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_reverse 0 78 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12754-136A9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2001hr%2c%20biol_rep2%20%28LK44%29.CNhs13373.12754-136A9.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12754-136A9 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_01hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12754-136A9\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF758RQJ GM12878 ARNT narrowPeak Transcription Factor ChIP-seq Peaks of ARNT in GM12878 from ENCODE 3 (ENCFF758RQJ) 0 78 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of ARNT in GM12878 from ENCODE 3 (ENCFF758RQJ)\ parent encTfChipPk off\ shortLabel GM12878 ARNT\ subGroups cellType=GM12878 factor=ARNT\ track encTfChipPkENCFF758RQJ\ wgEncodeRegDnaseUwGm12878Peak GM12878 Pk narrowPeak GM12878 B-lymphocyte, lymphoblastoid cell line DNaseI Peaks from ENCODE 1 78 85 152 255 170 203 255 1 0 0 regulation 1 color 85,152,255\ longLabel GM12878 B-lymphocyte, lymphoblastoid cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak on\ shortLabel GM12878 Pk\ subGroups view=a_Peaks cellType=GM12878 treatment=n_a tissue=blood cancer=normal\ track wgEncodeRegDnaseUwGm12878Peak\ wgEncodeRegDnaseUwGm12878Wig GM12878 Sg bigWig 0 7218.11 GM12878 B-lymphocyte, lymphoblastoid cell line DNaseI Signal from ENCODE 0 78 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel GM12878 B-lymphocyte, lymphoblastoid cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig on\ priority 1.73349\ shortLabel GM12878 Sg\ subGroups cellType=GM12878 treatment=n_a tissue=blood cancer=normal\ table wgEncodeRegDnaseUwGm12878Signal\ track wgEncodeRegDnaseUwGm12878Wig\ type bigWig 0 7218.11\ netHprcGCA_018503585v1 HG02818.mat netAlign GCA_018503585.1 chainHprcGCA_018503585v1 HG02818.mat HG02818.pri.mat.f1_v2 (May 2021 GCA_018503585.1_HG02818.pri.mat.f1_v2) HPRC project computed Chain Nets 1 78 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02818.mat HG02818.pri.mat.f1_v2 (May 2021 GCA_018503585.1_HG02818.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018503585.1\ parent hprcChainNetViewnet off\ priority 14\ shortLabel HG02818.mat\ subGroups view=net sample=s014 population=afr subpop=gwd hap=mat\ track netHprcGCA_018503585v1\ type netAlign GCA_018503585.1 chainHprcGCA_018503585v1\ AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_tpm_fwd AorticSmsToIL1b_02hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_forward 1 79 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12755-136B1 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2002hr%2c%20biol_rep2%20%28LK47%29.CNhs13374.12755-136B1.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12755-136B1 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_02hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12755-136B1\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_ctss_fwd AorticSmsToIL1b_02hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_forward 0 79 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12755-136B1 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2002hr%2c%20biol_rep2%20%28LK47%29.CNhs13374.12755-136B1.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12755-136B1 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_02hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12755-136B1\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwGm12865Peak GM12865 Pk narrowPeak GM12865 B-lymphocyte, lymphoblastoid cell line DNaseI Peaks from ENCODE 1 79 85 147 255 170 201 255 1 0 0 regulation 1 color 85,147,255\ longLabel GM12865 B-lymphocyte, lymphoblastoid cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel GM12865 Pk\ subGroups view=a_Peaks cellType=GM12865 treatment=n_a tissue=blood cancer=unknown\ track wgEncodeRegDnaseUwGm12865Peak\ wgEncodeRegDnaseUwGm12865Wig GM12865 Sg bigWig 0 8525.5 GM12865 B-lymphocyte, lymphoblastoid cell line DNaseI Signal from ENCODE 0 79 85 147 255 170 201 255 0 0 0 regulation 1 color 85,147,255\ longLabel GM12865 B-lymphocyte, lymphoblastoid cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.73856\ shortLabel GM12865 Sg\ subGroups cellType=GM12865 treatment=n_a tissue=blood cancer=unknown\ table wgEncodeRegDnaseUwGm12865Signal\ track wgEncodeRegDnaseUwGm12865Wig\ type bigWig 0 8525.5\ encTfChipPkENCFF096XRG GM12878 ASH2L narrowPeak Transcription Factor ChIP-seq Peaks of ASH2L in GM12878 from ENCODE 3 (ENCFF096XRG) 0 79 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of ASH2L in GM12878 from ENCODE 3 (ENCFF096XRG)\ parent encTfChipPk off\ shortLabel GM12878 ASH2L\ subGroups cellType=GM12878 factor=ASH2L\ track encTfChipPkENCFF096XRG\ chainHprcGCA_018504065v1 HG02723.mat chain GCA_018504065.1 HG02723.mat HG02723.pri.mat.f1_v2 (May 2021 GCA_018504065.1_HG02723.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 79 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02723.mat HG02723.pri.mat.f1_v2 (May 2021 GCA_018504065.1_HG02723.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018504065.1\ parent hprcChainNetViewchain off\ priority 15\ shortLabel HG02723.mat\ subGroups view=chain sample=s015 population=afr subpop=gwd hap=mat\ track chainHprcGCA_018504065v1\ type chain GCA_018504065.1\ AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_tpm_rev AorticSmsToIL1b_02hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_reverse 1 80 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12755-136B1 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2002hr%2c%20biol_rep2%20%28LK47%29.CNhs13374.12755-136B1.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12755-136B1 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_02hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12755-136B1\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_ctss_rev AorticSmsToIL1b_02hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_reverse 0 80 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12755-136B1 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2002hr%2c%20biol_rep2%20%28LK47%29.CNhs13374.12755-136B1.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12755-136B1 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_02hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12755-136B1\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF210HTZ GM12878 ATF2 1 narrowPeak Transcription Factor ChIP-seq Peaks of ATF2 in GM12878 from ENCODE 3 (ENCFF210HTZ) 0 80 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of ATF2 in GM12878 from ENCODE 3 (ENCFF210HTZ)\ parent encTfChipPk off\ shortLabel GM12878 ATF2 1\ subGroups cellType=GM12878 factor=ATF2\ track encTfChipPkENCFF210HTZ\ netHprcGCA_018504065v1 HG02723.mat netAlign GCA_018504065.1 chainHprcGCA_018504065v1 HG02723.mat HG02723.pri.mat.f1_v2 (May 2021 GCA_018504065.1_HG02723.pri.mat.f1_v2) HPRC project computed Chain Nets 1 80 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02723.mat HG02723.pri.mat.f1_v2 (May 2021 GCA_018504065.1_HG02723.pri.mat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018504065.1\ parent hprcChainNetViewnet off\ priority 15\ shortLabel HG02723.mat\ subGroups view=net sample=s015 population=afr subpop=gwd hap=mat\ track netHprcGCA_018504065v1\ type netAlign GCA_018504065.1 chainHprcGCA_018504065v1\ wgEncodeRegDnaseUwMonocytescd14ro01746Peak Monocyte-CD14+ Pk narrowPeak Monocytes-CD14+_RO01746 monocyte, CD14+ DNaseI Peaks from ENCODE 1 80 85 135 255 170 195 255 1 0 0 regulation 1 color 85,135,255\ longLabel Monocytes-CD14+_RO01746 monocyte, CD14+ DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel Monocyte-CD14+ Pk\ subGroups view=a_Peaks cellType=Monocytes_CD14_RO01746 treatment=n_a tissue=blood cancer=normal\ track wgEncodeRegDnaseUwMonocytescd14ro01746Peak\ wgEncodeRegDnaseUwMonocytescd14ro01746Wig Monocyte-CD14+ Sg bigWig 0 853.111 Monocytes-CD14+_RO01746 monocyte, CD14+ DNaseI Signal from ENCODE 0 80 85 135 255 170 195 255 0 0 0 regulation 1 color 85,135,255\ longLabel Monocytes-CD14+_RO01746 monocyte, CD14+ DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.75089\ shortLabel Monocyte-CD14+ Sg\ subGroups cellType=Monocytes_CD14_RO01746 treatment=n_a tissue=blood cancer=normal\ table wgEncodeRegDnaseUwMonocytescd14ro01746Signal\ track wgEncodeRegDnaseUwMonocytescd14ro01746Wig\ type bigWig 0 853.111\ AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_tpm_fwd AorticSmsToIL1b_02hrBr3+ bigWig Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_forward 1 81 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12853-137C9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2002hr%2c%20biol_rep3%20%28LK48%29.CNhs13582.12853-137C9.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12853-137C9 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_02hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12853-137C9\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_ctss_fwd AorticSmsToIL1b_02hrBr3+ bigWig Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_forward 0 81 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12853-137C9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2002hr%2c%20biol_rep3%20%28LK48%29.CNhs13582.12853-137C9.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12853-137C9 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_02hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12853-137C9\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF806KKM GM12878 ATF2 2 narrowPeak Transcription Factor ChIP-seq Peaks of ATF2 in GM12878 from ENCODE 3 (ENCFF806KKM) 0 81 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of ATF2 in GM12878 from ENCODE 3 (ENCFF806KKM)\ parent encTfChipPk off\ shortLabel GM12878 ATF2 2\ subGroups cellType=GM12878 factor=ATF2\ track encTfChipPkENCFF806KKM\ chainHprcGCA_018469925v1 HG02622.pat chain GCA_018469925.1 HG02622.pat HG02622.alt.pat.f1_v2 (May 2021 GCA_018469925.1_HG02622.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 81 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02622.pat HG02622.alt.pat.f1_v2 (May 2021 GCA_018469925.1_HG02622.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469925.1\ parent hprcChainNetViewchain off\ priority 2\ shortLabel HG02622.pat\ subGroups view=chain sample=s002 population=afr subpop=gwd hap=pat\ track chainHprcGCA_018469925v1\ type chain GCA_018469925.1\ wgEncodeRegDnaseUwHl60Peak HL-60 Pk narrowPeak HL-60 acute promyelocytic leukemia (APL) cell line DNaseI Peaks from ENCODE 1 81 85 124 255 170 189 255 1 0 0 regulation 1 color 85,124,255\ longLabel HL-60 acute promyelocytic leukemia (APL) cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HL-60 Pk\ subGroups view=a_Peaks cellType=HL-60 treatment=n_a tissue=blood cancer=cancer\ track wgEncodeRegDnaseUwHl60Peak\ wgEncodeRegDnaseUwHl60Wig HL-60 Sg bigWig 0 5012.92 HL-60 acute promyelocytic leukemia (APL) cell line DNaseI Signal from ENCODE 0 81 85 124 255 170 189 255 0 0 0 regulation 1 color 85,124,255\ longLabel HL-60 acute promyelocytic leukemia (APL) cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.76239\ shortLabel HL-60 Sg\ subGroups cellType=HL-60 treatment=n_a tissue=blood cancer=cancer\ table wgEncodeRegDnaseUwHl60Signal\ track wgEncodeRegDnaseUwHl60Wig\ type bigWig 0 5012.92\ AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_tpm_rev AorticSmsToIL1b_02hrBr3- bigWig Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_reverse 1 82 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12853-137C9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2002hr%2c%20biol_rep3%20%28LK48%29.CNhs13582.12853-137C9.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12853-137C9 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_02hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12853-137C9\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_ctss_rev AorticSmsToIL1b_02hrBr3- bigWig Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_reverse 0 82 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12853-137C9 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2002hr%2c%20biol_rep3%20%28LK48%29.CNhs13582.12853-137C9.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12853-137C9 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_02hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12853-137C9\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF495PWL GM12878 ATF7 narrowPeak Transcription Factor ChIP-seq Peaks of ATF7 in GM12878 from ENCODE 3 (ENCFF495PWL) 0 82 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of ATF7 in GM12878 from ENCODE 3 (ENCFF495PWL)\ parent encTfChipPk off\ shortLabel GM12878 ATF7\ subGroups cellType=GM12878 factor=ATF7\ track encTfChipPkENCFF495PWL\ netHprcGCA_018469925v1 HG02622.pat netAlign GCA_018469925.1 chainHprcGCA_018469925v1 HG02622.pat HG02622.alt.pat.f1_v2 (May 2021 GCA_018469925.1_HG02622.alt.pat.f1_v2) HPRC project computed Chain Nets 1 82 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02622.pat HG02622.alt.pat.f1_v2 (May 2021 GCA_018469925.1_HG02622.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469925.1\ parent hprcChainNetViewnet off\ priority 2\ shortLabel HG02622.pat\ subGroups view=net sample=s002 population=afr subpop=gwd hap=pat\ track netHprcGCA_018469925v1\ type netAlign GCA_018469925.1 chainHprcGCA_018469925v1\ wgEncodeRegDnaseUwNb4Peak NB4 Pk narrowPeak NB4 acute promyelocytic leukemia (APL) cell line DNaseI Peaks from ENCODE 1 82 85 112 255 170 183 255 1 0 0 regulation 1 color 85,112,255\ longLabel NB4 acute promyelocytic leukemia (APL) cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel NB4 Pk\ subGroups view=a_Peaks cellType=NB4 treatment=n_a tissue=bone_marrow cancer=cancer\ track wgEncodeRegDnaseUwNb4Peak\ wgEncodeRegDnaseUwNb4Wig NB4 Sg bigWig 0 7662.2 NB4 acute promyelocytic leukemia (APL) cell line DNaseI Signal from ENCODE 0 82 85 112 255 170 183 255 0 0 0 regulation 1 color 85,112,255\ longLabel NB4 acute promyelocytic leukemia (APL) cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.77436\ shortLabel NB4 Sg\ subGroups cellType=NB4 treatment=n_a tissue=bone_marrow cancer=cancer\ table wgEncodeRegDnaseUwNb4Signal\ track wgEncodeRegDnaseUwNb4Wig\ type bigWig 0 7662.2\ AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_tpm_fwd AorticSmsToIL1b_03hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_forward 1 83 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12658-134I3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2003hr%2c%20biol_rep1%20%28LK49%29.CNhs13355.12658-134I3.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12658-134I3 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_03hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12658-134I3\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_ctss_fwd AorticSmsToIL1b_03hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_forward 0 83 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12658-134I3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2003hr%2c%20biol_rep1%20%28LK49%29.CNhs13355.12658-134I3.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12658-134I3 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_03hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12658-134I3\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF725YZH GM12878 BACH1 narrowPeak Transcription Factor ChIP-seq Peaks of BACH1 in GM12878 from ENCODE 3 (ENCFF725YZH) 0 83 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of BACH1 in GM12878 from ENCODE 3 (ENCFF725YZH)\ parent encTfChipPk off\ shortLabel GM12878 BACH1\ subGroups cellType=GM12878 factor=BACH1\ track encTfChipPkENCFF725YZH\ wgEncodeRegDnaseUwH7hescPeak H7-ES Pk narrowPeak H7-hESC embryonic stem cell DNaseI Peaks from ENCODE 1 83 85 93 255 170 174 255 1 0 0 regulation 1 color 85,93,255\ longLabel H7-hESC embryonic stem cell DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak on\ shortLabel H7-ES Pk\ subGroups view=a_Peaks cellType=H7-hESC treatment=n_a tissue=embryo cancer=unknown\ track wgEncodeRegDnaseUwH7hescPeak\ wgEncodeRegDnaseUwH7hescWig H7-ES Sg bigWig 0 13035.4 H7-hESC embryonic stem cell DNaseI Signal from ENCODE 0 83 85 93 255 170 174 255 0 0 0 regulation 1 color 85,93,255\ longLabel H7-hESC embryonic stem cell DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig on\ priority 1.79509\ shortLabel H7-ES Sg\ subGroups cellType=H7-hESC treatment=n_a tissue=embryo cancer=unknown\ table wgEncodeRegDnaseUwH7hescSignal\ track wgEncodeRegDnaseUwH7hescWig\ type bigWig 0 13035.4\ chainHprcGCA_018469945v1 HG02630.pat chain GCA_018469945.1 HG02630.pat HG02630.alt.pat.f1_v2 (May 2021 GCA_018469945.1_HG02630.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 83 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02630.pat HG02630.alt.pat.f1_v2 (May 2021 GCA_018469945.1_HG02630.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018469945.1\ parent hprcChainNetViewchain off\ priority 4\ shortLabel HG02630.pat\ subGroups view=chain sample=s004 population=afr subpop=gwd hap=pat\ track chainHprcGCA_018469945v1\ type chain GCA_018469945.1\ AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_tpm_rev AorticSmsToIL1b_03hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_reverse 1 84 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12658-134I3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2003hr%2c%20biol_rep1%20%28LK49%29.CNhs13355.12658-134I3.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12658-134I3 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_03hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12658-134I3\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_ctss_rev AorticSmsToIL1b_03hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_reverse 0 84 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12658-134I3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2003hr%2c%20biol_rep1%20%28LK49%29.CNhs13355.12658-134I3.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12658-134I3 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_03hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12658-134I3\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF832YIE GM12878 BATF narrowPeak Transcription Factor ChIP-seq Peaks of BATF in GM12878 from ENCODE 3 (ENCFF832YIE) 0 84 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of BATF in GM12878 from ENCODE 3 (ENCFF832YIE)\ parent encTfChipPk off\ shortLabel GM12878 BATF\ subGroups cellType=GM12878 factor=BATF\ track encTfChipPkENCFF832YIE\ wgEncodeRegDnaseUwH7hescDiffprota5dPeak H7-ES diff 5d Pk narrowPeak H7-hESC embryonic stem cell (diff 5d) DNaseI Peaks from ENCODE 1 84 85 88 255 170 171 255 1 0 0 regulation 1 color 85,88,255\ longLabel H7-hESC embryonic stem cell (diff 5d) DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel H7-ES diff 5d Pk\ subGroups view=a_Peaks cellType=H7-hESC treatment=diffProtA_5d tissue=embryo cancer=unknown\ track wgEncodeRegDnaseUwH7hescDiffprota5dPeak\ wgEncodeRegDnaseUwH7hescDiffprota5dWig H7-ES diff 5d Sg bigWig 0 5836.88 H7-hESC embryonic stem cell (diff 5d) DNaseI Signal from ENCODE 0 84 85 88 255 170 171 255 0 0 0 regulation 1 color 85,88,255\ longLabel H7-hESC embryonic stem cell (diff 5d) DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.80059\ shortLabel H7-ES diff 5d Sg\ subGroups cellType=H7-hESC treatment=diffProtA_5d tissue=embryo cancer=unknown\ table wgEncodeRegDnaseUwH7hescDiffprota5dSignal\ track wgEncodeRegDnaseUwH7hescDiffprota5dWig\ type bigWig 0 5836.88\ netHprcGCA_018469945v1 HG02630.pat netAlign GCA_018469945.1 chainHprcGCA_018469945v1 HG02630.pat HG02630.alt.pat.f1_v2 (May 2021 GCA_018469945.1_HG02630.alt.pat.f1_v2) HPRC project computed Chain Nets 1 84 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02630.pat HG02630.alt.pat.f1_v2 (May 2021 GCA_018469945.1_HG02630.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018469945.1\ parent hprcChainNetViewnet off\ priority 4\ shortLabel HG02630.pat\ subGroups view=net sample=s004 population=afr subpop=gwd hap=pat\ track netHprcGCA_018469945v1\ type netAlign GCA_018469945.1 chainHprcGCA_018469945v1\ AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_tpm_fwd AorticSmsToIL1b_03hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_forward 1 85 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12756-136B2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2003hr%2c%20biol_rep2%20%28LK50%29.CNhs13375.12756-136B2.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12756-136B2 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_03hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12756-136B2\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_ctss_fwd AorticSmsToIL1b_03hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_forward 0 85 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12756-136B2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2003hr%2c%20biol_rep2%20%28LK50%29.CNhs13375.12756-136B2.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12756-136B2 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_03hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12756-136B2\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF383HAY GM12878 BCL11A narrowPeak Transcription Factor ChIP-seq Peaks of BCL11A in GM12878 from ENCODE 3 (ENCFF383HAY) 0 85 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of BCL11A in GM12878 from ENCODE 3 (ENCFF383HAY)\ parent encTfChipPk off\ shortLabel GM12878 BCL11A\ subGroups cellType=GM12878 factor=BCL11A\ track encTfChipPkENCFF383HAY\ wgEncodeRegDnaseUwH7hescDiffprota14dPeak H7-ES diff 14d Pk narrowPeak H7-hESC embryonic stem cell (diff 14d) DNaseI Peaks from ENCODE 1 85 89 85 255 172 170 255 1 0 0 regulation 1 color 89,85,255\ longLabel H7-hESC embryonic stem cell (diff 14d) DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel H7-ES diff 14d Pk\ subGroups view=a_Peaks cellType=H7-hESC treatment=diffProtA_14d tissue=embryo cancer=unknown\ track wgEncodeRegDnaseUwH7hescDiffprota14dPeak\ wgEncodeRegDnaseUwH7hescDiffprota14dWig H7-ES diff 14d Sg bigWig 0 21393.7 H7-hESC embryonic stem cell (diff 14d) DNaseI Signal from ENCODE 0 85 89 85 255 172 170 255 0 0 0 regulation 1 color 89,85,255\ longLabel H7-hESC embryonic stem cell (diff 14d) DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.80809\ shortLabel H7-ES diff 14d Sg\ subGroups cellType=H7-hESC treatment=diffProtA_14d tissue=embryo cancer=unknown\ table wgEncodeRegDnaseUwH7hescDiffprota14dSignal\ track wgEncodeRegDnaseUwH7hescDiffprota14dWig\ type bigWig 0 21393.7\ chainHprcGCA_018470425v1 HG02717.pat chain GCA_018470425.1 HG02717.pat HG02717.alt.pat.f1_v2 (May 2021 GCA_018470425.1_HG02717.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 85 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02717.pat HG02717.alt.pat.f1_v2 (May 2021 GCA_018470425.1_HG02717.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018470425.1\ parent hprcChainNetViewchain off\ priority 6\ shortLabel HG02717.pat\ subGroups view=chain sample=s006 population=afr subpop=gwd hap=pat\ track chainHprcGCA_018470425v1\ type chain GCA_018470425.1\ AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_tpm_rev AorticSmsToIL1b_03hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_reverse 1 86 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12756-136B2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2003hr%2c%20biol_rep2%20%28LK50%29.CNhs13375.12756-136B2.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12756-136B2 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_03hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12756-136B2\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_ctss_rev AorticSmsToIL1b_03hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_reverse 0 86 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12756-136B2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2003hr%2c%20biol_rep2%20%28LK50%29.CNhs13375.12756-136B2.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12756-136B2 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_03hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12756-136B2\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF247MHT GM12878 BCL3 narrowPeak Transcription Factor ChIP-seq Peaks of BCL3 in GM12878 from ENCODE 3 (ENCFF247MHT) 0 86 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of BCL3 in GM12878 from ENCODE 3 (ENCFF247MHT)\ parent encTfChipPk off\ shortLabel GM12878 BCL3\ subGroups cellType=GM12878 factor=BCL3\ track encTfChipPkENCFF247MHT\ netHprcGCA_018470425v1 HG02717.pat netAlign GCA_018470425.1 chainHprcGCA_018470425v1 HG02717.pat HG02717.alt.pat.f1_v2 (May 2021 GCA_018470425.1_HG02717.alt.pat.f1_v2) HPRC project computed Chain Nets 1 86 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02717.pat HG02717.alt.pat.f1_v2 (May 2021 GCA_018470425.1_HG02717.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018470425.1\ parent hprcChainNetViewnet off\ priority 6\ shortLabel HG02717.pat\ subGroups view=net sample=s006 population=afr subpop=gwd hap=pat\ track netHprcGCA_018470425v1\ type netAlign GCA_018470425.1 chainHprcGCA_018470425v1\ wgEncodeRegDnaseUwRptecPeak RPTEC Pk narrowPeak RPTEC renal proximal tubule epithelium DNaseI Peaks from ENCODE 1 86 100 85 255 177 170 255 1 0 0 regulation 1 color 100,85,255\ longLabel RPTEC renal proximal tubule epithelium DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel RPTEC Pk\ subGroups view=a_Peaks cellType=RPTEC treatment=n_a tissue=kidney cancer=normal\ track wgEncodeRegDnaseUwRptecPeak\ wgEncodeRegDnaseUwRptecWig RPTEC Sg bigWig 0 22767.8 RPTEC renal proximal tubule epithelium DNaseI Signal from ENCODE 0 86 100 85 255 177 170 255 0 0 0 regulation 1 color 100,85,255\ longLabel RPTEC renal proximal tubule epithelium DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.82024\ shortLabel RPTEC Sg\ subGroups cellType=RPTEC treatment=n_a tissue=kidney cancer=normal\ table wgEncodeRegDnaseUwRptecSignal\ track wgEncodeRegDnaseUwRptecWig\ type bigWig 0 22767.8\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_tpm_fwd AorticSmsToIL1b_04hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_forward 1 87 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12659-134I4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep1%20%28LK52%29.CNhs13682.12659-134I4.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12659-134I4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_04hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12659-134I4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_ctss_fwd AorticSmsToIL1b_04hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_forward 0 87 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12659-134I4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep1%20%28LK52%29.CNhs13682.12659-134I4.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12659-134I4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_04hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12659-134I4\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF622HGF GM12878 BHLHE40 1 narrowPeak Transcription Factor ChIP-seq Peaks of BHLHE40 in GM12878 from ENCODE 3 (ENCFF622HGF) 0 87 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of BHLHE40 in GM12878 from ENCODE 3 (ENCFF622HGF)\ parent encTfChipPk off\ shortLabel GM12878 BHLHE40 1\ subGroups cellType=GM12878 factor=BHLHE40\ track encTfChipPkENCFF622HGF\ chainHprcGCA_018470435v1 HG02572.pat chain GCA_018470435.1 HG02572.pat HG02572.alt.pat.f1_v2 (May 2021 GCA_018470435.1_HG02572.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 87 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02572.pat HG02572.alt.pat.f1_v2 (May 2021 GCA_018470435.1_HG02572.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018470435.1\ parent hprcChainNetViewchain off\ priority 7\ shortLabel HG02572.pat\ subGroups view=chain sample=s007 population=afr subpop=gwd hap=pat\ track chainHprcGCA_018470435v1\ type chain GCA_018470435.1\ wgEncodeRegDnaseUwHrpepicPeak HRPEpiC Pk narrowPeak HRPEpiC retinal pigment epithelium DNaseI Peaks from ENCODE 1 87 124 85 255 189 170 255 1 0 0 regulation 1 color 124,85,255\ longLabel HRPEpiC retinal pigment epithelium DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HRPEpiC Pk\ subGroups view=a_Peaks cellType=HRPEpiC treatment=n_a tissue=eye cancer=normal\ track wgEncodeRegDnaseUwHrpepicPeak\ wgEncodeRegDnaseUwHrpepicWig HRPEpiC Sg bigWig 0 32404.6 HRPEpiC retinal pigment epithelium DNaseI Signal from ENCODE 0 87 124 85 255 189 170 255 0 0 0 regulation 1 color 124,85,255\ longLabel HRPEpiC retinal pigment epithelium DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.84446\ shortLabel HRPEpiC Sg\ subGroups cellType=HRPEpiC treatment=n_a tissue=eye cancer=normal\ table wgEncodeRegDnaseUwHrpepicSignal\ track wgEncodeRegDnaseUwHrpepicWig\ type bigWig 0 32404.6\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_tpm_rev AorticSmsToIL1b_04hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_reverse 1 88 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12659-134I4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep1%20%28LK52%29.CNhs13682.12659-134I4.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12659-134I4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_04hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12659-134I4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_ctss_rev AorticSmsToIL1b_04hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_reverse 0 88 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12659-134I4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep1%20%28LK52%29.CNhs13682.12659-134I4.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12659-134I4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_04hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12659-134I4\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF370ZNL GM12878 BHLHE40 2 narrowPeak Transcription Factor ChIP-seq Peaks of BHLHE40 in GM12878 from ENCODE 3 (ENCFF370ZNL) 0 88 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of BHLHE40 in GM12878 from ENCODE 3 (ENCFF370ZNL)\ parent encTfChipPk off\ shortLabel GM12878 BHLHE40 2\ subGroups cellType=GM12878 factor=BHLHE40\ track encTfChipPkENCFF370ZNL\ netHprcGCA_018470435v1 HG02572.pat netAlign GCA_018470435.1 chainHprcGCA_018470435v1 HG02572.pat HG02572.alt.pat.f1_v2 (May 2021 GCA_018470435.1_HG02572.alt.pat.f1_v2) HPRC project computed Chain Nets 1 88 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02572.pat HG02572.alt.pat.f1_v2 (May 2021 GCA_018470435.1_HG02572.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018470435.1\ parent hprcChainNetViewnet off\ priority 7\ shortLabel HG02572.pat\ subGroups view=net sample=s007 population=afr subpop=gwd hap=pat\ track netHprcGCA_018470435v1\ type netAlign GCA_018470435.1 chainHprcGCA_018470435v1\ wgEncodeRegDnaseUwHmvecdlyadPeak HMVEC-dLy-Ad Pk narrowPeak HMVEC-dLy-Ad dermal MV endothelial cell, lymph DNaseI Peaks from ENCODE 1 88 133 85 255 194 170 255 1 0 0 regulation 1 color 133,85,255\ longLabel HMVEC-dLy-Ad dermal MV endothelial cell, lymph DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel HMVEC-dLy-Ad Pk\ subGroups view=a_Peaks cellType=HMVEC-dLy-Ad treatment=n_a tissue=blood_vessel cancer=normal\ track wgEncodeRegDnaseUwHmvecdlyadPeak\ wgEncodeRegDnaseUwHmvecdlyadWig HMVEC-dLy-Ad Sg bigWig 0 39771.9 HMVEC-dLy-Ad dermal MV endothelial cell, lymph DNaseI Signal from ENCODE 0 88 133 85 255 194 170 255 0 0 0 regulation 1 color 133,85,255\ longLabel HMVEC-dLy-Ad dermal MV endothelial cell, lymph DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.85388\ shortLabel HMVEC-dLy-Ad Sg\ subGroups cellType=HMVEC-dLy-Ad treatment=n_a tissue=blood_vessel cancer=normal\ table wgEncodeRegDnaseUwHmvecdlyadSignal\ track wgEncodeRegDnaseUwHmvecdlyadWig\ type bigWig 0 39771.9\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_tpm_fwd AorticSmsToIL1b_04hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_forward 1 89 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12757-136B3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep2%20%28LK53%29.CNhs13376.12757-136B3.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12757-136B3 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_04hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12757-136B3\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_ctss_fwd AorticSmsToIL1b_04hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_forward 0 89 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12757-136B3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep2%20%28LK53%29.CNhs13376.12757-136B3.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12757-136B3 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_04hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12757-136B3\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF592LPO GM12878 BMI1 narrowPeak Transcription Factor ChIP-seq Peaks of BMI1 in GM12878 from ENCODE 3 (ENCFF592LPO) 0 89 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of BMI1 in GM12878 from ENCODE 3 (ENCFF592LPO)\ parent encTfChipPk off\ shortLabel GM12878 BMI1\ subGroups cellType=GM12878 factor=BMI1\ track encTfChipPkENCFF592LPO\ wgEncodeRegDnaseUwHelas3Peak HeLa-S3 Pk narrowPeak HeLa-S3 cervical epithelial adenocarcinoma cell line DNaseI Peaks from ENCODE 1 89 157 85 255 206 170 255 1 0 0 regulation 1 color 157,85,255\ longLabel HeLa-S3 cervical epithelial adenocarcinoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak on\ shortLabel HeLa-S3 Pk\ subGroups view=a_Peaks cellType=HeLa-S3 treatment=n_a tissue=cervix cancer=cancer\ track wgEncodeRegDnaseUwHelas3Peak\ wgEncodeRegDnaseUwHelas3Wig HeLa-S3 Sg bigWig 0 26492 HeLa-S3 cervical epithelial adenocarcinoma cell line DNaseI Signal from ENCODE 0 89 157 85 255 206 170 255 0 0 0 regulation 1 color 157,85,255\ longLabel HeLa-S3 cervical epithelial adenocarcinoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig on\ priority 1.87897\ shortLabel HeLa-S3 Sg\ subGroups cellType=HeLa-S3 treatment=n_a tissue=cervix cancer=cancer\ table wgEncodeRegDnaseUwHelas3Signal\ track wgEncodeRegDnaseUwHelas3Wig\ type bigWig 0 26492\ chainHprcGCA_018470465v1 HG02886.pat chain GCA_018470465.1 HG02886.pat HG02886.alt.pat.f1_v2 (May 2021 GCA_018470465.1_HG02886.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 89 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02886.pat HG02886.alt.pat.f1_v2 (May 2021 GCA_018470465.1_HG02886.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018470465.1\ parent hprcChainNetViewchain off\ priority 10\ shortLabel HG02886.pat\ subGroups view=chain sample=s010 population=afr subpop=gwd hap=pat\ track chainHprcGCA_018470465v1\ type chain GCA_018470465.1\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_tpm_rev AorticSmsToIL1b_04hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_reverse 1 90 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12757-136B3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep2%20%28LK53%29.CNhs13376.12757-136B3.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12757-136B3 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_04hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12757-136B3\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_ctss_rev AorticSmsToIL1b_04hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_reverse 0 90 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12757-136B3 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep2%20%28LK53%29.CNhs13376.12757-136B3.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12757-136B3 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_04hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12757-136B3\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF005JKU GM12878 BRCA1 narrowPeak Transcription Factor ChIP-seq Peaks of BRCA1 in GM12878 from ENCODE 3 (ENCFF005JKU) 0 90 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of BRCA1 in GM12878 from ENCODE 3 (ENCFF005JKU)\ parent encTfChipPk off\ shortLabel GM12878 BRCA1\ subGroups cellType=GM12878 factor=BRCA1\ track encTfChipPkENCFF005JKU\ netHprcGCA_018470465v1 HG02886.pat netAlign GCA_018470465.1 chainHprcGCA_018470465v1 HG02886.pat HG02886.alt.pat.f1_v2 (May 2021 GCA_018470465.1_HG02886.alt.pat.f1_v2) HPRC project computed Chain Nets 1 90 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02886.pat HG02886.alt.pat.f1_v2 (May 2021 GCA_018470465.1_HG02886.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018470465.1\ parent hprcChainNetViewnet off\ priority 10\ shortLabel HG02886.pat\ subGroups view=net sample=s010 population=afr subpop=gwd hap=pat\ track netHprcGCA_018470465v1\ type netAlign GCA_018470465.1 chainHprcGCA_018470465v1\ wgEncodeRegDnaseUwSknmcPeak SK-N-MC Pk narrowPeak SK-N-MC neuroepithelioma cell line DNaseI Peaks from ENCODE 1 90 176 85 255 215 170 255 1 0 0 regulation 1 color 176,85,255\ longLabel SK-N-MC neuroepithelioma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel SK-N-MC Pk\ subGroups view=a_Peaks cellType=SK-N-MC treatment=n_a tissue=brain cancer=cancer\ track wgEncodeRegDnaseUwSknmcPeak\ wgEncodeRegDnaseUwSknmcWig SK-N-MC Sg bigWig 0 5864.79 SK-N-MC neuroepithelioma cell line DNaseI Signal from ENCODE 0 90 176 85 255 215 170 255 0 0 0 regulation 1 color 176,85,255\ longLabel SK-N-MC neuroepithelioma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.90393\ shortLabel SK-N-MC Sg\ subGroups cellType=SK-N-MC treatment=n_a tissue=brain cancer=cancer\ table wgEncodeRegDnaseUwSknmcSignal\ track wgEncodeRegDnaseUwSknmcWig\ type bigWig 0 5864.79\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_tpm_fwd AorticSmsToIL1b_04hrBr3+ bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_forward 1 91 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12855-137D2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep3%20%28LK54%29.CNhs13584.12855-137D2.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12855-137D2 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_04hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12855-137D2\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_ctss_fwd AorticSmsToIL1b_04hrBr3+ bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_forward 0 91 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12855-137D2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep3%20%28LK54%29.CNhs13584.12855-137D2.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12855-137D2 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_04hrBr3+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12855-137D2\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF070SOX GM12878 CBFB narrowPeak Transcription Factor ChIP-seq Peaks of CBFB in GM12878 from ENCODE 3 (ENCFF070SOX) 0 91 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CBFB in GM12878 from ENCODE 3 (ENCFF070SOX)\ parent encTfChipPk off\ shortLabel GM12878 CBFB\ subGroups cellType=GM12878 factor=CBFB\ track encTfChipPkENCFF070SOX\ chainHprcGCA_018473315v1 HG03540.pat chain GCA_018473315.1 HG03540.pat HG03540.alt.pat.f1_v2 (May 2021 GCA_018473315.1_HG03540.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 91 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG03540.pat HG03540.alt.pat.f1_v2 (May 2021 GCA_018473315.1_HG03540.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018473315.1\ parent hprcChainNetViewchain off\ priority 12\ shortLabel HG03540.pat\ subGroups view=chain sample=s012 population=afr subpop=gwd hap=pat\ track chainHprcGCA_018473315v1\ type chain GCA_018473315.1\ wgEncodeRegDnaseUwMcf7Peak MCF-7 Pk narrowPeak MCF-7 mammary adenocarcinoma cell line DNaseI Peaks from ENCODE 1 91 190 85 255 222 170 255 1 0 0 regulation 1 color 190,85,255\ longLabel MCF-7 mammary adenocarcinoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel MCF-7 Pk\ subGroups view=a_Peaks cellType=MCF-7 treatment=n_a tissue=breast cancer=cancer\ track wgEncodeRegDnaseUwMcf7Peak\ wgEncodeRegDnaseUwMcf7Wig MCF-7 Sg bigWig 0 15780.8 MCF-7 mammary adenocarcinoma cell line DNaseI Signal from ENCODE 0 91 190 85 255 222 170 255 0 0 0 regulation 1 color 190,85,255\ longLabel MCF-7 mammary adenocarcinoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.93061\ shortLabel MCF-7 Sg\ subGroups cellType=MCF-7 treatment=n_a tissue=breast cancer=cancer\ table wgEncodeRegDnaseUwMcf7Signal\ track wgEncodeRegDnaseUwMcf7Wig\ type bigWig 0 15780.8\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_tpm_rev AorticSmsToIL1b_04hrBr3- bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_reverse 1 92 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12855-137D2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep3%20%28LK54%29.CNhs13584.12855-137D2.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12855-137D2 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_04hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12855-137D2\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_ctss_rev AorticSmsToIL1b_04hrBr3- bigWig Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_reverse 0 92 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12855-137D2 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2004hr%2c%20biol_rep3%20%28LK54%29.CNhs13584.12855-137D2.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12855-137D2 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_04hrBr3-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12855-137D2\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF552QOA GM12878 CBX3 narrowPeak Transcription Factor ChIP-seq Peaks of CBX3 in GM12878 from ENCODE 3 (ENCFF552QOA) 0 92 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CBX3 in GM12878 from ENCODE 3 (ENCFF552QOA)\ parent encTfChipPk off\ shortLabel GM12878 CBX3\ subGroups cellType=GM12878 factor=CBX3\ track encTfChipPkENCFF552QOA\ netHprcGCA_018473315v1 HG03540.pat netAlign GCA_018473315.1 chainHprcGCA_018473315v1 HG03540.pat HG03540.alt.pat.f1_v2 (May 2021 GCA_018473315.1_HG03540.alt.pat.f1_v2) HPRC project computed Chain Nets 1 92 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG03540.pat HG03540.alt.pat.f1_v2 (May 2021 GCA_018473315.1_HG03540.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018473315.1\ parent hprcChainNetViewnet off\ priority 12\ shortLabel HG03540.pat\ subGroups view=net sample=s012 population=afr subpop=gwd hap=pat\ track netHprcGCA_018473315v1\ type netAlign GCA_018473315.1 chainHprcGCA_018473315v1\ wgEncodeRegDnaseUwMcf7Estradiolctrl0hrPeak MCF-7 estr 0h Pk narrowPeak MCF-7 mammary adenocarcinoma cell line (estradi 0h) DNaseI Peaks from ENCODE 1 92 192 85 255 223 170 255 1 0 0 regulation 1 color 192,85,255\ longLabel MCF-7 mammary adenocarcinoma cell line (estradi 0h) DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel MCF-7 estr 0h Pk\ subGroups view=a_Peaks cellType=MCF-7 treatment=Estradiol_ctrl_0hr tissue=breast cancer=cancer\ track wgEncodeRegDnaseUwMcf7Estradiolctrl0hrPeak\ wgEncodeRegDnaseUwMcf7Estradiolctrl0hrWig MCF-7 estr 0h Sg bigWig 0 23308.2 MCF-7 mammary adenocarcinoma cell line (estradi 0h) DNaseI Signal from ENCODE 0 92 192 85 255 223 170 255 0 0 0 regulation 1 color 192,85,255\ longLabel MCF-7 mammary adenocarcinoma cell line (estradi 0h) DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.93395\ shortLabel MCF-7 estr 0h Sg\ subGroups cellType=MCF-7 treatment=Estradiol_ctrl_0hr tissue=breast cancer=cancer\ table wgEncodeRegDnaseUwMcf7Estradiolctrl0hrSignal\ track wgEncodeRegDnaseUwMcf7Estradiolctrl0hrWig\ type bigWig 0 23308.2\ AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_tpm_fwd AorticSmsToIL1b_05hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_forward 1 93 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12660-134I5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2005hr%2c%20biol_rep1%20%28LK55%29.CNhs13356.12660-134I5.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12660-134I5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_05hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12660-134I5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_ctss_fwd AorticSmsToIL1b_05hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_forward 0 93 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12660-134I5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2005hr%2c%20biol_rep1%20%28LK55%29.CNhs13356.12660-134I5.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12660-134I5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_05hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12660-134I5\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF417SVR GM12878 CBX5 narrowPeak Transcription Factor ChIP-seq Peaks of CBX5 in GM12878 from ENCODE 3 (ENCFF417SVR) 0 93 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CBX5 in GM12878 from ENCODE 3 (ENCFF417SVR)\ parent encTfChipPk off\ shortLabel GM12878 CBX5\ subGroups cellType=GM12878 factor=CBX5\ track encTfChipPkENCFF417SVR\ chainHprcGCA_018503575v1 HG02818.pat chain GCA_018503575.1 HG02818.pat HG02818.alt.pat.f1_v2 (May 2021 GCA_018503575.1_HG02818.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 93 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02818.pat HG02818.alt.pat.f1_v2 (May 2021 GCA_018503575.1_HG02818.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018503575.1\ parent hprcChainNetViewchain off\ priority 13\ shortLabel HG02818.pat\ subGroups view=chain sample=s013 population=afr subpop=gwd hap=pat\ track chainHprcGCA_018503575v1\ type chain GCA_018503575.1\ wgEncodeRegDnaseUwMcf7Estradiol100nm1hrPeak MCF-7 estr 1h Pk narrowPeak MCF-7 mammary adenocarcinoma cell line (estradi 1h) DNaseI Peaks from ENCODE 1 93 192 85 255 223 170 255 1 0 0 regulation 1 color 192,85,255\ longLabel MCF-7 mammary adenocarcinoma cell line (estradi 1h) DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel MCF-7 estr 1h Pk\ subGroups view=a_Peaks cellType=MCF-7 treatment=Estradiol_100nM_1hr tissue=breast cancer=cancer\ track wgEncodeRegDnaseUwMcf7Estradiol100nm1hrPeak\ wgEncodeRegDnaseUwMcf7Estradiol100nm1hrWig MCF-7 estr 1h Sg bigWig 0 24234.6 MCF-7 mammary adenocarcinoma cell line (estradi 1h) DNaseI Signal from ENCODE 0 93 192 85 255 223 170 255 0 0 0 regulation 1 color 192,85,255\ longLabel MCF-7 mammary adenocarcinoma cell line (estradi 1h) DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.93373\ shortLabel MCF-7 estr 1h Sg\ subGroups cellType=MCF-7 treatment=Estradiol_100nM_1hr tissue=breast cancer=cancer\ table wgEncodeRegDnaseUwMcf7Estradiol100nm1hrSignal\ track wgEncodeRegDnaseUwMcf7Estradiol100nm1hrWig\ type bigWig 0 24234.6\ AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_tpm_rev AorticSmsToIL1b_05hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_reverse 1 94 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12660-134I5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2005hr%2c%20biol_rep1%20%28LK55%29.CNhs13356.12660-134I5.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12660-134I5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_05hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12660-134I5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_ctss_rev AorticSmsToIL1b_05hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_reverse 0 94 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12660-134I5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2005hr%2c%20biol_rep1%20%28LK55%29.CNhs13356.12660-134I5.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12660-134I5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_05hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12660-134I5\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF786YYI GM12878 CEBPB narrowPeak Transcription Factor ChIP-seq Peaks of CEBPB in GM12878 from ENCODE 3 (ENCFF786YYI) 0 94 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CEBPB in GM12878 from ENCODE 3 (ENCFF786YYI)\ parent encTfChipPk off\ shortLabel GM12878 CEBPB\ subGroups cellType=GM12878 factor=CEBPB\ track encTfChipPkENCFF786YYI\ netHprcGCA_018503575v1 HG02818.pat netAlign GCA_018503575.1 chainHprcGCA_018503575v1 HG02818.pat HG02818.alt.pat.f1_v2 (May 2021 GCA_018503575.1_HG02818.alt.pat.f1_v2) HPRC project computed Chain Nets 1 94 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02818.pat HG02818.alt.pat.f1_v2 (May 2021 GCA_018503575.1_HG02818.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018503575.1\ parent hprcChainNetViewnet off\ priority 13\ shortLabel HG02818.pat\ subGroups view=net sample=s013 population=afr subpop=gwd hap=pat\ track netHprcGCA_018503575v1\ type netAlign GCA_018503575.1 chainHprcGCA_018503575v1\ wgEncodeRegDnaseUwWerirb1Peak WERI-Rb-1 Pk narrowPeak WERI-Rb-1 retinoblastoma cell line DNaseI Peaks from ENCODE 1 94 211 85 255 233 170 255 1 0 0 regulation 1 color 211,85,255\ longLabel WERI-Rb-1 retinoblastoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel WERI-Rb-1 Pk\ subGroups view=a_Peaks cellType=WERI-Rb-1 treatment=n_a tissue=eye cancer=cancer\ track wgEncodeRegDnaseUwWerirb1Peak\ wgEncodeRegDnaseUwWerirb1Wig WERI-Rb-1 Sg bigWig 0 8726.43 WERI-Rb-1 retinoblastoma cell line DNaseI Signal from ENCODE 0 94 211 85 255 233 170 255 0 0 0 regulation 1 color 211,85,255\ longLabel WERI-Rb-1 retinoblastoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 1.96205\ shortLabel WERI-Rb-1 Sg\ subGroups cellType=WERI-Rb-1 treatment=n_a tissue=eye cancer=cancer\ table wgEncodeRegDnaseUwWerirb1Signal\ track wgEncodeRegDnaseUwWerirb1Wig\ type bigWig 0 8726.43\ AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_tpm_fwd AorticSmsToIL1b_05hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_forward 1 95 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12758-136B4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2005hr%2c%20biol_rep2%20%28LK56%29.CNhs13377.12758-136B4.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12758-136B4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_05hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12758-136B4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_ctss_fwd AorticSmsToIL1b_05hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_forward 0 95 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12758-136B4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2005hr%2c%20biol_rep2%20%28LK56%29.CNhs13377.12758-136B4.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12758-136B4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_05hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12758-136B4\ urlLabel FANTOM5 Details:\ wgEncodeRegDnaseUwBe2cPeak BE2_C Pk narrowPeak BE2_C neuroblastoma cell line DNaseI Peaks from ENCODE 1 95 237 85 255 246 170 255 1 0 0 regulation 1 color 237,85,255\ longLabel BE2_C neuroblastoma cell line DNaseI Peaks from ENCODE\ parent wgEncodeRegDnasePeak off\ shortLabel BE2_C Pk\ subGroups view=a_Peaks cellType=BE2_C treatment=n_a tissue=brain cancer=cancer\ track wgEncodeRegDnaseUwBe2cPeak\ wgEncodeRegDnaseUwBe2cWig BE2_C Sg bigWig 0 72865.5 BE2_C neuroblastoma cell line DNaseI Signal from ENCODE 0 95 237 85 255 246 170 255 0 0 0 regulation 1 color 237,85,255\ longLabel BE2_C neuroblastoma cell line DNaseI Signal from ENCODE\ parent wgEncodeRegDnaseWig off\ priority 2\ shortLabel BE2_C Sg\ subGroups cellType=BE2_C treatment=n_a tissue=brain cancer=cancer\ table wgEncodeRegDnaseUwBe2cSignal\ track wgEncodeRegDnaseUwBe2cWig\ type bigWig 0 72865.5\ encTfChipPkENCFF863CTN GM12878 CHD1 narrowPeak Transcription Factor ChIP-seq Peaks of CHD1 in GM12878 from ENCODE 3 (ENCFF863CTN) 0 95 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CHD1 in GM12878 from ENCODE 3 (ENCFF863CTN)\ parent encTfChipPk off\ shortLabel GM12878 CHD1\ subGroups cellType=GM12878 factor=CHD1\ track encTfChipPkENCFF863CTN\ chainHprcGCA_018504075v1 HG02723.pat chain GCA_018504075.1 HG02723.pat HG02723.alt.pat.f1_v2 (May 2021 GCA_018504075.1_HG02723.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 95 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02723.pat HG02723.alt.pat.f1_v2 (May 2021 GCA_018504075.1_HG02723.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018504075.1\ parent hprcChainNetViewchain off\ priority 16\ shortLabel HG02723.pat\ subGroups view=chain sample=s016 population=afr subpop=gwd hap=pat\ track chainHprcGCA_018504075v1\ type chain GCA_018504075.1\ AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_tpm_rev AorticSmsToIL1b_05hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_reverse 1 96 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12758-136B4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2005hr%2c%20biol_rep2%20%28LK56%29.CNhs13377.12758-136B4.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12758-136B4 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_05hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12758-136B4\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_ctss_rev AorticSmsToIL1b_05hrBr2- bigWig Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_reverse 0 96 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12758-136B4 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2005hr%2c%20biol_rep2%20%28LK56%29.CNhs13377.12758-136B4.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12758-136B4 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_05hrBr2-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12758-136B4\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF249SIN GM12878 CHD4 narrowPeak Transcription Factor ChIP-seq Peaks of CHD4 in GM12878 from ENCODE 3 (ENCFF249SIN) 0 96 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CHD4 in GM12878 from ENCODE 3 (ENCFF249SIN)\ parent encTfChipPk off\ shortLabel GM12878 CHD4\ subGroups cellType=GM12878 factor=CHD4\ track encTfChipPkENCFF249SIN\ netHprcGCA_018504075v1 HG02723.pat netAlign GCA_018504075.1 chainHprcGCA_018504075v1 HG02723.pat HG02723.alt.pat.f1_v2 (May 2021 GCA_018504075.1_HG02723.alt.pat.f1_v2) HPRC project computed Chain Nets 1 96 0 0 0 255 255 0 0 0 0 hprc 0 longLabel HG02723.pat HG02723.alt.pat.f1_v2 (May 2021 GCA_018504075.1_HG02723.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018504075.1\ parent hprcChainNetViewnet off\ priority 16\ shortLabel HG02723.pat\ subGroups view=net sample=s016 population=afr subpop=gwd hap=pat\ track netHprcGCA_018504075v1\ type netAlign GCA_018504075.1 chainHprcGCA_018504075v1\ wgEncodeRegDnaseUwK562Hotspot K562 Ht bigBed 6 + K562 lymphoblast chronic myeloid leukemia cell line DNaseI Hotspots from ENCODE 0 96 255 85 85 255 170 170 1 0 0 regulation 1 color 255,85,85\ longLabel K562 lymphoblast chronic myeloid leukemia cell line DNaseI Hotspots from ENCODE\ parent wgEncodeRegDnaseHotspot on\ shortLabel K562 Ht\ subGroups view=b_Hot cellType=K562 treatment=n_a tissue=bone_marrow cancer=cancer\ track wgEncodeRegDnaseUwK562Hotspot\ type bigBed 6 +\ wgEncodeRegDnaseUwA549Hotspot A549 Ht bigBed 6 + A549 lung adenocarcinoma cell line DNaseI Hotspots from ENCODE 0 97 254 93 85 254 174 170 1 0 0 regulation 1 color 254,93,85\ longLabel A549 lung adenocarcinoma cell line DNaseI Hotspots from ENCODE\ parent wgEncodeRegDnaseHotspot off\ shortLabel A549 Ht\ subGroups view=b_Hot cellType=A549 treatment=n_a tissue=lung cancer=cancer\ track wgEncodeRegDnaseUwA549Hotspot\ type bigBed 6 +\ AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_tpm_fwd AorticSmsToIL1b_06hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_forward 1 97 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12661-134I6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2006hr%2c%20biol_rep1%20%28LK58%29.CNhs13357.12661-134I6.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12661-134I6 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_06hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12661-134I6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_ctss_fwd AorticSmsToIL1b_06hrBr1+ bigWig Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_forward 0 97 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12661-134I6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2006hr%2c%20biol_rep1%20%28LK58%29.CNhs13357.12661-134I6.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12661-134I6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_06hrBr1+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12661-134I6\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF091YID GM12878 CREM narrowPeak Transcription Factor ChIP-seq Peaks of CREM in GM12878 from ENCODE 3 (ENCFF091YID) 0 97 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CREM in GM12878 from ENCODE 3 (ENCFF091YID)\ parent encTfChipPk off\ shortLabel GM12878 CREM\ subGroups cellType=GM12878 factor=CREM\ track encTfChipPkENCFF091YID\ chainHprcGCA_018504665v1 NA21309.pat chain GCA_018504665.1 NA21309.pat NA21309.alt.pat.f1_v2 (May 2021 GCA_018504665.1_NA21309.alt.pat.f1_v2) HPRC project computed Chained Alignments 3 97 0 0 0 255 255 0 1 0 0 hprc 1 longLabel NA21309.pat NA21309.alt.pat.f1_v2 (May 2021 GCA_018504665.1_NA21309.alt.pat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018504665.1\ parent hprcChainNetViewchain off\ priority 86\ shortLabel NA21309.pat\ subGroups view=chain sample=s086 population=other subpop=hapmap hap=pat\ track chainHprcGCA_018504665v1\ type chain GCA_018504665.1\ AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_tpm_rev AorticSmsToIL1b_06hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_reverse 1 98 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12661-134I6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2006hr%2c%20biol_rep1%20%28LK58%29.CNhs13357.12661-134I6.hg38.tpm.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12661-134I6 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_06hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_tpm_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12661-134I6\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_ctss_rev AorticSmsToIL1b_06hrBr1- bigWig Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_reverse 0 98 0 0 255 127 127 255 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12661-134I6 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2006hr%2c%20biol_rep1%20%28LK58%29.CNhs13357.12661-134I6.hg38.ctss.rev.bw\ color 0,0,255\ longLabel Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_reverse\ maxHeightPixels 100:8:8\ metadata ontology_id=12661-134I6 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_06hrBr1-\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=reverse\ track AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_ctss_rev\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12661-134I6\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF356LIU GM12878 CTCF 1 narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in GM12878 from ENCODE 3 (ENCFF356LIU) 0 98 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in GM12878 from ENCODE 3 (ENCFF356LIU)\ parent encTfChipPk on\ shortLabel GM12878 CTCF 1\ subGroups cellType=GM12878 factor=CTCF\ track encTfChipPkENCFF356LIU\ wgEncodeRegDnaseUwLncapHotspot LNCaP Ht bigBed 6 + LNCaP prostate adenocarcinoma cell line DNaseI Hotspots from ENCODE 0 98 255 102 85 255 178 170 1 0 0 regulation 1 color 255,102,85\ longLabel LNCaP prostate adenocarcinoma cell line DNaseI Hotspots from ENCODE\ parent wgEncodeRegDnaseHotspot off\ shortLabel LNCaP Ht\ subGroups view=b_Hot cellType=LNCaP treatment=n_a tissue=prostate cancer=cancer\ track wgEncodeRegDnaseUwLncapHotspot\ type bigBed 6 +\ netHprcGCA_018504665v1 NA21309.pat netAlign GCA_018504665.1 chainHprcGCA_018504665v1 NA21309.pat NA21309.alt.pat.f1_v2 (May 2021 GCA_018504665.1_NA21309.alt.pat.f1_v2) HPRC project computed Chain Nets 1 98 0 0 0 255 255 0 0 0 0 hprc 0 longLabel NA21309.pat NA21309.alt.pat.f1_v2 (May 2021 GCA_018504665.1_NA21309.alt.pat.f1_v2) HPRC project computed Chain Nets\ otherDb GCA_018504665.1\ parent hprcChainNetViewnet off\ priority 86\ shortLabel NA21309.pat\ subGroups view=net sample=s086 population=other subpop=hapmap hap=pat\ track netHprcGCA_018504665v1\ type netAlign GCA_018504665.1 chainHprcGCA_018504665v1\ AorticSmoothMuscleCellResponseToIL1b06hrBiolRep2LK59_CNhs13378_tpm_fwd AorticSmsToIL1b_06hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 06hr, biol_rep2 (LK59)_CNhs13378_12759-136B5_forward 1 99 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12759-136B5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2006hr%2c%20biol_rep2%20%28LK59%29.CNhs13378.12759-136B5.hg38.tpm.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 06hr, biol_rep2 (LK59)_CNhs13378_12759-136B5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12759-136B5 sequence_tech=hCAGE\ parent TSS_activity_TPM off\ shortLabel AorticSmsToIL1b_06hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b06hrBiolRep2LK59_CNhs13378_tpm_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12759-136B5\ urlLabel FANTOM5 Details:\ AorticSmoothMuscleCellResponseToIL1b06hrBiolRep2LK59_CNhs13378_ctss_fwd AorticSmsToIL1b_06hrBr2+ bigWig Aortic smooth muscle cell response to IL1b, 06hr, biol_rep2 (LK59)_CNhs13378_12759-136B5_forward 0 99 255 0 0 255 127 127 0 0 0 http://fantom.gsc.riken.jp/5/sstar/FF:12759-136B5 regulation 0 bigDataUrl /gbdb/hg38/fantom5/Aortic%20smooth%20muscle%20cell%20response%20to%20IL1b%2c%2006hr%2c%20biol_rep2%20%28LK59%29.CNhs13378.12759-136B5.hg38.ctss.fwd.bw\ color 255,0,0\ longLabel Aortic smooth muscle cell response to IL1b, 06hr, biol_rep2 (LK59)_CNhs13378_12759-136B5_forward\ maxHeightPixels 100:8:8\ metadata ontology_id=12759-136B5 sequence_tech=hCAGE\ parent TSS_activity_read_counts off\ shortLabel AorticSmsToIL1b_06hrBr2+\ subGroups sequenceTech=hCAGE category=AoSMC_response_to_IL1b strand=forward\ track AorticSmoothMuscleCellResponseToIL1b06hrBiolRep2LK59_CNhs13378_ctss_fwd\ type bigWig\ url http://fantom.gsc.riken.jp/5/sstar/FF:12759-136B5\ urlLabel FANTOM5 Details:\ encTfChipPkENCFF960ZGP GM12878 CTCF 2 narrowPeak Transcription Factor ChIP-seq Peaks of CTCF in GM12878 from ENCODE 3 (ENCFF960ZGP) 0 99 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CTCF in GM12878 from ENCODE 3 (ENCFF960ZGP)\ parent encTfChipPk off\ shortLabel GM12878 CTCF 2\ subGroups cellType=GM12878 factor=CTCF\ track encTfChipPkENCFF960ZGP\ chainHprcGCA_018504085v1 HG02080.mat chain GCA_018504085.1 HG02080.mat HG02080.pri.mat.f1_v2 (May 2021 GCA_018504085.1_HG02080.pri.mat.f1_v2) HPRC project computed Chained Alignments 3 99 0 0 0 255 255 0 1 0 0 hprc 1 longLabel HG02080.mat HG02080.pri.mat.f1_v2 (May 2021 GCA_018504085.1_HG02080.pri.mat.f1_v2) HPRC project computed Chained Alignments\ otherDb GCA_018504085.1\ parent hprcChainNetViewchain off\ priority 84\ shortLabel HG02080.mat\ subGroups view=chain sample=s084 population=eas subpop=khv hap=mat\ track chainHprcGCA_018504085v1\ type chain GCA_018504085.1\ wgEncodeRegDnaseUwHmecHotspot HMEC Ht bigBed 6 + HMEC mammary epithelium DNaseI Hotspots from ENCODE 0 99 255 112 85 255 183 170 1 0 0 regulation 1 color 255,112,85\ longLabel HMEC mammary epithelium DNaseI Hotspots from ENCODE\ parent wgEncodeRegDnaseHotspot off\ shortLabel HMEC Ht\ subGroups view=b_Hot cellType=HMEC treatment=n_a tissue=breast cancer=normal\ track wgEncodeRegDnaseUwHmecHotspot\ type bigBed 6 +\ est Human ESTs psl est Human ESTs Including Unspliced 0 100 0 0 0 127 127 127 1 0 0

Description

\ This track shows alignments between human expressed sequence tags \ (ESTs) in GenBank and the genome. ESTs are single-read sequences, \ typically about 500 bases in length, that usually represent fragments of \ transcribed genes.

\ NOTE: As of April, 2007, we no longer include GenBank sequences \ that contain the following URL as part of the record:\

\ http://fulllength.invitrogen.com\

\ Some of these entries are the result of alignment to pseudogenes,\ followed by "correction" of the EST to match the genomic sequence. \ It is therefore not the sequence of the actual EST and makes it appear that \ the EST is transcribed. Invitrogen no longer sells the clones.\

\ \

Display Conventions and Configuration

\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.

\ The strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.

\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.

\ To use the filter:\

Type a term in one or more of the text boxes to filter the EST\ display. For example, to apply the filter to all ESTs expressed in a specific\ organ, type the name of the organ in the tissue box. To view the list of \ valid terms for each text box, consult the table in the Table Browser that \ corresponds to the factor on which you wish to filter. For example, the \ "tissue" table contains all the types of tissues that can be \ entered into the tissue text box. Multiple terms may be entered at once, \ separated by a space. Wildcards may also be used in the\ filter.\
If filtering on more than one value, choose the desired combination\ logic. If "and" is selected, only ESTs that match all filter \ criteria will be highlighted. If "or" is selected, ESTs that \ match any one of the filter criteria will be highlighted.\
Choose the color or display characteristic that should be used to \ highlight or include/exclude the filtered items. If "exclude" is \ chosen, the browser will not display ESTs that match the filter criteria. \ If "include" is selected, the browser will display only those \ ESTs that match the filter criteria.\

\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those \ that differ from the genomic sequence. For more information about this option,\ click \ here.\ Several types of alignment gap may also be colored; \ for more information, click \ here.\

\ \

Methods

\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most — but not all — ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.

\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the \ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.

\ To generate this track, human ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence were kept.

\ \

\ \

\ This track follows the display conventions for\ \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.\

\ \

\ The description page for this track has a filter that can be used to change\ the display mode, alter the color, and include/exclude a subset of items\ within the track. This may be helpful when many items are shown in the track\ display, especially when only some are relevant to the current task.\

\ \

\ To use the filter:\

Type a term in one or more of the text boxes to filter the mRNA\ display. For example, to apply the filter to all mRNAs expressed in a specific\ organ, type the name of the organ in the tissue box. To view the list of\ valid terms for each text box, consult the table in the Table Browser that\ corresponds to the factor on which you wish to filter. For example, the\ "tissue" table contains all the types of tissues that can be\ entered into the tissue text box. Multiple terms may be entered at once,\ separated by a space. Wildcards may also be used in the filter.
If filtering on more than one value, choose the desired combination\ logic. If "and" is selected, only mRNAs that match all filter\ criteria will be highlighted. If "or" is selected, mRNAs that\ match any one of the filter criteria will be highlighted.
Choose the color or display characteristic that should be used to\ highlight or include/exclude the filtered items. If "exclude" is\ chosen, the browser will not display mRNAs that match the filter criteria.\ If "include" is selected, the browser will display only those\ mRNAs that match the filter criteria.

\ \

\ This track may also be configured to display codon coloring, a feature that\ allows the user to quickly compare mRNAs against the genomic sequence. For more\ information about this option, go to the\ \ Codon and Base Coloring for Alignment Tracks page.\ Several types of alignment gap may also be colored;\ for more information, go to the\ \ Alignment Insertion/Deletion Display Options page.\

\ \

Methods

\ \

\ GenBank human mRNAs were aligned against the genome using the\ blat program. When a single mRNA aligned in multiple places,\ the alignment having the highest base identity was found.\ Only alignments having a base identity level within 0.5% of\ the best and at least 96% base identity with the genomic sequence were kept.\

\ \

Credits

\ \

\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by\ scientists worldwide.\

\ \

References

\ Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\ \ GenBank.\ Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.\ PMID: 23193287; PMC: PMC3531190\

\ \

\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\ GenBank: update.\ Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\ PMID: 14681350; PMC: PMC308779\

\ \

\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.\ PMID: 11932250; PMC: PMC187518\

\ rna 1 baseColorDefault diffCodons\ baseColorUseCds genbank\ baseColorUseSequence genbank\ group rna\ indelDoubleInsert on\ indelPolyA on\ indelQueryInsert on\ longLabel Human mRNAs from GenBank\ shortLabel Human mRNAs\ showDiffBasesAllScales .\ spectrum on\ table all_mrna\ track mrna\ type psl .\ visibility hide\ tgpArchive 1000 Genomes 1000 Genomes Phase 3 0 100 0 0 0 127 127 127 0 0 0

Description

\ This supertrack is a collection of tracks from the\ 1000 Genomes Project showing\ paired-end accessible regions and integrated variant calls. More information about display\ conventions, methods, credits, and references can be found on each subtrack's description page.\

\ For more details, see:

\ \

Credits

\ Thanks to the International Genome Sample Resource (IGSR) for making these variant calls\ freely available.

\ varRep 0 cartVersion 2\ group varRep\ html ../tgpArchive\ longLabel 1000 Genomes Phase 3\ shortLabel 1000 Genomes\ superTrack on\ track tgpArchive\ visibility hide\ tgpTrios 1000 Genomes Trios vcfPhasedTrio Thousand Genomes Project Family VCF Trios 3 100 0 0 0 127 127 127 0 0 23 chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,

Description

\ This track shows approximately 4.5 million single nucleotide variants (SNVs) and\ 0.6 million short insertions/deletions (indels) from 7 different parent/child trios as\ produced by the\ International\ Genome Sample Resource (IGSR), from sequence data generated by the\ 1000 Genomes Project\ in its Phase 3 sequencing of 2,504 genomes from 16 populations worldwide.

\ Variants were called on the autosomes (chromosomes 1 through 22) and on the\ Pseudo-Autosomal Regions (PARs) of chromosome X.\ Therefore this track has no annotations on alternate haplotype sequences, fix patches,\ chromosome Y, or the non-PAR portion (the majority) of chromosome X.\

\ The variant genotypes have been phased (i.e., the two alleles of each diploid genotype\ have been assigned to two\ haplotypes,\ one inherited from each parent). This information allows us to illustrate which\ haplotypes in the child have been inherited from which parent.\

\ \

Trios from six different populations are available, including:\

YRI - Yoruban from Idaban, Nigeria
KHV - Kinh in Ho Chi Minh City, Vietnam
PUR - Puerto Ricans from Puerto Rico
CEU - CEPH Utah
CHS - Southern Han Chinese
MXL - Mexican Ancestry from Los Angeles

\ \

Display Conventions and Configuration

\ This track illustrates the vcfPhasedTrio track type, where two lines, one for each chromosome\ in the diploid genome, is drawn per sample in the underlying VCF. Variants in the window\ are then drawn on the haplotype line corresponding to which haplotype they belong to, such that\ variants on the same line were likely inherited together. The sorting routine is the same as\ what is used to draw the haplotype sorted display in the non-trio 1000 Genomes track, and is\ described here.\

\ \

\ The child haplotypes are drawn in the center of each group, flanked above and below by\ parent haplotypes, and variants are sorted to show the transmitted alleles:\

\
parent 1 untransmitted haploytpe \
parent 1 transmitted haplotype\
child haplotype inherited from parent 1\
child haplotype inherited from parent 2\
parent 2 transmitted haplotype\
parent 2 untransmitted haploytpe \

\ \

\ Track configuration options include:\

Showing the child haplotypes below the parent(s)
Toggling the haplotype labels with mother/father/child or VCF sample IDs
Hiding the parent samples

\ \

\ Allele coloring options include:\

No shading - the default option
Shading by functional effect of the variant relative to NCBI RefSeq Curated Transcripts:\
- reference alleles invisible
- alternate alleles in red for non-synonymous
- alternate alleles in green for synonymous
- alternate alleles in blue for UTR/noncoding
- alternate alleles in black otherwise
\
Child de novo alleles in red - all alternate alleles black except for cases where the child has\ an allele not present in either parent
Child alleles that are "inconsistent" with phasing in red - all alternate alleles black except for cases where the "inherited" child allele does not match the "transmitted" parent allele. Note that as the genomic location changes, and thus the alleles present to use for sorting change, whether an allele is marked as inconsistent can change as well. Because all the variants present in the window are considered a haplotype, what haplotypes are considered "inherited" and "transmitted" varies as the viewing location changes

\ \

\ From the subtrack configure menu, there is the option to manually rearrange \ the family order for each trio by dragging haplotypes. \

\ \

\ Clicking on a variant takes one to a details page with the standard VCF details, including\ INFO column annotations, the REF and ALT alleles, and the genotypes from all three samples.\

\ \

Methods

\ The genomes of 2,504 individuals were sequenced using both whole-genome sequencing\ (mean depth = 7.4x) and targeted exome sequencing (mean depth = 65.7x).\ Sequence reads were aligned to the reference genome using alt-aware BWA-MEM\ (Zheng-Bradley et al.).\ Variant discovery and quality control were performed as described in\ Lowy-Gallego et al.

\ See also:\

\ \

UCSC Methods

\ Trio samples were extracted out of both the main 1000 Genomes set, and the\ related samples using the pedigree information from 1000\ Genomes. Variants that were homozygous reference across all three samples were removed.\

\ \

Data Access

\ Trio VCFs are available for download from\ our download server.\

\ \

Credits

\ Thanks to the\ International Genome Sample\ Resource (IGSR)\ for making these variant calls freely available.\

\ \

References

\ \

\ Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P, 1000 Genomes Project\ Consortium.\ \ Alignment of 1000 Genomes Project reads to reference assembly GRCh38.\ Gigascience. 2017 Jul 1;6(7):1-8.\ PMID: 28531267; PMC: PMC5522380\

\ \

\ Fairley S, Lowy-Gallego E, Perry E, Flicek P.\ \ The International Genome Sample Resource (IGSR) collection of open human genomic variation\ resources.\ Nucleic Acids Res. 2019 Oct 4.\ PMID: 31584097\

\ \

\ Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P,\ 1000 Genomes Project Consortium.\ \ Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project [version 1; peer review: 2 not approved].\ Wellcome Open Research. 2019 Mar. 11.\

\ \

\ 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO,\ Marchini JL, McCarthy S, McVean GA et al.\ \ A global reference for human genetic variation.\ Nature. 2015 Oct 1;526(7571):68-74.\ PMID: 26432245\

\ varRep 0 chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX\ compositeTrack on\ geneTrack ncbiRefSeqCurated\ html tgpTrios\ longLabel Thousand Genomes Project Family VCF Trios\ maxWindowToDraw 5000000\ parent tgpArchive\ shortLabel 1000 Genomes Trios\ track tgpTrios\ type vcfPhasedTrio\ vcfDoFilter off\ vcfDoMaf off\ vcfDoQual off\ vcfUseAltSampleNames on\ visibility pack\ tgpPhase3 1000G Ph3 Vars vcfTabix 1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels 0 100 0 0 0 127 127 127 0 0 23 chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,

Description

\ This track shows approximately 73 million single nucleotide variants (SNVs) and\ 5 million short insertions/deletions (indels)\ produced by the\ International\ Genome Sample Resource (IGSR) from sequence data generated by the\ 1000 Genomes Project\ in its Phase 3 sequencing of 2,504 genomes from 16 populations worldwide.

\ The variant genotypes have been phased\ (i.e., the two alleles of each diploid genotype have been assigned to two\ haplotypes,\ one inherited from each parent).\ This extra information enables a clustering of independent haplotypes\ by local similarity for display.\

\ \

Display Conventions

\ \ \ \ In "dense" mode, a vertical line is drawn at the position of each\ variant.\ In "pack" mode, since these variants have been phased, the\ display shows a clustering of haplotypes in the viewed range, sorted\ by similarity of alleles weighted by proximity to a central variant.\ The clustering view can highlight local patterns of linkage.

\ In the clustering display, each sample's phased diploid genotype is split\ into two independent haplotypes.\ Each haplotype is placed in a horizontal row of pixels; when the number of\ haplotypes exceeds the number of vertical pixels for the track, multiple\ haplotypes fall in the same pixel row and pixels are averaged across haplotypes.

\ Each variant is a vertical bar with white (invisible) representing the reference allele\ and black representing the non-reference allele(s).\ Tick marks are drawn at the top and bottom of each variant's vertical bar\ to make the bar more visible when most alleles are reference alleles.\ The vertical bar for the central variant used in clustering is outlined in purple.\ In order to avoid long compute times, the range of alleles used in clustering\ may be limited; alleles used in clustering have purple tick marks at the\ top and bottom.

\ The clustering tree is displayed to the left of the main image.\ It does not represent relatedness of individuals; it simply shows the arrangement\ of local haplotypes by similarity. When a rightmost branch is purple, it means\ that all haplotypes in that branch are identical, at least within the range of\ variants used in clustering.\

\ \

Methods

\ phenDis 1 bigDataUrl /gbdb/hg38/abSplice/AbSplice.bb\ filter.spliceABscore 0.01\ filterLabel.maxScore Tissues\ filterLabel.spliceABscore Filter by minimum AbSplice score\ filterLimits.spliceABscore 0.01:1\ filterText.maxScore *\ group phenDis\ html abSplice\ itemRgb on\ longLabel Aberrant Splicing Prediction Scores\ mouseOver change: $name
gene: $ENSGid
max score: $spliceABscore
$maxScore\ noScoreFilter on\ shortLabel AbSplice Scores\ track abSplice\ type bigBed 9 +\ visibility hide\ affyArchive Affy Archive psl . Affymetrix Archive 0 100 0 0 0 127 127 127 0 0 0

Description

\ This supertrack is a collection of Affymetrix tracks showing the location of the consensus and\ exemplar sequences used for the selection of probes on the Affymetrix chips.\

Credits

\ Thanks to\ Affymetrix for the data underlying these tracks.\

\ expression 1 cartVersion 2\ group expression\ html ../affyArchive\ longLabel Affymetrix Archive\ shortLabel Affy Archive\ superTrack on\ track affyArchive\ type psl .\ visibility hide\ affyGnf1h Affy GNF1H psl . Alignments of Affymetrix Consensus/Exemplars from GNF1H 3 100 0 0 0 127 127 127 0 0 0

Description

This track shows the location of the sequences used for the selection of\ probes on the Affymetrix GNF1H chips. This contains 11406 predicted genes that do not overlap with\ the Affy U133A chip.

\ \

Methods

The sequences were mapped to the genome using blat followed by pslReps with the\ parameters:

-minCover=0.3 -minAli=0.95 -nearTop=0.005

\ \

Credits

Thanks to the Genomics\ Institute of the Novartis Research Foundation (GNF) for the data underlying this track.

\ \

References

\ Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G\ et al.\ \ A gene atlas of the mouse and human protein-encoding transcriptomes.\ Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7.\ PMID: 15075390; PMC: PMC395923\

\ expression 1 group expression\ longLabel Alignments of Affymetrix Consensus/Exemplars from GNF1H\ parent affyArchive\ shortLabel Affy GNF1H\ track affyGnf1h\ type psl .\ visibility pack\ affyU133 Affy U133 psl . Alignments of Affymetrix Consensus/Exemplars from HG-U133 3 100 0 0 0 127 127 127 0 0 0

Description

\ This track shows the location of the consensus and exemplar sequences used \ for the selection of probes on the Affymetrix HG-U133A and HG-U133B chips.

\ \

Methods

\ Consensus and exemplar sequences were downloaded from the\ Affymetrix Product Support\ and mapped to the genome using blat followed by pslReps with the \ parameters:

   -minCover=0.5 -minAli=0.97 -nearTop=0.005\

\ \

Credits

\ Thanks to Affymetrix for the data underlying this track.

\ expression 1 group expression\ longLabel Alignments of Affymetrix Consensus/Exemplars from HG-U133\ parent affyArchive\ shortLabel Affy U133\ track affyU133\ type psl .\ visibility pack\ affyU95 Affy U95 psl . Alignments of Affymetrix Consensus/Exemplars from HG-U95 3 100 0 0 0 127 127 127 0 0 0

Description

\ This track shows the location of the consensus and exemplar sequences used \ for the selection of probes on the Affymetrix HG-U95Av2 chip. For this chip, \ probes are predominantly designed from consensus sequences.

\ \

Methods

\ Consensus and exemplar sequences were downloaded from the\ Affymetrix Product Support\ and mapped to the genome using blat followed by pslReps with the \ parameters:

   -minCover=0.3 -minAli=0.95 -nearTop=0.005\

\ \

Credits

\ Thanks to Affymetrix for the data underlying this track.

\ expression 1 group expression\ longLabel Alignments of Affymetrix Consensus/Exemplars from HG-U95\ parent affyArchive\ shortLabel Affy U95\ track affyU95\ type psl .\ visibility pack\ altSeqLiftOverPsl Alt Haplotypes psl Reference Assembly Alternate Haplotype Sequence Alignments 3 100 0 0 100 127 127 177 0 0 0

Description

\ \

\ This track shows alignments of alternate locus (also known as "alternate haplotype")\ reference sequences to main chromosome sequences in the reference genome assembly.\ Some loci in the genome are highly variable, with sets of variants that tend\ to segregate into distinct haplotypes.\ Only one haplotype can be included in a reference assembly chromosome sequence.\ Instead of providing a separate complete chromosome sequence for each haplotype,\ which could cause confusion with divergent chromosome coordinates and\ ambiguity about which sequence is the official reference, the\ Genome Reference Consortium\ (GRC) adds alternate locus sequences, ranging from tens of thousands of bases\ up to low millions of bases in size, to represent the distinct haplotypes. \

\ \

Display Conventions and Configuration

\ \

Credits

\ The alignments were provided by NCBI as GFF files and translated into the PSL\ representation for browser display by UCSC.\

Methods

\ The Agilent arrays were downloaded from their \ Agilent SureDesign website tool on March 2022.

\ The Illumina 450k and 850k (EPIC) tracks were created using a few columns from the\ Infinium MethylationEPIC v1.0 B5 Manifest File (CSV Format)\ and was then converted into a bigBed.

\ The Illumina CytoSNP-850K track was created by downloading the\ CytoSNP-850K v1.2 Manifest File (CSV Format) (GRCh38) file and then converted\ into a bigBed file.\

\ The Affymetrix Cytoscan HD GeneChip Array track was created by converting the \ CytoScanHD_Accel_Array.na36.bed.zip\ into a bigBed file.\

\ \

Data Access

\ \

Credits

\ Thanks to the Aliglent and Illumina support teams for sharing the data and the UCSC Genome Browser\ engineers for configuring the data.

\ varRep 1 compositeTrack on\ group varRep\ longLabel Microarray Probesets\ shortLabel Array Probesets\ track genotypeArrays\ type bigBed 4\ visibility hide\ gold Assembly bed 3 + Assembly from Fragments 0 100 150 100 30 230 170 40 0 0 0

Description

\ This track shows the contigs used to construct the GRCh38 (hg38) genome assembly, as defined in the\ AGP file delivered with the sequence. \ For information on the AGP file format, see the NCBI \ AGP Specification. The NCBI website also provides an \ overview of genome assembly procedures, as well as \ specific information about the hg38 assembly.\

\ In dense mode, this track depicts the contigs that make up the \ currently viewed scaffold. \ Contig boundaries are distinguished by the use of alternating gold and brown \ coloration. Where gaps\ exist between contigs, spaces are shown between the gold and brown\ blocks. The relative order and orientation of the contigs\ within a scaffold is always known; therefore, a line is drawn in the graphical\ display to bridge the blocks.

\ Component types found in this track (with counts of that type in parenthesis):\

F - finished sequence (35,798)
O - other sequence (8,536)
W - whole genome shotgun (764)
P - pre draft (16)
D - draft sequence (8)
A - active finishing (8)

\ \

\ In addition to the standard nucleotide codes, the raw sequence files from NCBI also include\ IUPAC ambiguity codes for bases that could not be positively identified as A, C, G or T (see\ Wikipedia's IUPAC notation article for more information). As part of the UCSC\ assembly creation process, all IUPAC ambiguity characters are converted to Ns. The FASTA files\ available for download from UCSC reflect this. The raw data files containing the original IUPAC\ characters can be downloaded from the NCBI\ FTP site.\

\ \

\ The following table lists the counts by chromosome of the various IUPAC ambiguity characters\ in the original NCBI data files:\

\ \

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
chromosome
1 2 3 6 7 9 10 12 13 16 17 21 22 X Y Total
code
B 1 1 2
K 1 4 1 2 8
M 1 1 3 1 2 8
R 1 1 1 1 1 13 1 3 1 2 1 1 27
S 1 1 1 1 1 5
W 2 2 6 1 1 1 1 14
Y 4 3 1 2 2 8 2 2 5 2 2 2 35
Total 2 9 7 1 4 3 36 3 3 1 12 3 5 5 5 99
\

\ map 1 altColor 230,170,40\ color 150,100,30\ group map\ html gold\ longLabel Assembly from Fragments\ shortLabel Assembly\ track gold\ type bed 3 +\ visibility hide\ assemblyContainer Assembly Tracks Assembly identifiers, clones, and markers 0 100 0 0 0 127 127 127 0 0 0

Description

\ This is a container track for data related to the genome assembly. \ It contains tracks about the assembly identifiers, certain clones, and STS markers. \ Click into any of the sub-tracks to see information\ details on the specific annotations.

\ map 0 cartVersion 4\ group map\ longLabel Assembly identifiers, clones, and markers\ shortLabel Assembly Tracks\ superTrack on\ track assemblyContainer\ augustusGene AUGUSTUS genePred AUGUSTUS ab initio gene predictions v3.1 3 100 180 0 0 217 127 127 0 0 0

Description

\ \

\ This track shows ab initio predictions from the program\ AUGUSTUS (version 3.1).\ The predictions are based on the genome sequence alone.\

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Methods

\ \

\ Statistical signal models were built for splice sites, branch-point\ patterns, translation start sites, and the poly-A signal.\ Furthermore, models were built for the sequence content of\ protein-coding and non-coding regions as well as for the length distributions\ of different exon and intron types. Detailed descriptions of most of these different models\ can be found in Mario Stanke's\ dissertation.\ This track shows the most likely gene structure according to a\ Semi-Markov Conditional Random Field model.\ Alternative splicing transcripts were obtained with\ a sampling algorithm (--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2\ --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2).\

\ \

\ The different models used by Augustus were trained on a number of different species-specific\ gene sets, which included 1000-2000 training gene structures. The --species option allows\ one to choose the species used for training the models. Different training species were used\ for the --species option when generating these predictions for different groups of\ assemblies.\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Assembly Group Training Species
Fish zebrafish\ \
Birds chicken\ \
Human and all other vertebrates human\ \
Nematodes caenorhabditis
Drosophila fly
A. mellifera honeybee1
A. gambiae culex
S. cerevisiae saccharomyces
\

\ This table describes which training species was used for a particular group of assemblies.\ When available, the closest related training species was used.\

\ \

Credits

\ \ Thanks to the\ Stanke lab\ for providing the AUGUSTUS program. The training for the chicken version was\ done by Stefanie König and the training for the\ human and zebrafish versions was done by Mario Stanke.\ \

References

\ \

\ Stanke M, Diekhans M, Baertsch R, Haussler D.\ \ Using native and syntenically mapped cDNA alignments to improve de novo gene finding.\ Bioinformatics. 2008 Mar 1;24(5):637-44.\ PMID: 18218656\

\ \

\ Stanke M, Waack S.\ \ Gene prediction with a hidden Markov model and a new intron submodel.\ Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25.\ PMID: 14534192\

\ genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ color 180,0,0\ group genes\ html ../../augustusGene\ longLabel AUGUSTUS ab initio gene predictions v3.1\ parent genePredArchive\ shortLabel AUGUSTUS\ track augustusGene\ type genePred\ visibility pack\ avada Avada Variants bigBed 9 + Avada Variants extracted from full text publications 1 100 0 0 0 127 127 127 0 0 0

\ \

\ The AVADA VCF file was reformatted at UCSC to the bigBed format.\ The program that performs the conversion is available on\ Github. The paper reference information was added from\ MEDLINE and is used Courtesy of the U.S. National Library of Medicine, according \ to its \ Terms and Conditions.

\ \

Credits

\ Thanks to Gill Bejerano and Johannes Birgmeier for making the data available.\

\ \

References

\ Johannes Birgmeier, Cole A. Deisseroth, Laura E. Hayward, Luisa M. T. Galhardo, Andrew P. Tierno, Karthik A. Jagadeesh, Peter D. Stenson, David N. Cooper, Jonathan A. Bernstein, Maximilian Haeussler, and Gill Bejerano.\ \ AVADA: Towards Automated Pathogenic Variant Evidence Retrieval Directly from the Full Text Literature. .\ Genetics in Medicine. 2019.\ PMID: 31467448\

\ phenDis 1 bigDataUrl /gbdb/hg38/bbi/avada.bb\ dataVersion release 1\ exonNumbers off\ longLabel Avada Variants extracted from full text publications\ mouseOverField _mouseOver\ noScoreFilter on\ parent varsInPubs pack\ shortLabel Avada Variants\ track avada\ type bigBed 9 +\ urls pmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" doi="https://doi.org/$$" ensId="http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?g=$$" entrezs="https://www.ncbi.nlm.nih.gov/gene/$$" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$"\ visibility dense\ cons470wayViewphyloP Basewise Conservation (phyloP) bed 4 Multiz Alignment & Conservation (470 mammals) 2 100 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Multiz Alignment & Conservation (470 mammals)\ parent cons470way\ shortLabel Basewise Conservation (phyloP)\ track cons470wayViewphyloP\ view phyloP\ viewLimits -20.0:11.936\ viewLimitsMax -20:11.936\ visibility full\ cons447wayViewphyloP Basewise Conservation (phyloP) bed 4 Cactus Alignment & Conservation on 447 mammal species, including Zoonomia genomes 2 100 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Cactus Alignment & Conservation on 447 mammal species, including Zoonomia genomes\ parent cons447way\ shortLabel Basewise Conservation (phyloP)\ track cons447wayViewphyloP\ view phyloP\ viewLimits -20.0:11.936\ visibility full\ bismap Bismap bigWig Single-read and multi-read mappability after bisulfite conversion 2 100 0 0 0 127 127 127 0 0 0

Description

\ These tracks indicate regions with uniquely mappable reads of particular lengths before and after\ bisulfite conversion. Both Umap and Bismap tracks contain single-read mappability and multi-read\ mappability tracks for four different read lengths: 24 bp, 36 bp, 50 bp, and 100 bp.

\ You can use these tracks for many purposes, including filtering unreliable signal from\ sequencing assays. The Bismap track can help filter unreliable signal from sequencing assays\ involving bisulfite conversion, such as whole-genome bisulfite sequencing or reduced representation\ bisulfite sequencing.

\ \ \

Bismap single-read and multi-read mappability

Bismap single-read mappability

These tracks mark any region of the bisulfite-converted genome that is uniquely mappable by\ at least one k-mer on the specified strand. Mappability of the forward strand was\ generated by converting all instances of cytosine to thymine. Similarly, mappability of the\ reverse strand was generated by converting all instances of guanine to adenine.

To calculate the single-read mappability, you must find the overlap of a given region with\ the region that is uniquely mappable on both strands. Regions not uniquely mappable on both\ strands or have a low multi-read mappability might bias the downstream analysis.

Bismap multi-read mappability

These tracks represent the probability that a randomly selected k-mer which overlaps\ with a given position is uniquely mappable. Multi-read mappability track is calculated for\ k-mers that are uniquely mappable on both strands, and thus there is no strand\ specification.

\ \ \

Umap single-read and multi-read mappability

Umap single-read mappability: \
These tracks mark any region of the genome that is uniquely mappable by at least one\ k-mer. To calculate the single-read mappability, you must find the overlap of a given\ region with this track.
Umap multi-read mappability: \
These tracks represent the probability that a randomly selected k-mer which overlaps\ with a given position is uniquely mappable.

\ \

For greater detail and explanatory diagrams, see the\ preprint, the\ Umap and Bismap project website, or the\ Umap and Bismap software\ documentation.\ \

Data Access

\ The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, genome annotation is stored in a bigBed\ or bigWig file that can be downloaded from the\ download\ server. Individual regions or the whole genome annotation can be obtained using our tool\ bigBedToBed or bigWigToWig, which can be compiled from the source code or\ downloaded as a precompiled binary for your system. Instructions for downloading source code and\ binaries can be found here.\ The tool can also be used to obtain only features within a given range, for example:

\ bigBedToBed -chrom=chr6 -start=0 -end=1000000\ http://hgdownload.soe.ucsc.edu/gbdb/hg38/hoffmanMappability/k24.Unique.Mappability.bb stdout\
\ bigWigToWig -chrom=chr6 -start=0 -end=1000000\ http://hgdownload.soe.ucsc.edu/gbdb/hg38/hoffmanMappability/k24.Umap.MultiTrackMappability.bw\ stdout\

\ Please refer to our mailing list archives for questions, or our\ Data Access FAQ for more\ information.

\ \

Credits

\ Anshul Kundaje (Stanford\ University) created the original Umap software in MATLAB. The original Umap repository is available\ here.\ Mehran Karimzadeh (Michael Hoffman\ lab, Princess Margaret Cancer Centre) implemented the Python version of Umap and added features,\ including Bismap.

\ \

References

\ Karimzadeh M, Ernst C, Kundaje A, Hoffman MM.,\ Umap and Bismap:\ quantifying genome and methylome mappability\ bioRxiv bioRxiv, p. 095463, 2016.; doi: https://doi.org/10.1101/095463.

\ map 0 compositeTrack on\ group map\ html mappability\ longLabel Single-read and multi-read mappability after bisulfite conversion\ noInherit on\ parent mappability\ shortLabel Bismap\ subGroup1 view Views SR=Single-read MR=Multi-read\ track bismap\ type bigWig\ visibility full\ bloodHao Blood (PBMC) Hao Peripheral blood mononuclear cells (PBMC) from Hao et al 2020 0 100 0 0 0 127 127 127 0 0 0

Description

\ This track displays data from Integrated analysis of\ multimodal single-cell data. Human peripheral blood mononuclear cells\ (PBMCs) taken from pre-vaccinated and post-vaccinated individuals were profiled\ using both CITE-seq and ECCITE-seq. A total of 57 cell type clusters were\ identified and each cluster included cells from all 24 samples with rare\ exceptions. This dataset contains three annotations for cell clustering: Level\ 1 (8 cell types), Level 2 (30 cell types), Level 3 (57 cell types).

\ \

\ This track collection contains six bar chart tracks of RNA expression in PBMCs\ where cells are grouped by cell type level 1 \ (Blood PBMC Cells), cell type level 2 \ (Blood PBMC Cells 2), \ cell type level 3 (Blood PBMC Cells 3), donor \ (Blood PBMC Donor), phase of cell cycle \ (Blood PBMC Phase), or time into experiment \ (Blood PBMC Time). The default track displayed \ is Blood PBMC Cells.

\ \

Display Conventions

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \
Color Cell classification
immune
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes.

\ \

Method

\ PBMC samples were taken from 8 volunteers ages 20-49 enrolled in an HIV\ vaccine trial (NCT01578889). A total of 24 blood samples were collected at 3\ time points: day 0 (the day before), day 3, and day 7 after the administration\ of a VSV-vectored HIV vaccine. Samples were collected at these different time\ points to minimize batch effects. Cells were then divided into separate\ aliquots for modified versions of the 3' CITE-seq and 5' ECCITE-seq staining\ protocols. In the 3' CITE-seq staining protocol, the samples are simultaneously\ stained with the antibody and unique hashtag. Whereas, 5' ECCITE-seq samples\ are stained first with a unique hashtag. 3' libraries were loaded into 8 lanes\ of a 10x Genomics Chip B using the 10x Genomics 3' v3 kit. 5' libraries\ were loaded into 2 lanes of a 10x Genomics Chip A using the 10x Genomics V(D)J\ kit (v1). Both 3' and 5' libraries were pooled together and sequenced on an\ Illumina Novaseq S4 flowcell. In total, 210,911 cells were profiled after \ quality control and doublet filtration.

\ \

\ The cell/gene matrix and cell-level metadata was downloaded from the UCSC Cell \ Browser. The UCSC command line utility matrixClusterColumns, matrixToBarChart, \ and bedToBigBed were used to transform these into a bar chart format bigBed file \ that can be visualized. The coloring was done by defining colors for the broad \ level cell classes and then using another UCSC utility, hcaColorCells, to interpolate \ the colors across all cell types. The UCSC utilities can be found on\ our download server.

\ \

Data Access

\ \

Credit

\ Thanks to Yuhan Hao, Stephanie Hao, and to the many authors who worked on\ producing and publishing this data set. The data were integrated into the UCSC\ Genome Browser by Jim Kent and Brittney Wick then reviewed by Jairo Navarro. The UCSC \ work was paid for by the Chan Zuckerberg Initiative.

\ \

References

\ Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M\ et al.\ \ Integrated analysis of multimodal single-cell data.\ Cell. 2021 Jun 24;184(13):3573-3587.e29.\ PMID: 34062119; PMC: PMC8238499\

\ singleCell 0 group singleCell\ longLabel Peripheral blood mononuclear cells (PBMC) from Hao et al 2020\ shortLabel Blood (PBMC) Hao\ superTrack on\ track bloodHao\ visibility hide\ bloodHaoCellType Blood PBMC Cells bigBarChart Blood (PBMCs) binned by cell type (level 1) from Hao et al 2020 3 100 0 0 0 127 127 127 0 0 0 https://cells.ucsc.edu/?ds=multimodal-pbmc+sct&gene=$$

Description

\ \

Display Conventions

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \
Color Cell classification
immune
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes.

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \
Color Cell classification
immune
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes.

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \
Color Cell classification
immune
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes.

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \
Color Cell classification
immune
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes.

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \
Color Cell classification
immune
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes.

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \
Color Cell classification
immune
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes.

Gap Annotation

\ The Display chains between alignments configuration option\ enables display of gaps between alignment blocks in the pairwise alignments in\ a manner similar to the Chain track display. Missing sequence in any\ assembly is highlighted in the track display by regions of yellow when zoomed\ out and by Ns when displayed at base level. The following conventions are used:\

Single line: No bases in the aligned species. Possibly due to a\ lineage-specific insertion between the aligned blocks in the human genome\ or a lineage-specific deletion between the aligned blocks in the aligning\ species.\
Double line: Aligning species has one or more unalignable bases in\ the gap region. Possibly due to excessive evolutionary distance between\ species or independent indels in the region between the aligned blocks in both\ species.\
Pale yellow coloring: Aligning species has Ns in the gap region.\ Reflects uncertainty in the relationship between the DNA of both species, due\ to lack of sequence in relevant portions of the aligning species.\

\ \

Genomic Breaks

\ Discontinuities in the genomic context (chromosome, scaffold or region) of the\ aligned DNA in the aligning species are shown as follows:\

\ Vertical blue bar: Represents a discontinuity that persists indefinitely\ on either side, e.g. a large region of DNA on either side of the bar\ comes from a different chromosome in the aligned species due to a large scale\ rearrangement.\
\ Green square brackets: Enclose shorter alignments consisting of DNA from\ one genomic context in the aligned species nested inside a larger chain of\ alignments from a different genomic context. The alignment within the\ brackets may represent a short misalignment, a lineage-specific insertion of a\ transposon in the human genome that aligns to a paralogous copy somewhere\ else in the aligned species, or other similar occurrence.\

\ \

Base Level

\ No codon translation: The gene annotation is not used; the bases are\ displayed without translation.\
\ Use default species reading frames for translation: The annotations from\ the genome displayed in the Default species to establish reading frame\ pull-down menu are used to translate all the aligned species present in the\ alignment.\
\ Use reading frames for species if available, otherwise no translation:\ Codon translation is performed only for those species where the region is\ annotated as protein coding.\
Use reading frames for species if available, otherwise use default species:\ Codon translation is done on those species that are annotated as being protein\ coding over the aligned region using species-specific annotation; the remaining\ species are translated using the default species annotation.\

\ Codon translation uses the following gene tracks as the basis for translation:\

\ \ \ \ \ \
Gene Track Species
RefSeq Genes Bos mutus, Canis lupus familiaris, Carlito syrichta, Cercocebus atys, Chinchilla lanigera, Colobus angolensis, Condylura cristata, Dipodomys ordii, Elephantulus edwardii, Eptesicus fuscus, Felis catus, Felis catus fca126, Fukomys damarensis, Homo sapiesn, Ictidomys tridecemlineatus, Macaca mulatta, Macaca nemestrina, Marmota marmota, Microtus ochrogaster, Miniopterus natalensis, Mus musculus, Mus pahari, Myotis brandtii, Myotis davidii, Myotis lucifugus, Odobenus rosmarus, Orcinus orca, Otolemur garnettii, Peromyscus maniculatus, Piliocolobus tephrosceles, Propithecus coquerelli, Pteropus alecto, Pteropus vampyrus, Rattus norvegicus, Rhinopithecus roxellana, Saimiri boliviensis, Sorex araneus, Sus scrofa, Theropithecus gelada, Tupaia chinensis
Ensembl Genes Cavia aperea
Augustus Genes Eidolon helvum, Pteronotus parnellii
no annotation Acinonyx jubatus, Acomys cahirinus, Ailuropoda melanoleuca, Ailurus fulgens, Allactaga bullata, Allenopithecus nigroviridis, Allochrocebus lhoesti, Allochrocebus preussi, Allochrocebus solatus, Alouatta belzebul, Alouatta caraya, Alouatta discolor, Alouatta juara, Alouatta macconnelli, Alouatta nigerrima, Alouatta palliata, Alouatta puruensis, Alouatta seniculus, Ammotragus lervia, Anoura caudifer, Antilocapra americana, Aotus azarae, Aotus griseimembra, Aotus nancymaae, Aotus trivirgatus, Aotus vociferans, Aplodontia rufa, Arctocebus calabarensis, Artibeus jamaicensis, Ateles geoffroyi_a, Ateles geoffroyi_b, Ateles belzebuth, Ateles chamek, Ateles marginatus, Ateles paniscus, Avahi laniger, Avahi peyrierasi, Balaenoptera acutorostrata, Balaenoptera bonaerensis, Beatragus hunteri, Bison bison, Bos indicus, Bos taurus, Bubalus bubalis, Cacajao ayresi, Cacajao calvus, Cacajao hosomi, Cacajao melanocephalus, Callibella humilis, Callimico goeldii, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Camelus bactrianus, Camelus dromedarius, Camelus ferus, Canis lupus VD, Canis lupus dingo, Canis lupus orion, Capra aegagrus, Capra hircus, Capromys pilorides, Carollia perspicillata, Castor canadensis, Catagonus wagneri, Cavia porcellus, Cavia tschudii, Cebuella niveiventris, Cebuella pygmaea, Cebus albifrons, Cebus olivaceus, Cebus unicolor, Cephalopachus bancanus, Ceratotherium simum, Ceratotherium simum cottoni, Cercocebus chrysogaster, Cercocebus lunulatus, Cercocebus torquatus, Cercopithecus ascanius, Cercopithecus cephus, Cercopithecus diana, Cercopithecus hamlyni, Cercopithecus lowei, Cercopithecus albogularis, Cercopithecus mona, Cercopithecus neglectus, Cercopithecus nictitans, Cercopithecus petaurista, Cercopithecus pogonias, Cercopithecus roloway, Chaetophractus vellerosus, Cheirogaleus major, Cheirogaleus medius, Cheracebus lucifer, Cheracebus lugens, Cheracebus regulus, Cheracebus torquatus, Chiropotes albinasus, Chiropotes israelita, Chiropotes sagulatus, Chlorocebus aethiops, Chlorocebus pygerythrus, Chlorocebus sabaeus, Choloepus didactylus, Choloepus hoffmanni, Chrysochloris asiatica, Colobus guereza, Colobus polykomos, Craseonycteris thonglongyai, Cricetomys gambianus, Cricetulus griseus, Crocidura indochinensis, Cryptoprocta ferox, Ctenodactylus gundi, Ctenomys sociabilis, Cuniculus paca, Dasyprocta punctata, Dasypus novemcinctus, Daubentonia madagascariensis, Delphinapterus leucas, Desmodus rotundus, Dicerorhinus sumatrensis, Diceros bicornis, Dinomys branickii, Dipodomys stephensi, Dolichotis patagonum, Echinops telfairi, Elaphurus davidianus, Ellobius lutescens, Ellobius talpinus, Enhydra lutris, Equus asinus, Equus caballus, Equus przewalskii, Erinaceus europaeus, Erythrocebus patas, Eschrichtius robustus, Eubalaena japonica, Eulemur albifrons, Eulemur collaris, Eulemur coronatus, Eulemur flavifrons, Eulemur fulvus, Eulemur macaco, Eulemur mongoz, Eulemur rubriventer, Eulemur rufus, Eulemur sanfordi, Felis nigripes, Galago moholi, Galago senegalensis, Galagoides demidoff, Galeopterus variegatus, Giraffa tippelskirchi, Glis glis, Gorilla beringei, Gorilla gorilla, Graphiurus murinus, Hapalemur alaotrensis, Hapalemur gilberti, Hapalemur griseus, Hapalemur meridionalis, Hapalemur occidentalis, Helogale parvula, Hemitragus hylocrius, Heterocephalus glaber, Heterohyrax brucei, Hippopotamus amphibius, Hipposideros armiger, Hipposideros galeritus, Hoolock leuconedys, Hyaena hyaena, Hydrochoerus hydrochaeris, Hylobates abbotti, Hylobates agilis, Hylobates klossii, Hylobates pileatus, Hylobates muelleri, Hylobates pileatus, Hystrix cristata, Indri indri, Inia geoffrensis, Jaculus jaculus, Kogia breviceps, Lagothrix lagothricha, Lasiurus borealis, Lemur catta, Leontocebus fuscicollis, Leontocebus illigeri, Leontocebus nigricollis, Leontopithecus chrysomelas, Leontopithecus rosalia, Lepilemur ankaranensis, Lepilemur dorsalis, Lepilemur ruficaudatus, Lepilemur septentrionalis, Leptonychotes weddellii, Lepus americanus, Lipotes vexillifer, Lophocebus aterrimus, Loris lydekkerianus, Loris tardigradus, Loxodonta africana, Lycaon pictus, Macaca arctoides, Macaca assamensis, Macaca cyclopis, Macaca fascicularis, Macaca fuscata, Macaca leonina, Macaca maura, Macaca nigra, Macaca radiata, Macaca siberu, Macaca silenus, Macaca thibetana, Macaca tonkeana, Macroglossus sobrinus, Mandrillus leucophaeus, Mandrillus sphinx, Manis javanica, Manis pentadactyla, Megaderma lyra, Mellivora capensis, Meriones unguiculatus, Mesocricetus auratus, Mesoplodon bidens, Mico argentatus, Mico humeralifer, Mico schneideri, Microcebus murinus, Microgale talazaci, Micronycteris hirsuta, Miniopterus schreibersii, Miopithecus ogouensis, Mirounga angustirostris, Mirza zaza, Monodon monoceros, Mormoops blainvillei, Moschus moschiferus, Mungos mungo, Murina feae, Mus caroli, Mus spretus, Muscardinus avellanarius, Mustela putorius, Myocastor coypus, Myotis myotis, Myrmecophaga tridactyla, Nannospalax galili, Nasalis larvatus, Neomonachus schauinslandi, Neophocaena asiaeorientalis, Noctilio leporinus, Nomascus annamensis, Nomascus concolor, Nomascus gabriellae, Nomascus siki_a, Nomascus siki_b, Nyctereutes procyonoides, Nycticebus bengalensis, Nycticebus coucang, Nycticebus pygmaeus, Ochotona princeps, Octodon degus, Odocoileus virginianus, Okapia johnstoni, Ondatra zibethicus, Onychomys torridus, Orycteropus afer, Oryctolagus cuniculus, Otocyon megalotis, Otolemur crassicaudatus, Ovis aries, Ovis canadensis, Pan paniscus, Pan troglodytes, Panthera onca, Panthera pardus, Panthera tigris, Pantholops hodgsonii, Papio anubis, Papio cynocephalus, Papio hamadryas, Papio kindae, Papio papio, Papio ursinus, Paradoxurus hermaphroditus, Perodicticus ibeanus, Perodicticus potto, Perognathus longimembris, Petromus typicus, Phocoena phocoena, Piliocolobus badius, Piliocolobus gordonorum, Piliocolobus kirkii, Pipistrellus pipistrellus, Pithecia albicans, Pithecia chrysocephala, Pithecia hirsuta, Pithecia mittermeieri, Pithecia pissinattii, Pithecia pithecia, Pithecia vanzolinii, Platanista gangetica, Plecturocebus bernhardi, Plecturocebus brunneus, Plecturocebus caligatus, Plecturocebus cinerascens, Plecturocebus cupreus, Plecturocebus dubius, Plecturocebus grovesi, Plecturocebus hoffmannsi, Plecturocebus miltoni, Plecturocebus moloch, Pongo abelii, Pongo pygmaeus, Presbytis comata, Presbytis mitrata, Procavia capensis, Prolemur simus, Propithecus coronatus, Propithecus diadema, Propithecus edwardsi, Propithecus perrieri, Propithecus tattersalli, Propithecus verreauxi, Psammomys obesus, Pteronura brasiliensis, Puma concolor, Pygathrix cinerea, Pygathrix nigripes, Pygathrix nigripes, Rangifer tarandus, Rhinolophus sinicus, Rhinopithecus bieti, Rhinopithecus strykeri, Rousettus aegyptiacus, Saguinus bicolor, Saguinus geoffroyi, Saguinus imperator, Saguinus inustus, Saguinus labiatus, Saguinus midas, Saguinus mystax, Saguinus oedipus, Saiga tatarica, Saimiri cassiquiarensis, Saimiri macrodon, Saimiri oerstedii, Saimiri sciureus, Saimiri ustus, Sapajus apella, Sapajus macrocephalus, Scalopus aquaticus, Semnopithecus entellus, Semnopithecus hypoleucos, Semnopithecus johnii, Semnopithecus priam, Semnopithecus schistaceus, Semnopithecus vetulus, Sigmodon hispidus, Solenodon paradoxus, Spermophilus dauricus, Spilogale gracilis, Suricata suricatta, Symphalangus syndactylus, Tadarida brasiliensis, Tamandua tetradactyla, Tapirus indicus, Tapirus terrestris, Tarsius lariang, Tarsius wallacei, Thryonomys swinderianus, Tolypeutes matacus, Tonatia saurophila, Trachypithecus auratus, Trachypithecus crepusculus, Trachypithecus cristatus, Trachypithecus francoisi, Trachypithecus geei, Trachypithecus germaini, Trachypithecus hatinhensis, Trachypithecus laotum, Trachypithecus leucocephalus, Trachypithecus melamera, Trachypithecus obscurus, Trachypithecus phayrei, Trachypithecus pileatus, Tragulus javanicus, Trichechus manatus, Tupaia tana, Tursiops truncatus, Uropsilus gracilis, Ursus maritimus, Varecia rubra, Varecia variegata, Vicugna pacos, Vulpes lagopus, Xerus inauris, Zalophus californianus, Zapus hudsonius, Ziphius cavirostris\
\ Table 2. Gene tracks used for codon translation.\

\ \

Methods

\ This alignment was created by making three edits (using Cactus) to the\ 241-way mammalian Zoonomia Cactus alignment\ (\ https://cglgenomics.ucsc.edu/data/cactus/).\

One additional cat genome, "Felis_catus_fca126" (GCA_018350175.1) was\ added as a sister taxa to the existing "Felis_catus" species
Five additional canine genomes were also added: canFam4,\ "Canis_lupus_dingo" (GCA_003254725.1), "Canis_lupus_orion"\ (GCA_905319855.2), "Nyctereutes_procyonoides" (GCA_905146905.1) and\ "Otocyon_megalotis" (GCA_017311455.1). "Canis_lupus" from the Zoonomia\ alignment was also renamed "Canis_lupus_VD" to reflect the fact that it\ corresponds to a "village dog" and not "wolf" sample.
The 43-species primates clade from the Zoonomia alignment was removed\ and replaced with the 243-way primates alignment from Identification of\ constrained sequence elements across 239 primate genomes, increasing the alignment by 200\ additional primate species.

\ \

Phylogenic tree

\ The phylogenic tree was established by the research described\ in A global catalog of whole-genome diversity from 233 primate\ species.\ \

Sequences

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
count common
name clade scientific name
(link to browser when existing) taxon id
link to NCBI
001 human primates catarrhini Homo sapiens/hg38
reference species 9606
002 western gorilla primates catarrhini Gorilla gorilla
GCA_900006655.3_Susie3 9593
003 Sumatran orangutan primates catarrhini Pongo abelii
GCA_002880775.3_Susie_PABv2 9601
004 Eastern Gorilla primates catarrhini Gorilla beringei 499232
005 chimpanzee primates catarrhini Pan troglodytes
GCA_002880755.3_Clint_PTRv2 9598
006 Bornean orangutan primates catarrhini Pongo pygmaeus 9600
007 Rhesus monkey primates catarrhini Macaca mulatta
rheMac10 9544
008 gelada primates catarrhini Theropithecus gelada
GCF_003255815.1_Tgel_1.0 9565
009 stump-tailed macaque primates catarrhini Macaca arctoides 9540
010 Northern Talapoin Monkey primates catarrhini Miopithecus ogouensis 100488
011 crab-eating macaque primates catarrhini Macaca fascicularis 9541
012 Allen's swamp monkey primates catarrhini Allenopithecus nigroviridis 54135
013 siamang primates catarrhini Symphalangus syndactylus 9590
014 black crested mangabey primates catarrhini Lophocebus aterrimus 75566
015 drill primates catarrhini Mandrillus leucophaeus 9568
016 Bonnet Macaque primates catarrhini Macaca radiata 9548
017 Red-capped Mangabey primates catarrhini Cercocebus torquatus 9530
018 Golden-bellied Mangabey primates catarrhini Cercocebus chrysogaster 75569
019 Owl-faced Monkey primates catarrhini Cercopithecus hamlyni 9536
020 Siberut Macaque primates catarrhini Macaca siberu 244255
021 pig-tailed macaque primates catarrhini Macaca nemestrina
GCF_000956065.1_Mnem_1.0 9545
022 White-naped Mangabey primates catarrhini Cercocebus lunulatus (Cercocebus atys lunulatus) 75570
023 Tonkean Macaque primates catarrhini Macaca tonkeana 40843
024 Diana Monkey primates catarrhini Cercopithecus diana 36224
025 red guenon primates catarrhini Erythrocebus patas 9538
026 Northern Pig-tailed Macaque primates catarrhini Macaca leonina 90387
027 Moor Macaque primates catarrhini Macaca maura 90383
028 Guinea Baboon primates catarrhini Papio papio 100937
029 hamadryas baboon primates catarrhini Papio hamadryas 9557
030 liontail macaque primates catarrhini Macaca silenus 54601
031 olive baboon primates catarrhini Papio anubis
GCA_000264685.2_Panu_3.0 9555
032 Roloway Monkey primates catarrhini Cercopithecus roloway 1137049
033 Kinda Baboon primates catarrhini Papio kindae 208091
034 Chacma Baboon primates catarrhini Papio ursinus 36229
035 Sun-tailed Monkey primates catarrhini Allochrocebus solatus 147650
036 golden snub-nosed monkey primates catarrhini Rhinopithecus roxellana
GCF_007565055.1_ASM756505v1 61622
037 Vervet Monkey primates catarrhini Chlorocebus pygerythrus 60710
038 sooty mangabey primates catarrhini Cercocebus atys
GCF_000955945.1_Caty_1.0 9531
039 green monkey primates catarrhini Chlorocebus sabaeus
GCA_000409795.2_Chlorocebus_sabeus_1.1 60711
040 De Brazza's monkey primates catarrhini Cercopithecus neglectus 36227
041 Yellow Baboon primates catarrhini Papio cynocephalus 9556
042 Celebes crested macaque primates catarrhini Macaca nigra 54600
043 proboscis monkey primates catarrhini Nasalis larvatus 43780
044 Preuss's Monkey primates catarrhini Allochrocebus preussi 147649
045 Putty-nosed Monkey primates catarrhini Cercopithecus nictitans 36228
046 Javan Surili primates catarrhini Presbytis comata 78452
047 Sykes' Monkey primates catarrhini Cercopithecus albogularis 36225
048 LHoests Monkey primates catarrhini Allochrocebus lhoesti 100224
049 Crowned Monkey primates catarrhini Cercopithecus pogonias 102108
050 Southern Mitered Langur primates catarrhini Presbytis mitrata (Presbytis melalophos mitrata) 272115
051 Grey-shanked Douc Langur primates catarrhini Pygathrix cinerea 693712
052 Mona monkey primates catarrhini Cercopithecus mona 36226
053 Spot-nosed Monkey primates catarrhini Cercopithecus petaurista 100487
054 grivet primates catarrhini Chlorocebus aethiops 9534
055 Lowes Monkey primates catarrhini Cercopithecus lowei 304410
056 Northern Yellow-cheeked Crested Gibbon primates catarrhini Nomascus annamensis 1616038
057 Red-cheeked Gibbon primates catarrhini Nomascus gabriellae 61852
058 Japanese macaque primates catarrhini Macaca fuscata 9542
059 Western Red Colobus primates catarrhini Piliocolobus badius 164648
060 southern white-cheeked gibbon primates catarrhini Nomascus siki_a 9586
061 Taiwan macaque primates catarrhini Macaca cyclopis 78449
062 black-shanked douc langur primates catarrhini Pygathrix nigripes 310352
063 King Colobus primates catarrhini Colobus polykomos 9572
064 Black Crested Gibbon primates catarrhini Nomascus concolor 29089
065 Udzungwa Red Colobus primates catarrhini Piliocolobus gordonorum 591933
066 Gee's Golden Langur primates catarrhini Trachypithecus geei 164650
067 Kloss's Gibbon primates catarrhini Hylobates klossii 9587
068 Spectacled Leaf Monkey primates catarrhini Trachypithecus obscurus 54181
069 Zanzibar Red Colobus primates catarrhini Piliocolobus kirkii 591937
070 Indochinese Silvered Langur primates catarrhini Trachypithecus germaini 271260
071 Hatinh Langur primates catarrhini Trachypithecus hatinhensis 867383
072 Moustached Monkey primates catarrhini Cercopithecus cephus 9535
073 Laotian Langur primates catarrhini Trachypithecus laotum 465718
074 Francois's langur primates catarrhini Trachypithecus francoisi 54180
075 Purple-faced Langur primates catarrhini Semnopithecus vetulus (Trachypithecus vetulus) 54137
076 Capped Langur primates catarrhini Trachypithecus pileatus 164651
077 Ugandan red Colobus primates catarrhini Piliocolobus tephrosceles
GCF_002776525.2_ASM277652v2 591936
078 Spangled Ebony Langur primates catarrhini Trachypithecus auratus 222416
079 Red-tailed Monkey primates catarrhini Cercopithecus ascanius 36223
080 Silvery Lutung primates catarrhini Trachypithecus cristatus 122765
081 Nilgiri Langur primates catarrhini Semnopithecus johnii (Trachypithecus johnii) 66063
082 Indochinese grey langur primates catarrhini Trachypithecus crepusculus (Trachypithecus phayrei crepuscula) 272121
083 White-headed langur primates catarrhini Trachypithecus leucocephalus (Trachypithecus poliocephalus) 465719
084 pygmy chimpanzee primates catarrhini Pan paniscus
GCA_000258655.2_panpan1.1 9597
085 northern white-cheeked gibbon primates catarrhini Nomascus siki_b 9586
086 Agile Gibbon primates catarrhini Hylobates agilis 9579
087 Phayre's Leaf-monkey primates catarrhini Trachypithecus melamera n/a
088 Nepal Gray Langur primates catarrhini Semnopithecus schistaceus 2804203
089 Abbott's Gray Gibbon primates catarrhini Hylobates abbotti (Hylobates muelleri abbotti) 716694
090 Bornean Gibbon primates catarrhini Hylobates muelleri 9588
091 Tufted Gray Langur primates catarrhini Semnopithecus priam 1208733
092 Black-footed Gray Langur primates catarrhini Semnopithecus hypoleucos 1208734
093 mantled guereza primates catarrhini Colobus guereza 33548
094 Hanuman langur primates catarrhini Semnopithecus entellus 88029
095 pileated gibbon primates catarrhini Hylobates pileatus 9589
096 black snub-nosed monkey primates catarrhini Rhinopithecus bieti 61621
097 Burmese snub-nosed monkey primates catarrhini Rhinopithecus strykeri 1194336
098 Angolan colobus primates catarrhini Colobus angolensis
colAng1 54131
099 Pileated Gibbon primates catarrhini Hylobates pileatus 9589
100 black-shanked douc langur primates catarrhini Pygathrix nigripes 310352
101 Milne-edwards' Macaque primates catarrhini Macaca thibetana 54602
102 Phayre's Leaf-monkey primates catarrhini Trachypithecus phayrei 61618
103 Assam macaque primates catarrhini Macaca assamensis 9551
104 Eastern hoolock gibbon primates catarrhini Hoolock leuconedys 61851
105 mandrill primates catarrhini Mandrillus sphinx 9561
106 White-faced Saki primates platyrrhini Pithecia chrysocephala 2946515
107 Monk Saki primates platyrrhini Pithecia hirsuta 2946516
108 white-faced saki primates platyrrhini Pithecia pithecia 43777
109 Mittermeier's Tapaj�s saki primates platyrrhini Pithecia mittermeieri 2946517
110 Buffy Saki primates platyrrhini Pithecia albicans 2946514
111 Pissinatti's saki primates platyrrhini Pithecia pissinattii (Pithecia pissinatti) 2946518
112 Vanzolini's Bald-faced Saki primates platyrrhini Pithecia vanzolinii 2946519
113 Bald-headed Uacari primates platyrrhini Cacajao calvus 30596
114 Ayres Black Uakari primates platyrrhini Cacajao ayresi 535896
115 Black-headed Uacari primates platyrrhini Cacajao melanocephalus 70825
116 Black-headed Uacari primates platyrrhini Cacajao hosomi 535897
117 Reddish-brown bearded saki primates platyrrhini Chiropotes sagulatus (Chiropotes chiropotes) 658221
118 brown-backed bearded saki primates platyrrhini Chiropotes israelita 280163
119 Collared Titi Monkey primates platyrrhini Cheracebus lugens 210166
120 Brown Titi Monkey primates platyrrhini Plecturocebus brunneus 1812042
121 Hoffmanns's titi monkey primates platyrrhini Plecturocebus hoffmannsi 78255
122 Milton's Titi Monkey primates platyrrhini Plecturocebus miltoni 1812038
123 Widow Monkey primates platyrrhini Cheracebus torquatus 30592
124 Ashy Black Titi Monkey primates platyrrhini Plecturocebus cinerascens 1812037
125 Prince Bernhard's Titi Monkey primates platyrrhini Plecturocebus bernhardi 1812036
126 Yellow-handed Titi Monkey primates platyrrhini Cheracebus lucifer 2487712
127 Coppery Titi Monkey primates platyrrhini Plecturocebus cupreus 202457
128 Chestnut-bellied Titi primates platyrrhini Plecturocebus caligatus 867332
129 Hershkovitzs Titi primates platyrrhini Plecturocebus dubius 2946520
130 Red-bellied Titi Monkey primates platyrrhini Plecturocebus moloch 9523
131 Groves' Titi primates platyrrhini Plecturocebus grovesi 2488670
132 black-handed spider monkey primates platyrrhini Ateles geoffroyi_a 9509
133 Widow Monkey primates platyrrhini Cheracebus regulus 1812110
134 Guiana Spider Monkey primates platyrrhini Ateles paniscus 9510
135 Black-faced Black Spider Monkey primates platyrrhini Ateles chamek 118643
136 White-cheeked Spider Monkey primates platyrrhini Ateles marginatus 1529884
137 White-bellied Spider Monkey primates platyrrhini Ateles belzebuth 9507
138 Common Woolly Monkey primates platyrrhini Lagothrix lagothricha (Lagothrix lagotricha) 9519
139 large-headed capuchin primates platyrrhini Sapajus macrocephalus (Sapajus apella macrocephalus) 1547595
140 Spixs White-fronted Capuchin primates platyrrhini Cebus unicolor 1985288
141 Central American spider monkey primates platyrrhini Ateles geoffroyi_b 9509
142 Guinan Weeper Capuchin primates platyrrhini Cebus olivaceus 37295
143 mantled howler monkey primates platyrrhini Alouatta palliata 30589
144 white-fronted capuchin primates platyrrhini Cebus albifrons 9514
145 Northern Night Monkey primates platyrrhini Aotus trivirgatus 9505
146 Grey-handed Night Monkey primates platyrrhini Aotus griseimembra 292213
147 Black-and-gold Howler Monkey primates platyrrhini Alouatta caraya 9502
148 Spixs Night Monkey primates platyrrhini Aotus vociferans 57176
149 Red-handed Howler Monkey primates platyrrhini Alouatta belzebul 30590
150 Red-handed Howler Monkey primates platyrrhini Alouatta discolor 2905217
151 Azara's Night Monkey primates platyrrhini Aotus azarae (Aotus azarai) 30591
152 Pur�s Red Howler Monkey primates platyrrhini Alouatta puruensis (Alouatta seniculus puruensis) 1347729
153 Black Howler Monkey primates platyrrhini Alouatta nigerrima (Alouatta belzebul) 30590
154 Guianan Red Howler Monkey primates platyrrhini Alouatta macconnelli 198115
155 Colombian Red Howler Monkey primates platyrrhini Alouatta juara 2946512
156 Colombian Red Howler Monkey primates platyrrhini Alouatta seniculus 9503
157 tufted capuchin primates platyrrhini Sapajus apella 9515
158 Ma's night monkey primates platyrrhini Aotus nancymaae
GCA_000952055.2_Anan_2.0 37293
159 Bolivian squirrel monkey primates platyrrhini Saimiri boliviensis
GCF_016699345.1_BCM_Sbol_2.0 27679
160 White-nosed Saki primates platyrrhini Chiropotes albinasus 198627
161 Black Mantle Tamarin primates platyrrhini Leontocebus nigricollis 9489
162 brown-mantled tamarin primates platyrrhini Leontocebus fuscicollis 9487
163 Illiger's saddle-back tamarin primates platyrrhini Leontocebus illigeri (Leontocebus fuscicollis illigeri) 881947
164 Cotton-headed Tamarin primates platyrrhini Saguinus oedipus 9490
165 Pied Tamarin primates platyrrhini Saguinus bicolor 37588
166 Geoffroy's Tamarin primates platyrrhini Saguinus geoffroyi 43778
167 White-fronted Titi Monkey primates platyrrhini Saguinus inustus 1079039
168 Moustached Tamarin primates platyrrhini Saguinus mystax 9488
169 tamarin primates platyrrhini Saguinus imperator 9491
170 Guianan Squirrel Monkey primates platyrrhini Saimiri sciureus 9521
171 Red-chested Mustached Tamarin primates platyrrhini Saguinus labiatus 78454
172 Goeldi's Monkey primates platyrrhini Callimico goeldii 9495
173 Black-crowned Central American Squirrel Monkey primates platyrrhini Saimiri oerstedii 70928
174 Golden-headed Lion Tamarin primates platyrrhini Leontopithecus chrysomelas 57374
175 golden lion tamarin primates platyrrhini Leontopithecus rosalia 30588
176 Humboldt's Squirrel Monkey primates platyrrhini Saimiri cassiquiarensis 2946521
177 bare-eared squirrel monkey primates platyrrhini Saimiri ustus 66265
178 Ecuadorian squirrel monkey primates platyrrhini Saimiri macrodon 2946522
179 white-tufted-ear marmoset primates platyrrhini Callithrix jacchus 9483
180 Eastern Pygmy Marmoset primates platyrrhini Cebuella niveiventris 2826950
181 Western Pygmy Marmoset primates platyrrhini Cebuella pygmaea 9493
182 Black And White Tassel-ear Marmoset primates platyrrhini Mico humeralifer 52232
183 Black-crowned Dwarf Marmoset primates platyrrhini Callibella humilis (Mico humilis) 666519
184 Mico schneideri primates platyrrhini Mico schneideri n/a
185 Silvery Marmoset primates platyrrhini Mico argentatus 9482
186 Midas tamarin primates platyrrhini Saguinus midas 30586
187 Wieds Marmoset primates platyrrhini Callithrix kuhlii 867363
188 Geoffroy's Tufted-ear Marmoset primates platyrrhini Callithrix geoffroyi 52231
189 Horsfield's tarsier primates tarsiidae Cephalopachus bancanus 9477
190 Philippine tarsier primates tarsiidae Carlito syrichta
tarSyr2 1868482
191 Lariang Tarsier primates tarsiidae Tarsius lariang 630277
192 Wallace's Tarsier primates tarsiidae Tarsius wallacei 981131
193 aye-aye primates strepsirrhini Daubentonia madagascariensis 31869
194 Crowned Sifaka primates strepsirrhini Propithecus coronatus (Propithecus deckenii coronatus) 475619
195 Perrier's Sifaka primates strepsirrhini Propithecus perrieri 989338
196 ruffed lemur primates strepsirrhini Varecia variegata 9455
197 Diademed Sifaka primates strepsirrhini Propithecus diadema 83281
198 Milne-Edwards Sifaka primates strepsirrhini Propithecus edwardsi 543559
199 babakoto primates strepsirrhini Indri indri 34827
200 Golden-crowned Sifaka primates strepsirrhini Propithecus tattersalli 30601
201 Eastern Woolly Lemur primates strepsirrhini Avahi laniger 122246
202 Verreauxs Sifaka primates strepsirrhini Propithecus verreauxi 34825
203 Peyrieras Woolly Lemur primates strepsirrhini Avahi peyrierasi 1313323
204 Red Ruffed Lemur primates strepsirrhini Varecia rubra 554167
205 greater bamboo lemur primates strepsirrhini Prolemur simus 1328070
206 Red-bellied Lemur primates strepsirrhini Eulemur rubriventer 34829
207 mongoose lemur primates strepsirrhini Eulemur mongoz 34828
208 Geoffroys Dwarf Lemur primates strepsirrhini Cheirogaleus major 47177
209 Crowned Lemur primates strepsirrhini Eulemur coronatus 13514
210 black lemur primates strepsirrhini Eulemur macaco 30602
211 lesser dwarf lemur primates strepsirrhini Cheirogaleus medius 9460
212 Sclater's lemur primates strepsirrhini Eulemur flavifrons 87288
213 Coquerel's sifaka primates strepsirrhini Propithecus coquerelli (Propithecus coquereli)
proCoq1 379532
214 Collared Brown Lemur primates strepsirrhini Eulemur collaris (Eulemur fulvus collaris) 47178
215 Red-tailed Sportive Lemur primates strepsirrhini Lepilemur ruficaudatus 78866
216 Red Brown Lemur primates strepsirrhini Eulemur rufus 859983
217 Sanfords Brown Lemur primates strepsirrhini Eulemur sanfordi 122225
218 White-fronted Lemur primates strepsirrhini Eulemur albifrons 1215604
219 Gray's Sportive Lemur primates strepsirrhini Lepilemur dorsalis 78583
220 brown lemur primates strepsirrhini Eulemur fulvus 13515
221 Sahafary Sportive Lemur primates strepsirrhini Lepilemur septentrionalis 78584
222 Sambirano Lesser Bamboo Lemur primates strepsirrhini Hapalemur occidentalis 867377
223 Alaotra Reed Lemur primates strepsirrhini Hapalemur alaotrensis (Hapalemur griseus alaotrensis) 122220
224 Eastern Lesser Bamboo Lemur primates strepsirrhini Hapalemur griseus 13557
225 Ankarana Sportive Lemur primates strepsirrhini Lepilemur ankaranensis 342401
226 ring-tailed lemur primates strepsirrhini Lemur catta 9447
227 gray bamboo lemur primates strepsirrhini Hapalemur gilberti 3043110
228 Rusty-gray Lesser Bamboo Lemur primates strepsirrhini Hapalemur meridionalis 3043112
229 Demidoffs Dwarf Galago primates strepsirrhini Galagoides demidoff 89672
230 northern giant mouse lemur primates strepsirrhini Mirza zaza 339999
231 gray mouse lemur primates strepsirrhini Microcebus murinus
GCA_000165445.3_Mmur_3.0 30608
232 small-eared galago primates strepsirrhini Otolemur garnettii
otoGar3 30611
233 Northern Lesser Galago primates strepsirrhini Galago senegalensis 9465
234 Thick-tailed Greater Galago primates strepsirrhini Otolemur crassicaudatus 9463
235 Grey Slender Loris primates strepsirrhini Loris lydekkerianus 300163
236 slender loris primates strepsirrhini Loris tardigradus 9468
237 West African Potto primates strepsirrhini Perodicticus potto 9472
238 East African Potto primates strepsirrhini Perodicticus ibeanus (Perodicticus potto ibeanus) 261737
239 Moholi bushbaby primates strepsirrhini Galago moholi 30609
240 Pygmy Slow Loris primates strepsirrhini Nycticebus pygmaeus (Xanthonycticebus pygmaeus) 101278
241 Bengal slow loris primates strepsirrhini Nycticebus bengalensis 261741
242 Calabar Angwantibo primates strepsirrhini Arctocebus calabarensis 261739
243 slow loris primates strepsirrhini Nycticebus coucang 9470
244 jaguar carnivora Panthera onca
GCA_004023805.1_PanOnc_v1_BIUU 9690
245 leopard carnivora Panthera pardus
GCA_001857705.1_PanPar1.0 9691
246 giant panda carnivora Ailuropoda melanoleuca
GCA_002007445.1_ASM200744v1 9646
247 Hawaiian monk seal carnivora Neomonachus schauinslandi
GCA_002201575.1_ASM220157v1 29088
248 California sea lion carnivora Zalophus californianus
GCA_004024565.1_ZalCal_v1_BIUU 9704
249 Greenland wolf carnivora Canis lupus orion
GCA_905319855.2_mCanLor1.2 2605939
250 Pacific walrus carnivora Odobenus rosmarus
odoRosDiv1 9707
251 domestic cat (Fca126) carnivora Felis catus fca126 (Felis catus)
GCF_018350175.1_F.catus_Fca126_mat1.0 9685
252 northern elephant seal carnivora Mirounga angustirostris
GCA_004023865.1_MirAng_v1_BIUU 9716
253 domestic cat carnivora Felis catus
felCat8 9685
254 domestic dog (BS72/Village Dog) carnivora Canis lupus familiaris
GCA_004027395.1_CanFam_VD_v1_BIUU
255 German Shepherd dog (Mischka) carnivora Canis lupus familiaris (CanFam4) (Canis lupus familiaris)
canFam4
256 dingo carnivora Canis lupus dingo 286419
257 raccoon dog carnivora Nyctereutes procyonoides 34880
258 fossa carnivora Cryptoprocta ferox 94188
259 polar bear carnivora Ursus maritimus
GCA_000687225.1_UrsMar_1.0 29073
260 Asian palm civet carnivora Paradoxurus hermaphroditus
GCA_004024585.1_ParHer_v1_BIUU 71117
261 African hunting dog carnivora Lycaon pictus
GCA_001887905.1_LycPicSAfr1.0 9622
262 Arctic fox carnivora Vulpes lagopus
GCA_004023825.1_VulLag_v1_BIUU 494514
263 dog carnivora Canis lupus familiaris
GCF_000002285.3_CanFam3.1 9615
264 striped hyena carnivora Hyaena hyaena
GCA_004023945.1_HyaHya_v1_BIUU 95912
265 n/a carnivora Acinonyx jubatus
GCA_001443585.1_aciJub1 32536
266 tiger carnivora Panthera tigris
GCA_000464555.1_PanTig1.0 9694
267 Sea otter carnivora Enhydra lutris
GCA_002288905.2_ASM228890v2 34882
268 giant otter carnivora Pteronura brasiliensis 9672
269 bat-eared fox carnivora Otocyon megalotis 9624
270 Weddell seal carnivora Leptonychotes weddellii
GCA_000349705.1_LepWed1.0 9713
271 Lesser panda carnivora Ailurus fulgens
GCA_002007465.1_ASM200746v1 9649
272 ratel carnivora Mellivora capensis
GCA_004024625.1_MelCap_v1_BIUU 9664
273 banded mongoose carnivora Mungos mungo
GCA_004023785.1_MunMun_v1_BIUU 210652
274 dwarf mongoose carnivora Helogale parvula
GCA_004023845.1_HelPar_v1_BIUU 210647
275 meerkat carnivora Suricata suricatta
GCA_004023905.1_SurSur_v1_BIUU 37032
276 puma carnivora Puma concolor
GCA_003327715.1_PumCon1.0 9696
277 black-footed cat carnivora Felis nigripes
GCA_004023925.1_FelNig_v1_BIUU 61379
278 European polecat carnivora Mustela putorius
GCA_000239315.1_MusPutFurMale1.0 9668
279 western spotted skunk carnivora Spilogale gracilis
GCA_004023965.1_SpiGra_v1_BIUU 30551
280 Sumatran rhinoceros laurasiatheria Dicerorhinus sumatrensis
GCA_002844835.1_ASM284483v1 89632
281 black rhinoceros laurasiatheria Diceros bicornis
GCA_004027315.1_DicBicMic_v1_BIUU 9805
282 Asiatic tapir laurasiatheria Tapirus indicus
GCA_004024905.1_TapInd_v1_BIUU 9802
283 Brazilian tapir laurasiatheria Tapirus terrestris
GCA_004025025.1_TapTer_v1_BIUU 9801
284 northern white rhinoceros laurasiatheria Ceratotherium simum cottoni 310713
285 ass laurasiatheria Equus asinus
GCA_001305755.1_ASM130575v1 9793
286 Southern white rhinoceros laurasiatheria Ceratotherium simum
GCA_000283155.1_CerSimSim1.0 9807
287 Przewalski's horse laurasiatheria Equus przewalskii
GCA_000696695.1_Burgud 9798
288 horse laurasiatheria Equus caballus
GCA_000002305.1_EquCab2.0 9796
289 Malayan pangolin laurasiatheria Manis javanica
GCA_001685135.1_ManJav1.0 9974
290 Chinese pangolin laurasiatheria Manis pentadactyla
GCA_000738955.1_M_pentadactyla-1.1.1 143292
291 Hispaniolan solenodon laurasiatheria Solenodon paradoxus 79805
292 eastern mole laurasiatheria Scalopus aquaticus
GCA_004024925.1_ScaAqu_v1_BIUU 71119
293 gracile shrew mole laurasiatheria Uropsilus gracilis
GCA_004024945.1_UroGra_v1_BIUU 182669
294 star-nosed mole laurasiatheria Condylura cristata
GCF_000260355.1_ConCri1.0 143302
295 western European hedgehog laurasiatheria Erinaceus europaeus
GCA_000296755.1_EriEur2.0 9365
296 European shrew laurasiatheria Sorex araneus
sorAra2 42254
297 Indochinese shrew laurasiatheria Crocidura indochinensis
GCA_004027635.1_CroInd_v1_BIUU 876679
298 Hoffmann's two-fingered sloth xenarthra Choloepus hoffmanni
GCA_000164785.2_C_hoffmanni-2.0.1 9358
299 nine-banded armadillo xenarthra Dasypus novemcinctus
GCA_000208655.2_Dasnov3.0 9361
300 giant anteater xenarthra Myrmecophaga tridactyla
GCA_004026745.1_MyrTri_v1_BIUU 71006
301 southern tamandua xenarthra Tamandua tetradactyla
GCA_004025105.1_TamTet_v1_BIUU 48850
302 placentals xenarthra Tolypeutes matacus 183749
303 southern two-toed sloth xenarthra Choloepus didactylus
GCA_004027855.1_ChoDid_v1_BIUU 27675
304 screaming hairy armadillo xenarthra Chaetophractus vellerosus
GCA_004027955.1_ChaVel_v1_BIUU 340076
305 North Pacific right whale artiodactyla Eubalaena japonica 302098
306 grey whale artiodactyla Eschrichtius robustus 9764
307 hippopotamus artiodactyla Hippopotamus amphibius
GCA_004027065.1_HipAmp_v1_BIUU 9833
308 Minke whale artiodactyla Balaenoptera acutorostrata
GCA_000493695.1_BalAcu1.0 9767
309 beluga whale artiodactyla Delphinapterus leucas
GCA_002288925.2_ASM228892v2 9749
310 Antarctic minke whale artiodactyla Balaenoptera bonaerensis
GCA_000978805.1_ASM97880v1 33556
311 boutu artiodactyla Inia geoffrensis 9725
312 harbor porpoise artiodactyla Phocoena phocoena 9742
313 narwhal artiodactyla Monodon monoceros
GCA_004026685.1_MonMon_M_v1_BIUU 40151
314 Yangtze River dolphin artiodactyla Lipotes vexillifer
GCA_000442215.1_Lipotes_vexillifer_v1 118797
315 killer whale artiodactyla Orcinus orca
orcOrc1 9733
316 Ganges River dolphin artiodactyla Platanista gangetica 118798
317 Yangtze finless porpoise artiodactyla Neophocaena asiaeorientalis
GCA_003031525.1_Neophocaena_asiaeorientalis_V1 189058
318 Sowerby's beaked whale artiodactyla Mesoplodon bidens 48745
319 alpaca artiodactyla Vicugna pacos
GCA_000767525.1_Vi_pacos_V1.0 30538
320 Cuvier's beaked whale" artiodactyla Ziphius cavirostris 9760
321 Bactrian camel artiodactyla Camelus bactrianus
GCA_000767855.1_Ca_bactrianus_MBC_1.0 9837
322 Arabian camel artiodactyla Camelus dromedarius
GCA_000767585.1_PRJNA234474_Ca_dromedarius_V1.0 9838
323 wild Bactrian camel artiodactyla Camelus ferus
GCA_000311805.2_CB1 419612
324 pygmy sperm whale artiodactyla Kogia breviceps 27615
325 Chacoan peccary artiodactyla Catagonus wagneri
GCA_004024745.1_CatWag_v1_BIUU 51154
326 reindeer artiodactyla Rangifer tarandus
GCA_004026565.1_RanTarSib_v1_BIUU 9870
327 Pere David's deer artiodactyla Elaphurus davidianus
GCA_002443075.1_Milu1.0 43332
328 okapi artiodactyla Okapia johnstoni
GCA_001660835.1_ASM166083v1 86973
329 Masai giraffe artiodactyla Giraffa tippelskirchi
GCA_001651235.1_ASM165123v1 439328
330 Siberian musk deer artiodactyla Moschus moschiferus
GCA_004024705.1_MosMos_v1_BIUU 68415
331 water buffalo artiodactyla Bubalus bubalis
GCA_000471725.1_UMD_CASPUR_WB_2.0 89462
332 cow artiodactyla Bos taurus
GCA_000003205.6_Btau_5.0.1 9913
333 pronghorn artiodactyla Antilocapra americana
GCA_004027515.1_AntAmePen_v1_BIUU 9891
334 white-tailed deer artiodactyla Odocoileus virginianus
GCA_002102435.1_Ovir.te_1.0 9874
335 aoudad artiodactyla Ammotragus lervia
GCA_002201775.1_ALER1.0 9899
336 bighorn sheep artiodactyla Ovis canadensis
GCA_004026945.1_OviCan_v1_BIUU 37174
337 goat artiodactyla Capra hircus
GCA_001704415.1_ARS1 9925
338 Nilgiri tahr artiodactyla Hemitragus hylocrius
GCA_004026825.1_HemHyl_v1_BIUU 330464
339 hirola artiodactyla Beatragus hunteri
GCA_004027495.1_BeaHun_v1_BIUU 59527
340 wild yak artiodactyla Bos mutus
bosMut1 72004
341 American bison artiodactyla Bison bison
GCA_000754665.1_Bison_UMD1.0 9901
342 sheep artiodactyla Ovis aries
GCA_000298735.2_Oar_v4.0 9940
343 chiru artiodactyla Pantholops hodgsonii
GCA_000400835.1_PHO1.0 59538
344 wild goat artiodactyla Capra aegagrus
GCA_000978405.1_CapAeg_1.0 9923
345 Java mouse-deer artiodactyla Tragulus javanicus
GCA_004024965.1_TraJav_v1_BIUU 9849
346 pig artiodactyla Sus scrofa
susScr3 9823
347 zebu cattle artiodactyla Bos indicus
GCA_000247795.2_Bos_indicus_1.0 9915
348 common bottlenose dolphin artiodactyla Tursiops truncatus
GCA_001922835.1_NIST_Tur_tru_v1 9739
349 Saiga antelope artiodactyla Saiga tatarica
GCA_004024985.1_SaiTat_v1_BIUU 34875
350 Chinese rufous horseshoe bat chiroptera Rhinolophus sinicus
GCA_001888835.1_ASM188883v1 89399
351 black flying fox chiroptera Pteropus alecto
pteAle1 9402
352 Cantor's roundleaf bat chiroptera Hipposideros galeritus 58069
353 Egyptian rousette chiroptera Rousettus aegyptiacus
GCA_004024865.1_RouAeg_v1_BIUU 9407
354 long-tongued fruit bat chiroptera Macroglossus sobrinus 326083
355 large flying fox chiroptera Pteropus vampyrus
GCF_000151845.1_Pvam_2.0 132908
356 Brazilian free-tailed bat chiroptera Tadarida brasiliensis
GCA_004025005.1_TadBra_v1_BIUU 9438
357 great roundleaf bat chiroptera Hipposideros armiger
GCA_001890085.1_ASM189008v1 186990
358 straw-colored fruit bat chiroptera Eidolon helvum
eidHel1 77214
359 Antillean ghost-faced bat chiroptera Mormoops blainvillei
GCA_004026545.1_MorMeg_v1_BIUU 118852
360 tailed tailless bat chiroptera Anoura caudifer
GCA_004027475.1_AnoCau_v1_BIUU 27642
361 common vampire bat chiroptera Desmodus rotundus
GCA_002940915.2_ASM294091v2 9430
362 hairy big-eared bat chiroptera Micronycteris hirsuta
GCA_004026765.1_MicHir_v1_BIUU 148065
363 stripe-headed round-eared bat chiroptera Tonatia saurophila
GCA_004024845.1_TonSau_v1_BIUU 171122
364 Seba's short-tailed bat chiroptera Carollia perspicillata
GCA_004027735.1_CarPer_v1_BIUU 40233
365 Jamaican fruit-eating bat chiroptera Artibeus jamaicensis
GCA_004027435.1_ArtJam_v1_BIUU 9417
366 Indian false vampire chiroptera Megaderma lyra
GCA_004026885.1_MegLyr_v1_BIUU 9413
367 Schreibers' long-fingered bat chiroptera Miniopterus schreibersii
GCA_004026525.1_MinSch_v1_BIUU 9433
368 greater bulldog bat chiroptera Noctilio leporinus
GCA_004026585.1_NocLep_v1_BIUU 94963
369 Natal long-fingered bat chiroptera Miniopterus natalensis
GCF_001595765.1_Mnat.v1 291302
370 hog-nosed bat chiroptera Craseonycteris thonglongyai
GCA_004027555.1_CraTho_v1_BIUU 208972
371 Parnell's mustached bat chiroptera Pteronotus parnellii
ptePar1 59476
372 greater mouse-eared bat chiroptera Myotis myotis
GCA_004026985.1_MyoMyo_v1_BIUU 51298
373 Ashy-gray tube-nosed bat chiroptera Murina feae (Murina aurata feae)
GCA_004026665.1_MurFea_v1_BIUU 1453894
374 David's myotis chiroptera Myotis davidii
myoDav1 225400
375 Brandt's bat chiroptera Myotis brandtii
myoBra1 109478
376 big brown bat chiroptera Eptesicus fuscus
GCF_000308155.1_EptFus1.0 29078
377 red bat chiroptera Lasiurus borealis
GCA_004026805.1_LasBor_v1_BIUU 258930
378 little brown bat chiroptera Myotis lucifugus
myoLuc2 59463
379 common pipistrelle chiroptera Pipistrellus pipistrellus
GCA_004026625.1_PipPip_v1_BIUU 59474
380 African savanna elephant afrotheria Loxodonta africana
GCA_000001905.1_Loxafr3.0 9785
381 Florida manatee afrotheria Trichechus manatus
GCA_000243295.1_TriManLat1.0 9778
382 yellow-spotted hyrax afrotheria Heterohyrax brucei
GCA_004026845.1_HetBruBak_v1_BIUU 77598
383 Cape rock hyrax afrotheria Procavia capensis
GCA_004026925.1_ProCapCap_v1_BIUU 9813
384 aardvark afrotheria Orycteropus afer 9818
385 Cape golden mole afrotheria Chrysochloris asiatica
GCA_004027935.1_ChrAsi_v1_BIUU 185453
386 Cape elephant shrew afrotheria Elephantulus edwardii
eleEdw1 28737
387 Talazac's shrew tenrec afrotheria Microgale talazaci (Nesogale talazaci)
GCA_004026705.1_MicTal_v1_BIUU 2583312
388 small Madagascar hedgehog afrotheria Echinops telfairi
GCA_000313985.1_EchTel2.0 9371
389 Sunda flying lemur euarchontoglires Galeopterus variegatus
GCA_004027255.1_GalVar_v1_BIUU 482537
390 Chinese tree shrew euarchontoglires Tupaia chinensis
tupChi1 246437
391 South African ground squirrel euarchontoglires Xerus inauris
GCA_004024805.1_XerIna_v1_BIUU 234690
392 large tree shrew euarchontoglires Tupaia tana 70687
393 mountain beaver euarchontoglires Aplodontia rufa
GCA_004027875.1_AplRuf_v1_BIUU 51342
394 Alpine marmot euarchontoglires Marmota marmota
GCF_001458135.1_marMar2.1 9993
395 Daurian ground squirrel euarchontoglires Spermophilus dauricus
GCA_002406435.1_ASM240643v1 99837
396 crested porcupine euarchontoglires Hystrix cristata
GCA_004026905.1_HysCri_v1_BIUU 10137
397 thirteen-lined ground squirrel euarchontoglires Ictidomys tridecemlineatus
speTri2 43179
398 American beaver euarchontoglires Castor canadensis
GCA_004027675.1_CasCan_v1_BIUU 51338
399 long-tailed chinchilla euarchontoglires Chinchilla lanigera
chiLan1 34839
400 punctate agouti euarchontoglires Dasyprocta punctata 34846
401 pacarana euarchontoglires Dinomys branickii
GCA_004027595.1_DinBra_v1_BIUU 108858
402 fat dormouse euarchontoglires Glis glis
GCA_004027185.1_GliGli_v1_BIUU 41261
403 northern gundi euarchontoglires Ctenodactylus gundi
GCA_004027205.1_CteGun_v1_BIUU 10166
404 naked mole-rat euarchontoglires Heterocephalus glaber
GCA_000247695.1_HetGla_female_1.0 10181
405 Patagonian cavy euarchontoglires Dolichotis patagonum
GCA_004027295.1_DolPat_v1_BIUU 29091
406 capybara euarchontoglires Hydrochoerus hydrochaeris
GCA_004027455.1_HydHyd_v1_BIUU 10149
407 Montane guinea pig euarchontoglires Cavia tschudii
GCA_004027695.1_CavTsc_v1_BIUU 143287
408 domestic guinea pig euarchontoglires Cavia porcellus
GCA_000151735.1_Cavpor3.0 10141
409 degu euarchontoglires Octodon degus
GCA_000260255.1_OctDeg1.0 10160
410 lowland paca euarchontoglires Cuniculus paca 108852
411 social tuco-tuco euarchontoglires Ctenomys sociabilis
GCA_004027165.1_CteSoc_v1_BIUU 43321
412 Damara mole-rat euarchontoglires Fukomys damarensis
fukDam1 885580
413 woodland dormouse euarchontoglires Graphiurus murinus 51346
414 Desmarest's hutia euarchontoglires Capromys pilorides
GCA_004027915.1_CapPil_v1_BIUU 34842
415 Upper Galilee mountains blind mole rat euarchontoglires Nannospalax galili
GCA_000622305.1_S.galili_v1.0 1026970
416 nutria euarchontoglires Myocastor coypus
GCA_004027025.1_MyoCoy_v1_BIUU 10157
417 hazel dormouse euarchontoglires Muscardinus avellanarius
GCA_004027005.1_MusAve_v1_BIUU 39082
418 dassie-rat euarchontoglires Petromus typicus
GCA_004026965.1_PetTyp_v1_BIUU 10183
419 greater cane rat euarchontoglires Thryonomys swinderianus
GCA_004025085.1_ThrSwi_v1_BIUU 10169
420 snowshoe hare euarchontoglires Lepus americanus
GCA_004026855.1_LepAme_v1_BIUU 48086
421 Gambian giant pouched rat euarchontoglires Cricetomys gambianus
GCA_004027575.1_CriGam_v1_BIUU 10085
422 Prairie deer mouse euarchontoglires Peromyscus maniculatus
GCF_000500345.1_Pman_1.0 10042
423 southern grasshopper mouse euarchontoglires Onychomys torridus
GCA_004026725.1_OnyTor_v1_BIUU 38674
424 rabbit euarchontoglires Oryctolagus cuniculus
GCA_000003625.1_OryCun2.0 9986
425 muskrat euarchontoglires Ondatra zibethicus
GCA_004026605.1_OndZib_v1_BIUU 10060
426 northern mole vole euarchontoglires Ellobius talpinus
GCA_001685095.1_ETalpinus_0.1 329620
427 Mongolian gerbil euarchontoglires Meriones unguiculatus
GCA_004026785.1_MerUng_v1_BIUU 10047
428 fat sand rat euarchontoglires Psammomys obesus
GCA_002215935.1_ASM221593v1 48139
429 house mouse euarchontoglires Mus musculus
mm10 10090
430 Chinese hamster euarchontoglires Cricetulus griseus
GCA_900186095.1_CHOK1S_HZDv1 10029
431 Norway rat euarchontoglires Rattus norvegicus
GCF_000001895.5_Rnor_6.0 10116
432 western wild mouse euarchontoglires Mus spretus
GCA_001624865.1_SPRET_EiJ_v1 10096
433 meadow jumping mouse euarchontoglires Zapus hudsonius
GCA_004024765.1_ZapHud_v1_BIUU 160400
434 prairie vole euarchontoglires Microtus ochrogaster
micOch1 79684
435 Ryukyu mouse euarchontoglires Mus caroli
GCA_900094665.2_CAROLI_EIJ_v1.1 10089
436 Egyptian spiny mouse euarchontoglires Acomys cahirinus
GCA_004027535.1_AcoCah_v1_BIUU 10068
437 Gobi jerboa euarchontoglires Allactaga bullata (Orientallactaga bullata)
GCA_004027895.1_AllBul_v1_BIUU 1041416
438 shrew mouse euarchontoglires Mus pahari
GCF_900095145.1_PAHARI_EIJ_v1.1 10093
439 Transcaucasian mole vole euarchontoglires Ellobius lutescens
GCA_001685075.1_ASM168507v1 39086
440 hispid cotton rat euarchontoglires Sigmodon hispidus
GCA_004025045.1_SigHis_v1_BIUU 42415
441 lesser Egyptian jerboa euarchontoglires Jaculus jaculus
GCA_000280705.1_JacJac1.0 51337
442 Brazilian guinea pig euarchontoglires Cavia aperea
cavApe1 37548
443 golden hamster euarchontoglires Mesocricetus auratus
GCA_000349665.1_MesAur1.0 10036
444 Stephens's kangaroo rat euarchontoglires Dipodomys stephensi
GCA_004024685.1_DipSte_v1_BIUU 323379
445 American pika euarchontoglires Ochotona princeps
GCA_000292845.1_OchPri3.0 9978
446 Ord's kangaroo rat euarchontoglires Dipodomys ordii
dipOrd2 10020
447 little pocket mouse euarchontoglires Perognathus longimembris 38669

\ Table 1. Genome assemblies included in the 447-way Conservation track.\

\ \ \

References

\ Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F\ et al.\ \ Identification of constrained sequence elements across 239 primate genomes.\ Nature. 2023 Nov 29;.\ DOI: 10.1038/s41586-023-06798-8; PMID: 38030727\

\ Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J,\ Rousselle M et al.\ \ A global catalog of whole-genome diversity from 233 primate species.\ Science. 2023 Jun 2;380(6648):906-913.\ DOI: 10.1126/science.abn7829;\ PMID: 37262161\

\ Zoonomia Consortium.\ \ A comparative genomics multitool for scientific discovery and conservation.\ Nature. 2020 Nov;587(7833):240-245.\ DOI: 10.1038/s41586-020-2876-6; PMID: 33177664; PMC: PMC7759459\

\ Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC et\ al.\ \ Dense sampling of bird diversity increases power of comparative genomics.\ Nature. 2020 Nov;587(7833):252-257.\ DOI: 10.1038/s41586-020-2873-9; PMID: 33177665; PMC: PMC7759463\

\ compGeno 1 compositeTrack on\ dragAndDrop subTracks\ group compGeno\ html cactus447way\ longLabel Cactus Alignment & Conservation on 447 mammal species, including Zoonomia genomes\ shortLabel Cactus 447-way\ subGroup1 view Views align=Multiz_Alignments phyloP=Basewise_Conservation_(phyloP)\ track cons447way\ type bed 4\ visibility hide\ cactus447way Cactus 447-way bigMaf Cactus alignment on 447 mammal species, including Zoonomia genomes 3 100 0 10 100 0 90 10 0 0 0

Data Access

\ Downloads for data in this track are available from the directory:\

\ Cactus 447-way alignments (MAF format), and phylogenetic trees\ PhyloP conservation (WIG format)\

\ \

Display Conventions and Configuration

\ To view detailed information about the alignments at a specific\ position, zoom the display in to 30,000 or fewer bases, then click on\ the alignment.

\ \

Gap Annotation

Single line: No bases in the aligned species. Possibly due to a\ lineage-specific insertion between the aligned blocks in the human genome\ or a lineage-specific deletion between the aligned blocks in the aligning\ species.\
Double line: Aligning species has one or more unalignable bases in\ the gap region. Possibly due to excessive evolutionary distance between\ species or independent indels in the region between the aligned blocks in both\ species.\
Pale yellow coloring: Aligning species has Ns in the gap region.\ Reflects uncertainty in the relationship between the DNA of both species, due\ to lack of sequence in relevant portions of the aligning species.\

\ \

Genomic Breaks

\ Discontinuities in the genomic context (chromosome, scaffold or region) of the\ aligned DNA in the aligning species are shown as follows:\

\ Vertical blue bar: Represents a discontinuity that persists indefinitely\ on either side, e.g. a large region of DNA on either side of the bar\ comes from a different chromosome in the aligned species due to a large scale\ rearrangement.\
\ Green square brackets: Enclose shorter alignments consisting of DNA from\ one genomic context in the aligned species nested inside a larger chain of\ alignments from a different genomic context. The alignment within the\ brackets may represent a short misalignment, a lineage-specific insertion of a\ transposon in the human genome that aligns to a paralogous copy somewhere\ else in the aligned species, or other similar occurrence.\

\ \

Base Level

\ No codon translation: The gene annotation is not used; the bases are\ displayed without translation.\
\ Use default species reading frames for translation: The annotations from\ the genome displayed in the Default species to establish reading frame\ pull-down menu are used to translate all the aligned species present in the\ alignment.\
\ Use reading frames for species if available, otherwise no translation:\ Codon translation is performed only for those species where the region is\ annotated as protein coding.\
Use reading frames for species if available, otherwise use default species:\ Codon translation is done on those species that are annotated as being protein\ coding over the aligned region using species-specific annotation; the remaining\ species are translated using the default species annotation.\

\ Codon translation uses the following gene tracks as the basis for translation:\

\ \ \ \ \ \
Gene Track Species
RefSeq Genes Bos mutus, Canis lupus familiaris, Carlito syrichta, Cercocebus atys, Chinchilla lanigera, Colobus angolensis, Condylura cristata, Dipodomys ordii, Elephantulus edwardii, Eptesicus fuscus, Felis catus, Felis catus fca126, Fukomys damarensis, Homo sapiesn, Ictidomys tridecemlineatus, Macaca mulatta, Macaca nemestrina, Marmota marmota, Microtus ochrogaster, Miniopterus natalensis, Mus musculus, Mus pahari, Myotis brandtii, Myotis davidii, Myotis lucifugus, Odobenus rosmarus, Orcinus orca, Otolemur garnettii, Peromyscus maniculatus, Piliocolobus tephrosceles, Propithecus coquerelli, Pteropus alecto, Pteropus vampyrus, Rattus norvegicus, Rhinopithecus roxellana, Saimiri boliviensis, Sorex araneus, Sus scrofa, Theropithecus gelada, Tupaia chinensis
Ensembl Genes Cavia aperea
Augustus Genes Eidolon helvum, Pteronotus parnellii
no annotation Acinonyx jubatus, Acomys cahirinus, Ailuropoda melanoleuca, Ailurus fulgens, Allactaga bullata, Allenopithecus nigroviridis, Allochrocebus lhoesti, Allochrocebus preussi, Allochrocebus solatus, Alouatta belzebul, Alouatta caraya, Alouatta discolor, Alouatta juara, Alouatta macconnelli, Alouatta nigerrima, Alouatta palliata, Alouatta puruensis, Alouatta seniculus, Ammotragus lervia, Anoura caudifer, Antilocapra americana, Aotus azarae, Aotus griseimembra, Aotus nancymaae, Aotus trivirgatus, Aotus vociferans, Aplodontia rufa, Arctocebus calabarensis, Artibeus jamaicensis, Ateles geoffroyi_a, Ateles geoffroyi_b, Ateles belzebuth, Ateles chamek, Ateles marginatus, Ateles paniscus, Avahi laniger, Avahi peyrierasi, Balaenoptera acutorostrata, Balaenoptera bonaerensis, Beatragus hunteri, Bison bison, Bos indicus, Bos taurus, Bubalus bubalis, Cacajao ayresi, Cacajao calvus, Cacajao hosomi, Cacajao melanocephalus, Callibella humilis, Callimico goeldii, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Camelus bactrianus, Camelus dromedarius, Camelus ferus, Canis lupus VD, Canis lupus dingo, Canis lupus orion, Capra aegagrus, Capra hircus, Capromys pilorides, Carollia perspicillata, Castor canadensis, Catagonus wagneri, Cavia porcellus, Cavia tschudii, Cebuella niveiventris, Cebuella pygmaea, Cebus albifrons, Cebus olivaceus, Cebus unicolor, Cephalopachus bancanus, Ceratotherium simum, Ceratotherium simum cottoni, Cercocebus chrysogaster, Cercocebus lunulatus, Cercocebus torquatus, Cercopithecus ascanius, Cercopithecus cephus, Cercopithecus diana, Cercopithecus hamlyni, Cercopithecus lowei, Cercopithecus albogularis, Cercopithecus mona, Cercopithecus neglectus, Cercopithecus nictitans, Cercopithecus petaurista, Cercopithecus pogonias, Cercopithecus roloway, Chaetophractus vellerosus, Cheirogaleus major, Cheirogaleus medius, Cheracebus lucifer, Cheracebus lugens, Cheracebus regulus, Cheracebus torquatus, Chiropotes albinasus, Chiropotes israelita, Chiropotes sagulatus, Chlorocebus aethiops, Chlorocebus pygerythrus, Chlorocebus sabaeus, Choloepus didactylus, Choloepus hoffmanni, Chrysochloris asiatica, Colobus guereza, Colobus polykomos, Craseonycteris thonglongyai, Cricetomys gambianus, Cricetulus griseus, Crocidura indochinensis, Cryptoprocta ferox, Ctenodactylus gundi, Ctenomys sociabilis, Cuniculus paca, Dasyprocta punctata, Dasypus novemcinctus, Daubentonia madagascariensis, Delphinapterus leucas, Desmodus rotundus, Dicerorhinus sumatrensis, Diceros bicornis, Dinomys branickii, Dipodomys stephensi, Dolichotis patagonum, Echinops telfairi, Elaphurus davidianus, Ellobius lutescens, Ellobius talpinus, Enhydra lutris, Equus asinus, Equus caballus, Equus przewalskii, Erinaceus europaeus, Erythrocebus patas, Eschrichtius robustus, Eubalaena japonica, Eulemur albifrons, Eulemur collaris, Eulemur coronatus, Eulemur flavifrons, Eulemur fulvus, Eulemur macaco, Eulemur mongoz, Eulemur rubriventer, Eulemur rufus, Eulemur sanfordi, Felis nigripes, Galago moholi, Galago senegalensis, Galagoides demidoff, Galeopterus variegatus, Giraffa tippelskirchi, Glis glis, Gorilla beringei, Gorilla gorilla, Graphiurus murinus, Hapalemur alaotrensis, Hapalemur gilberti, Hapalemur griseus, Hapalemur meridionalis, Hapalemur occidentalis, Helogale parvula, Hemitragus hylocrius, Heterocephalus glaber, Heterohyrax brucei, Hippopotamus amphibius, Hipposideros armiger, Hipposideros galeritus, Hoolock leuconedys, Hyaena hyaena, Hydrochoerus hydrochaeris, Hylobates abbotti, Hylobates agilis, Hylobates klossii, Hylobates pileatus, Hylobates muelleri, Hylobates pileatus, Hystrix cristata, Indri indri, Inia geoffrensis, Jaculus jaculus, Kogia breviceps, Lagothrix lagothricha, Lasiurus borealis, Lemur catta, Leontocebus fuscicollis, Leontocebus illigeri, Leontocebus nigricollis, Leontopithecus chrysomelas, Leontopithecus rosalia, Lepilemur ankaranensis, Lepilemur dorsalis, Lepilemur ruficaudatus, Lepilemur septentrionalis, Leptonychotes weddellii, Lepus americanus, Lipotes vexillifer, Lophocebus aterrimus, Loris lydekkerianus, Loris tardigradus, Loxodonta africana, Lycaon pictus, Macaca arctoides, Macaca assamensis, Macaca cyclopis, Macaca fascicularis, Macaca fuscata, Macaca leonina, Macaca maura, Macaca nigra, Macaca radiata, Macaca siberu, Macaca silenus, Macaca thibetana, Macaca tonkeana, Macroglossus sobrinus, Mandrillus leucophaeus, Mandrillus sphinx, Manis javanica, Manis pentadactyla, Megaderma lyra, Mellivora capensis, Meriones unguiculatus, Mesocricetus auratus, Mesoplodon bidens, Mico argentatus, Mico humeralifer, Mico schneideri, Microcebus murinus, Microgale talazaci, Micronycteris hirsuta, Miniopterus schreibersii, Miopithecus ogouensis, Mirounga angustirostris, Mirza zaza, Monodon monoceros, Mormoops blainvillei, Moschus moschiferus, Mungos mungo, Murina feae, Mus caroli, Mus spretus, Muscardinus avellanarius, Mustela putorius, Myocastor coypus, Myotis myotis, Myrmecophaga tridactyla, Nannospalax galili, Nasalis larvatus, Neomonachus schauinslandi, Neophocaena asiaeorientalis, Noctilio leporinus, Nomascus annamensis, Nomascus concolor, Nomascus gabriellae, Nomascus siki_a, Nomascus siki_b, Nyctereutes procyonoides, Nycticebus bengalensis, Nycticebus coucang, Nycticebus pygmaeus, Ochotona princeps, Octodon degus, Odocoileus virginianus, Okapia johnstoni, Ondatra zibethicus, Onychomys torridus, Orycteropus afer, Oryctolagus cuniculus, Otocyon megalotis, Otolemur crassicaudatus, Ovis aries, Ovis canadensis, Pan paniscus, Pan troglodytes, Panthera onca, Panthera pardus, Panthera tigris, Pantholops hodgsonii, Papio anubis, Papio cynocephalus, Papio hamadryas, Papio kindae, Papio papio, Papio ursinus, Paradoxurus hermaphroditus, Perodicticus ibeanus, Perodicticus potto, Perognathus longimembris, Petromus typicus, Phocoena phocoena, Piliocolobus badius, Piliocolobus gordonorum, Piliocolobus kirkii, Pipistrellus pipistrellus, Pithecia albicans, Pithecia chrysocephala, Pithecia hirsuta, Pithecia mittermeieri, Pithecia pissinattii, Pithecia pithecia, Pithecia vanzolinii, Platanista gangetica, Plecturocebus bernhardi, Plecturocebus brunneus, Plecturocebus caligatus, Plecturocebus cinerascens, Plecturocebus cupreus, Plecturocebus dubius, Plecturocebus grovesi, Plecturocebus hoffmannsi, Plecturocebus miltoni, Plecturocebus moloch, Pongo abelii, Pongo pygmaeus, Presbytis comata, Presbytis mitrata, Procavia capensis, Prolemur simus, Propithecus coronatus, Propithecus diadema, Propithecus edwardsi, Propithecus perrieri, Propithecus tattersalli, Propithecus verreauxi, Psammomys obesus, Pteronura brasiliensis, Puma concolor, Pygathrix cinerea, Pygathrix nigripes, Pygathrix nigripes, Rangifer tarandus, Rhinolophus sinicus, Rhinopithecus bieti, Rhinopithecus strykeri, Rousettus aegyptiacus, Saguinus bicolor, Saguinus geoffroyi, Saguinus imperator, Saguinus inustus, Saguinus labiatus, Saguinus midas, Saguinus mystax, Saguinus oedipus, Saiga tatarica, Saimiri cassiquiarensis, Saimiri macrodon, Saimiri oerstedii, Saimiri sciureus, Saimiri ustus, Sapajus apella, Sapajus macrocephalus, Scalopus aquaticus, Semnopithecus entellus, Semnopithecus hypoleucos, Semnopithecus johnii, Semnopithecus priam, Semnopithecus schistaceus, Semnopithecus vetulus, Sigmodon hispidus, Solenodon paradoxus, Spermophilus dauricus, Spilogale gracilis, Suricata suricatta, Symphalangus syndactylus, Tadarida brasiliensis, Tamandua tetradactyla, Tapirus indicus, Tapirus terrestris, Tarsius lariang, Tarsius wallacei, Thryonomys swinderianus, Tolypeutes matacus, Tonatia saurophila, Trachypithecus auratus, Trachypithecus crepusculus, Trachypithecus cristatus, Trachypithecus francoisi, Trachypithecus geei, Trachypithecus germaini, Trachypithecus hatinhensis, Trachypithecus laotum, Trachypithecus leucocephalus, Trachypithecus melamera, Trachypithecus obscurus, Trachypithecus phayrei, Trachypithecus pileatus, Tragulus javanicus, Trichechus manatus, Tupaia tana, Tursiops truncatus, Uropsilus gracilis, Ursus maritimus, Varecia rubra, Varecia variegata, Vicugna pacos, Vulpes lagopus, Xerus inauris, Zalophus californianus, Zapus hudsonius, Ziphius cavirostris\
\ Table 2. Gene tracks used for codon translation.\

\ \

Methods

\ This alignment was created by making three edits (using Cactus) to the\ 241-way mammalian Zoonomia Cactus alignment\ (\ https://cglgenomics.ucsc.edu/data/cactus/).\

One additional cat genome, "Felis_catus_fca126" (GCA_018350175.1) was\ added as a sister taxa to the existing "Felis_catus" species
Five additional canine genomes were also added: canFam4,\ "Canis_lupus_dingo" (GCA_003254725.1), "Canis_lupus_orion"\ (GCA_905319855.2), "Nyctereutes_procyonoides" (GCA_905146905.1) and\ "Otocyon_megalotis" (GCA_017311455.1). "Canis_lupus" from the Zoonomia\ alignment was also renamed "Canis_lupus_VD" to reflect the fact that it\ corresponds to a "village dog" and not "wolf" sample.
The 43-species primates clade from the Zoonomia alignment was removed\ and replaced with the 243-way primates alignment from Identification of\ constrained sequence elements across 239 primate genomes, increasing the alignment by 200\ additional primate species.

\ \

Phylogenic tree

\ The phylogenic tree was established by the research described\ in A global catalog of whole-genome diversity from 233 primate\ species.\ \

Sequences

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
count common
name clade scientific name
(link to browser when existing) taxon id
link to NCBI
001 human primates catarrhini Homo sapiens/hg38
reference species 9606
002 western gorilla primates catarrhini Gorilla gorilla
GCA_900006655.3_Susie3 9593
003 Sumatran orangutan primates catarrhini Pongo abelii
GCA_002880775.3_Susie_PABv2 9601
004 Eastern Gorilla primates catarrhini Gorilla beringei 499232
005 chimpanzee primates catarrhini Pan troglodytes
GCA_002880755.3_Clint_PTRv2 9598
006 Bornean orangutan primates catarrhini Pongo pygmaeus 9600
007 Rhesus monkey primates catarrhini Macaca mulatta
rheMac10 9544
008 gelada primates catarrhini Theropithecus gelada
GCF_003255815.1_Tgel_1.0 9565
009 stump-tailed macaque primates catarrhini Macaca arctoides 9540
010 Northern Talapoin Monkey primates catarrhini Miopithecus ogouensis 100488
011 crab-eating macaque primates catarrhini Macaca fascicularis 9541
012 Allen's swamp monkey primates catarrhini Allenopithecus nigroviridis 54135
013 siamang primates catarrhini Symphalangus syndactylus 9590
014 black crested mangabey primates catarrhini Lophocebus aterrimus 75566
015 drill primates catarrhini Mandrillus leucophaeus 9568
016 Bonnet Macaque primates catarrhini Macaca radiata 9548
017 Red-capped Mangabey primates catarrhini Cercocebus torquatus 9530
018 Golden-bellied Mangabey primates catarrhini Cercocebus chrysogaster 75569
019 Owl-faced Monkey primates catarrhini Cercopithecus hamlyni 9536
020 Siberut Macaque primates catarrhini Macaca siberu 244255
021 pig-tailed macaque primates catarrhini Macaca nemestrina
GCF_000956065.1_Mnem_1.0 9545
022 White-naped Mangabey primates catarrhini Cercocebus lunulatus (Cercocebus atys lunulatus) 75570
023 Tonkean Macaque primates catarrhini Macaca tonkeana 40843
024 Diana Monkey primates catarrhini Cercopithecus diana 36224
025 red guenon primates catarrhini Erythrocebus patas 9538
026 Northern Pig-tailed Macaque primates catarrhini Macaca leonina 90387
027 Moor Macaque primates catarrhini Macaca maura 90383
028 Guinea Baboon primates catarrhini Papio papio 100937
029 hamadryas baboon primates catarrhini Papio hamadryas 9557
030 liontail macaque primates catarrhini Macaca silenus 54601
031 olive baboon primates catarrhini Papio anubis
GCA_000264685.2_Panu_3.0 9555
032 Roloway Monkey primates catarrhini Cercopithecus roloway 1137049
033 Kinda Baboon primates catarrhini Papio kindae 208091
034 Chacma Baboon primates catarrhini Papio ursinus 36229
035 Sun-tailed Monkey primates catarrhini Allochrocebus solatus 147650
036 golden snub-nosed monkey primates catarrhini Rhinopithecus roxellana
GCF_007565055.1_ASM756505v1 61622
037 Vervet Monkey primates catarrhini Chlorocebus pygerythrus 60710
038 sooty mangabey primates catarrhini Cercocebus atys
GCF_000955945.1_Caty_1.0 9531
039 green monkey primates catarrhini Chlorocebus sabaeus
GCA_000409795.2_Chlorocebus_sabeus_1.1 60711
040 De Brazza's monkey primates catarrhini Cercopithecus neglectus 36227
041 Yellow Baboon primates catarrhini Papio cynocephalus 9556
042 Celebes crested macaque primates catarrhini Macaca nigra 54600
043 proboscis monkey primates catarrhini Nasalis larvatus 43780
044 Preuss's Monkey primates catarrhini Allochrocebus preussi 147649
045 Putty-nosed Monkey primates catarrhini Cercopithecus nictitans 36228
046 Javan Surili primates catarrhini Presbytis comata 78452
047 Sykes' Monkey primates catarrhini Cercopithecus albogularis 36225
048 LHoests Monkey primates catarrhini Allochrocebus lhoesti 100224
049 Crowned Monkey primates catarrhini Cercopithecus pogonias 102108
050 Southern Mitered Langur primates catarrhini Presbytis mitrata (Presbytis melalophos mitrata) 272115
051 Grey-shanked Douc Langur primates catarrhini Pygathrix cinerea 693712
052 Mona monkey primates catarrhini Cercopithecus mona 36226
053 Spot-nosed Monkey primates catarrhini Cercopithecus petaurista 100487
054 grivet primates catarrhini Chlorocebus aethiops 9534
055 Lowes Monkey primates catarrhini Cercopithecus lowei 304410
056 Northern Yellow-cheeked Crested Gibbon primates catarrhini Nomascus annamensis 1616038
057 Red-cheeked Gibbon primates catarrhini Nomascus gabriellae 61852
058 Japanese macaque primates catarrhini Macaca fuscata 9542
059 Western Red Colobus primates catarrhini Piliocolobus badius 164648
060 southern white-cheeked gibbon primates catarrhini Nomascus siki_a 9586
061 Taiwan macaque primates catarrhini Macaca cyclopis 78449
062 black-shanked douc langur primates catarrhini Pygathrix nigripes 310352
063 King Colobus primates catarrhini Colobus polykomos 9572
064 Black Crested Gibbon primates catarrhini Nomascus concolor 29089
065 Udzungwa Red Colobus primates catarrhini Piliocolobus gordonorum 591933
066 Gee's Golden Langur primates catarrhini Trachypithecus geei 164650
067 Kloss's Gibbon primates catarrhini Hylobates klossii 9587
068 Spectacled Leaf Monkey primates catarrhini Trachypithecus obscurus 54181
069 Zanzibar Red Colobus primates catarrhini Piliocolobus kirkii 591937
070 Indochinese Silvered Langur primates catarrhini Trachypithecus germaini 271260
071 Hatinh Langur primates catarrhini Trachypithecus hatinhensis 867383
072 Moustached Monkey primates catarrhini Cercopithecus cephus 9535
073 Laotian Langur primates catarrhini Trachypithecus laotum 465718
074 Francois's langur primates catarrhini Trachypithecus francoisi 54180
075 Purple-faced Langur primates catarrhini Semnopithecus vetulus (Trachypithecus vetulus) 54137
076 Capped Langur primates catarrhini Trachypithecus pileatus 164651
077 Ugandan red Colobus primates catarrhini Piliocolobus tephrosceles
GCF_002776525.2_ASM277652v2 591936
078 Spangled Ebony Langur primates catarrhini Trachypithecus auratus 222416
079 Red-tailed Monkey primates catarrhini Cercopithecus ascanius 36223
080 Silvery Lutung primates catarrhini Trachypithecus cristatus 122765
081 Nilgiri Langur primates catarrhini Semnopithecus johnii (Trachypithecus johnii) 66063
082 Indochinese grey langur primates catarrhini Trachypithecus crepusculus (Trachypithecus phayrei crepuscula) 272121
083 White-headed langur primates catarrhini Trachypithecus leucocephalus (Trachypithecus poliocephalus) 465719
084 pygmy chimpanzee primates catarrhini Pan paniscus
GCA_000258655.2_panpan1.1 9597
085 northern white-cheeked gibbon primates catarrhini Nomascus siki_b 9586
086 Agile Gibbon primates catarrhini Hylobates agilis 9579
087 Phayre's Leaf-monkey primates catarrhini Trachypithecus melamera n/a
088 Nepal Gray Langur primates catarrhini Semnopithecus schistaceus 2804203
089 Abbott's Gray Gibbon primates catarrhini Hylobates abbotti (Hylobates muelleri abbotti) 716694
090 Bornean Gibbon primates catarrhini Hylobates muelleri 9588
091 Tufted Gray Langur primates catarrhini Semnopithecus priam 1208733
092 Black-footed Gray Langur primates catarrhini Semnopithecus hypoleucos 1208734
093 mantled guereza primates catarrhini Colobus guereza 33548
094 Hanuman langur primates catarrhini Semnopithecus entellus 88029
095 pileated gibbon primates catarrhini Hylobates pileatus 9589
096 black snub-nosed monkey primates catarrhini Rhinopithecus bieti 61621
097 Burmese snub-nosed monkey primates catarrhini Rhinopithecus strykeri 1194336
098 Angolan colobus primates catarrhini Colobus angolensis
colAng1 54131
099 Pileated Gibbon primates catarrhini Hylobates pileatus 9589
100 black-shanked douc langur primates catarrhini Pygathrix nigripes 310352
101 Milne-edwards' Macaque primates catarrhini Macaca thibetana 54602
102 Phayre's Leaf-monkey primates catarrhini Trachypithecus phayrei 61618
103 Assam macaque primates catarrhini Macaca assamensis 9551
104 Eastern hoolock gibbon primates catarrhini Hoolock leuconedys 61851
105 mandrill primates catarrhini Mandrillus sphinx 9561
106 White-faced Saki primates platyrrhini Pithecia chrysocephala 2946515
107 Monk Saki primates platyrrhini Pithecia hirsuta 2946516
108 white-faced saki primates platyrrhini Pithecia pithecia 43777
109 Mittermeier's Tapaj�s saki primates platyrrhini Pithecia mittermeieri 2946517
110 Buffy Saki primates platyrrhini Pithecia albicans 2946514
111 Pissinatti's saki primates platyrrhini Pithecia pissinattii (Pithecia pissinatti) 2946518
112 Vanzolini's Bald-faced Saki primates platyrrhini Pithecia vanzolinii 2946519
113 Bald-headed Uacari primates platyrrhini Cacajao calvus 30596
114 Ayres Black Uakari primates platyrrhini Cacajao ayresi 535896
115 Black-headed Uacari primates platyrrhini Cacajao melanocephalus 70825
116 Black-headed Uacari primates platyrrhini Cacajao hosomi 535897
117 Reddish-brown bearded saki primates platyrrhini Chiropotes sagulatus (Chiropotes chiropotes) 658221
118 brown-backed bearded saki primates platyrrhini Chiropotes israelita 280163
119 Collared Titi Monkey primates platyrrhini Cheracebus lugens 210166
120 Brown Titi Monkey primates platyrrhini Plecturocebus brunneus 1812042
121 Hoffmanns's titi monkey primates platyrrhini Plecturocebus hoffmannsi 78255
122 Milton's Titi Monkey primates platyrrhini Plecturocebus miltoni 1812038
123 Widow Monkey primates platyrrhini Cheracebus torquatus 30592
124 Ashy Black Titi Monkey primates platyrrhini Plecturocebus cinerascens 1812037
125 Prince Bernhard's Titi Monkey primates platyrrhini Plecturocebus bernhardi 1812036
126 Yellow-handed Titi Monkey primates platyrrhini Cheracebus lucifer 2487712
127 Coppery Titi Monkey primates platyrrhini Plecturocebus cupreus 202457
128 Chestnut-bellied Titi primates platyrrhini Plecturocebus caligatus 867332
129 Hershkovitzs Titi primates platyrrhini Plecturocebus dubius 2946520
130 Red-bellied Titi Monkey primates platyrrhini Plecturocebus moloch 9523
131 Groves' Titi primates platyrrhini Plecturocebus grovesi 2488670
132 black-handed spider monkey primates platyrrhini Ateles geoffroyi_a 9509
133 Widow Monkey primates platyrrhini Cheracebus regulus 1812110
134 Guiana Spider Monkey primates platyrrhini Ateles paniscus 9510
135 Black-faced Black Spider Monkey primates platyrrhini Ateles chamek 118643
136 White-cheeked Spider Monkey primates platyrrhini Ateles marginatus 1529884
137 White-bellied Spider Monkey primates platyrrhini Ateles belzebuth 9507
138 Common Woolly Monkey primates platyrrhini Lagothrix lagothricha (Lagothrix lagotricha) 9519
139 large-headed capuchin primates platyrrhini Sapajus macrocephalus (Sapajus apella macrocephalus) 1547595
140 Spixs White-fronted Capuchin primates platyrrhini Cebus unicolor 1985288
141 Central American spider monkey primates platyrrhini Ateles geoffroyi_b 9509
142 Guinan Weeper Capuchin primates platyrrhini Cebus olivaceus 37295
143 mantled howler monkey primates platyrrhini Alouatta palliata 30589
144 white-fronted capuchin primates platyrrhini Cebus albifrons 9514
145 Northern Night Monkey primates platyrrhini Aotus trivirgatus 9505
146 Grey-handed Night Monkey primates platyrrhini Aotus griseimembra 292213
147 Black-and-gold Howler Monkey primates platyrrhini Alouatta caraya 9502
148 Spixs Night Monkey primates platyrrhini Aotus vociferans 57176
149 Red-handed Howler Monkey primates platyrrhini Alouatta belzebul 30590
150 Red-handed Howler Monkey primates platyrrhini Alouatta discolor 2905217
151 Azara's Night Monkey primates platyrrhini Aotus azarae (Aotus azarai) 30591
152 Pur�s Red Howler Monkey primates platyrrhini Alouatta puruensis (Alouatta seniculus puruensis) 1347729
153 Black Howler Monkey primates platyrrhini Alouatta nigerrima (Alouatta belzebul) 30590
154 Guianan Red Howler Monkey primates platyrrhini Alouatta macconnelli 198115
155 Colombian Red Howler Monkey primates platyrrhini Alouatta juara 2946512
156 Colombian Red Howler Monkey primates platyrrhini Alouatta seniculus 9503
157 tufted capuchin primates platyrrhini Sapajus apella 9515
158 Ma's night monkey primates platyrrhini Aotus nancymaae
GCA_000952055.2_Anan_2.0 37293
159 Bolivian squirrel monkey primates platyrrhini Saimiri boliviensis
GCF_016699345.1_BCM_Sbol_2.0 27679
160 White-nosed Saki primates platyrrhini Chiropotes albinasus 198627
161 Black Mantle Tamarin primates platyrrhini Leontocebus nigricollis 9489
162 brown-mantled tamarin primates platyrrhini Leontocebus fuscicollis 9487
163 Illiger's saddle-back tamarin primates platyrrhini Leontocebus illigeri (Leontocebus fuscicollis illigeri) 881947
164 Cotton-headed Tamarin primates platyrrhini Saguinus oedipus 9490
165 Pied Tamarin primates platyrrhini Saguinus bicolor 37588
166 Geoffroy's Tamarin primates platyrrhini Saguinus geoffroyi 43778
167 White-fronted Titi Monkey primates platyrrhini Saguinus inustus 1079039
168 Moustached Tamarin primates platyrrhini Saguinus mystax 9488
169 tamarin primates platyrrhini Saguinus imperator 9491
170 Guianan Squirrel Monkey primates platyrrhini Saimiri sciureus 9521
171 Red-chested Mustached Tamarin primates platyrrhini Saguinus labiatus 78454
172 Goeldi's Monkey primates platyrrhini Callimico goeldii 9495
173 Black-crowned Central American Squirrel Monkey primates platyrrhini Saimiri oerstedii 70928
174 Golden-headed Lion Tamarin primates platyrrhini Leontopithecus chrysomelas 57374
175 golden lion tamarin primates platyrrhini Leontopithecus rosalia 30588
176 Humboldt's Squirrel Monkey primates platyrrhini Saimiri cassiquiarensis 2946521
177 bare-eared squirrel monkey primates platyrrhini Saimiri ustus 66265
178 Ecuadorian squirrel monkey primates platyrrhini Saimiri macrodon 2946522
179 white-tufted-ear marmoset primates platyrrhini Callithrix jacchus 9483
180 Eastern Pygmy Marmoset primates platyrrhini Cebuella niveiventris 2826950
181 Western Pygmy Marmoset primates platyrrhini Cebuella pygmaea 9493
182 Black And White Tassel-ear Marmoset primates platyrrhini Mico humeralifer 52232
183 Black-crowned Dwarf Marmoset primates platyrrhini Callibella humilis (Mico humilis) 666519
184 Mico schneideri primates platyrrhini Mico schneideri n/a
185 Silvery Marmoset primates platyrrhini Mico argentatus 9482
186 Midas tamarin primates platyrrhini Saguinus midas 30586
187 Wieds Marmoset primates platyrrhini Callithrix kuhlii 867363
188 Geoffroy's Tufted-ear Marmoset primates platyrrhini Callithrix geoffroyi 52231
189 Horsfield's tarsier primates tarsiidae Cephalopachus bancanus 9477
190 Philippine tarsier primates tarsiidae Carlito syrichta
tarSyr2 1868482
191 Lariang Tarsier primates tarsiidae Tarsius lariang 630277
192 Wallace's Tarsier primates tarsiidae Tarsius wallacei 981131
193 aye-aye primates strepsirrhini Daubentonia madagascariensis 31869
194 Crowned Sifaka primates strepsirrhini Propithecus coronatus (Propithecus deckenii coronatus) 475619
195 Perrier's Sifaka primates strepsirrhini Propithecus perrieri 989338
196 ruffed lemur primates strepsirrhini Varecia variegata 9455
197 Diademed Sifaka primates strepsirrhini Propithecus diadema 83281
198 Milne-Edwards Sifaka primates strepsirrhini Propithecus edwardsi 543559
199 babakoto primates strepsirrhini Indri indri 34827
200 Golden-crowned Sifaka primates strepsirrhini Propithecus tattersalli 30601
201 Eastern Woolly Lemur primates strepsirrhini Avahi laniger 122246
202 Verreauxs Sifaka primates strepsirrhini Propithecus verreauxi 34825
203 Peyrieras Woolly Lemur primates strepsirrhini Avahi peyrierasi 1313323
204 Red Ruffed Lemur primates strepsirrhini Varecia rubra 554167
205 greater bamboo lemur primates strepsirrhini Prolemur simus 1328070
206 Red-bellied Lemur primates strepsirrhini Eulemur rubriventer 34829
207 mongoose lemur primates strepsirrhini Eulemur mongoz 34828
208 Geoffroys Dwarf Lemur primates strepsirrhini Cheirogaleus major 47177
209 Crowned Lemur primates strepsirrhini Eulemur coronatus 13514
210 black lemur primates strepsirrhini Eulemur macaco 30602
211 lesser dwarf lemur primates strepsirrhini Cheirogaleus medius 9460
212 Sclater's lemur primates strepsirrhini Eulemur flavifrons 87288
213 Coquerel's sifaka primates strepsirrhini Propithecus coquerelli (Propithecus coquereli)
proCoq1 379532
214 Collared Brown Lemur primates strepsirrhini Eulemur collaris (Eulemur fulvus collaris) 47178
215 Red-tailed Sportive Lemur primates strepsirrhini Lepilemur ruficaudatus 78866
216 Red Brown Lemur primates strepsirrhini Eulemur rufus 859983
217 Sanfords Brown Lemur primates strepsirrhini Eulemur sanfordi 122225
218 White-fronted Lemur primates strepsirrhini Eulemur albifrons 1215604
219 Gray's Sportive Lemur primates strepsirrhini Lepilemur dorsalis 78583
220 brown lemur primates strepsirrhini Eulemur fulvus 13515
221 Sahafary Sportive Lemur primates strepsirrhini Lepilemur septentrionalis 78584
222 Sambirano Lesser Bamboo Lemur primates strepsirrhini Hapalemur occidentalis 867377
223 Alaotra Reed Lemur primates strepsirrhini Hapalemur alaotrensis (Hapalemur griseus alaotrensis) 122220
224 Eastern Lesser Bamboo Lemur primates strepsirrhini Hapalemur griseus 13557
225 Ankarana Sportive Lemur primates strepsirrhini Lepilemur ankaranensis 342401
226 ring-tailed lemur primates strepsirrhini Lemur catta 9447
227 gray bamboo lemur primates strepsirrhini Hapalemur gilberti 3043110
228 Rusty-gray Lesser Bamboo Lemur primates strepsirrhini Hapalemur meridionalis 3043112
229 Demidoffs Dwarf Galago primates strepsirrhini Galagoides demidoff 89672
230 northern giant mouse lemur primates strepsirrhini Mirza zaza 339999
231 gray mouse lemur primates strepsirrhini Microcebus murinus
GCA_000165445.3_Mmur_3.0 30608
232 small-eared galago primates strepsirrhini Otolemur garnettii
otoGar3 30611
233 Northern Lesser Galago primates strepsirrhini Galago senegalensis 9465
234 Thick-tailed Greater Galago primates strepsirrhini Otolemur crassicaudatus 9463
235 Grey Slender Loris primates strepsirrhini Loris lydekkerianus 300163
236 slender loris primates strepsirrhini Loris tardigradus 9468
237 West African Potto primates strepsirrhini Perodicticus potto 9472
238 East African Potto primates strepsirrhini Perodicticus ibeanus (Perodicticus potto ibeanus) 261737
239 Moholi bushbaby primates strepsirrhini Galago moholi 30609
240 Pygmy Slow Loris primates strepsirrhini Nycticebus pygmaeus (Xanthonycticebus pygmaeus) 101278
241 Bengal slow loris primates strepsirrhini Nycticebus bengalensis 261741
242 Calabar Angwantibo primates strepsirrhini Arctocebus calabarensis 261739
243 slow loris primates strepsirrhini Nycticebus coucang 9470
244 jaguar carnivora Panthera onca
GCA_004023805.1_PanOnc_v1_BIUU 9690
245 leopard carnivora Panthera pardus
GCA_001857705.1_PanPar1.0 9691
246 giant panda carnivora Ailuropoda melanoleuca
GCA_002007445.1_ASM200744v1 9646
247 Hawaiian monk seal carnivora Neomonachus schauinslandi
GCA_002201575.1_ASM220157v1 29088
248 California sea lion carnivora Zalophus californianus
GCA_004024565.1_ZalCal_v1_BIUU 9704
249 Greenland wolf carnivora Canis lupus orion
GCA_905319855.2_mCanLor1.2 2605939
250 Pacific walrus carnivora Odobenus rosmarus
odoRosDiv1 9707
251 domestic cat (Fca126) carnivora Felis catus fca126 (Felis catus)
GCF_018350175.1_F.catus_Fca126_mat1.0 9685
252 northern elephant seal carnivora Mirounga angustirostris
GCA_004023865.1_MirAng_v1_BIUU 9716
253 domestic cat carnivora Felis catus
felCat8 9685
254 domestic dog (BS72/Village Dog) carnivora Canis lupus familiaris
GCA_004027395.1_CanFam_VD_v1_BIUU
255 German Shepherd dog (Mischka) carnivora Canis lupus familiaris (CanFam4) (Canis lupus familiaris)
canFam4
256 dingo carnivora Canis lupus dingo 286419
257 raccoon dog carnivora Nyctereutes procyonoides 34880
258 fossa carnivora Cryptoprocta ferox 94188
259 polar bear carnivora Ursus maritimus
GCA_000687225.1_UrsMar_1.0 29073
260 Asian palm civet carnivora Paradoxurus hermaphroditus
GCA_004024585.1_ParHer_v1_BIUU 71117
261 African hunting dog carnivora Lycaon pictus
GCA_001887905.1_LycPicSAfr1.0 9622
262 Arctic fox carnivora Vulpes lagopus
GCA_004023825.1_VulLag_v1_BIUU 494514
263 dog carnivora Canis lupus familiaris
GCF_000002285.3_CanFam3.1 9615
264 striped hyena carnivora Hyaena hyaena
GCA_004023945.1_HyaHya_v1_BIUU 95912
265 n/a carnivora Acinonyx jubatus
GCA_001443585.1_aciJub1 32536
266 tiger carnivora Panthera tigris
GCA_000464555.1_PanTig1.0 9694
267 Sea otter carnivora Enhydra lutris
GCA_002288905.2_ASM228890v2 34882
268 giant otter carnivora Pteronura brasiliensis 9672
269 bat-eared fox carnivora Otocyon megalotis 9624
270 Weddell seal carnivora Leptonychotes weddellii
GCA_000349705.1_LepWed1.0 9713
271 Lesser panda carnivora Ailurus fulgens
GCA_002007465.1_ASM200746v1 9649
272 ratel carnivora Mellivora capensis
GCA_004024625.1_MelCap_v1_BIUU 9664
273 banded mongoose carnivora Mungos mungo
GCA_004023785.1_MunMun_v1_BIUU 210652
274 dwarf mongoose carnivora Helogale parvula
GCA_004023845.1_HelPar_v1_BIUU 210647
275 meerkat carnivora Suricata suricatta
GCA_004023905.1_SurSur_v1_BIUU 37032
276 puma carnivora Puma concolor
GCA_003327715.1_PumCon1.0 9696
277 black-footed cat carnivora Felis nigripes
GCA_004023925.1_FelNig_v1_BIUU 61379
278 European polecat carnivora Mustela putorius
GCA_000239315.1_MusPutFurMale1.0 9668
279 western spotted skunk carnivora Spilogale gracilis
GCA_004023965.1_SpiGra_v1_BIUU 30551
280 Sumatran rhinoceros laurasiatheria Dicerorhinus sumatrensis
GCA_002844835.1_ASM284483v1 89632
281 black rhinoceros laurasiatheria Diceros bicornis
GCA_004027315.1_DicBicMic_v1_BIUU 9805
282 Asiatic tapir laurasiatheria Tapirus indicus
GCA_004024905.1_TapInd_v1_BIUU 9802
283 Brazilian tapir laurasiatheria Tapirus terrestris
GCA_004025025.1_TapTer_v1_BIUU 9801
284 northern white rhinoceros laurasiatheria Ceratotherium simum cottoni 310713
285 ass laurasiatheria Equus asinus
GCA_001305755.1_ASM130575v1 9793
286 Southern white rhinoceros laurasiatheria Ceratotherium simum
GCA_000283155.1_CerSimSim1.0 9807
287 Przewalski's horse laurasiatheria Equus przewalskii
GCA_000696695.1_Burgud 9798
288 horse laurasiatheria Equus caballus
GCA_000002305.1_EquCab2.0 9796
289 Malayan pangolin laurasiatheria Manis javanica
GCA_001685135.1_ManJav1.0 9974
290 Chinese pangolin laurasiatheria Manis pentadactyla
GCA_000738955.1_M_pentadactyla-1.1.1 143292
291 Hispaniolan solenodon laurasiatheria Solenodon paradoxus 79805
292 eastern mole laurasiatheria Scalopus aquaticus
GCA_004024925.1_ScaAqu_v1_BIUU 71119
293 gracile shrew mole laurasiatheria Uropsilus gracilis
GCA_004024945.1_UroGra_v1_BIUU 182669
294 star-nosed mole laurasiatheria Condylura cristata
GCF_000260355.1_ConCri1.0 143302
295 western European hedgehog laurasiatheria Erinaceus europaeus
GCA_000296755.1_EriEur2.0 9365
296 European shrew laurasiatheria Sorex araneus
sorAra2 42254
297 Indochinese shrew laurasiatheria Crocidura indochinensis
GCA_004027635.1_CroInd_v1_BIUU 876679
298 Hoffmann's two-fingered sloth xenarthra Choloepus hoffmanni
GCA_000164785.2_C_hoffmanni-2.0.1 9358
299 nine-banded armadillo xenarthra Dasypus novemcinctus
GCA_000208655.2_Dasnov3.0 9361
300 giant anteater xenarthra Myrmecophaga tridactyla
GCA_004026745.1_MyrTri_v1_BIUU 71006
301 southern tamandua xenarthra Tamandua tetradactyla
GCA_004025105.1_TamTet_v1_BIUU 48850
302 placentals xenarthra Tolypeutes matacus 183749
303 southern two-toed sloth xenarthra Choloepus didactylus
GCA_004027855.1_ChoDid_v1_BIUU 27675
304 screaming hairy armadillo xenarthra Chaetophractus vellerosus
GCA_004027955.1_ChaVel_v1_BIUU 340076
305 North Pacific right whale artiodactyla Eubalaena japonica 302098
306 grey whale artiodactyla Eschrichtius robustus 9764
307 hippopotamus artiodactyla Hippopotamus amphibius
GCA_004027065.1_HipAmp_v1_BIUU 9833
308 Minke whale artiodactyla Balaenoptera acutorostrata
GCA_000493695.1_BalAcu1.0 9767
309 beluga whale artiodactyla Delphinapterus leucas
GCA_002288925.2_ASM228892v2 9749
310 Antarctic minke whale artiodactyla Balaenoptera bonaerensis
GCA_000978805.1_ASM97880v1 33556
311 boutu artiodactyla Inia geoffrensis 9725
312 harbor porpoise artiodactyla Phocoena phocoena 9742
313 narwhal artiodactyla Monodon monoceros
GCA_004026685.1_MonMon_M_v1_BIUU 40151
314 Yangtze River dolphin artiodactyla Lipotes vexillifer
GCA_000442215.1_Lipotes_vexillifer_v1 118797
315 killer whale artiodactyla Orcinus orca
orcOrc1 9733
316 Ganges River dolphin artiodactyla Platanista gangetica 118798
317 Yangtze finless porpoise artiodactyla Neophocaena asiaeorientalis
GCA_003031525.1_Neophocaena_asiaeorientalis_V1 189058
318 Sowerby's beaked whale artiodactyla Mesoplodon bidens 48745
319 alpaca artiodactyla Vicugna pacos
GCA_000767525.1_Vi_pacos_V1.0 30538
320 Cuvier's beaked whale" artiodactyla Ziphius cavirostris 9760
321 Bactrian camel artiodactyla Camelus bactrianus
GCA_000767855.1_Ca_bactrianus_MBC_1.0 9837
322 Arabian camel artiodactyla Camelus dromedarius
GCA_000767585.1_PRJNA234474_Ca_dromedarius_V1.0 9838
323 wild Bactrian camel artiodactyla Camelus ferus
GCA_000311805.2_CB1 419612
324 pygmy sperm whale artiodactyla Kogia breviceps 27615
325 Chacoan peccary artiodactyla Catagonus wagneri
GCA_004024745.1_CatWag_v1_BIUU 51154
326 reindeer artiodactyla Rangifer tarandus
GCA_004026565.1_RanTarSib_v1_BIUU 9870
327 Pere David's deer artiodactyla Elaphurus davidianus
GCA_002443075.1_Milu1.0 43332
328 okapi artiodactyla Okapia johnstoni
GCA_001660835.1_ASM166083v1 86973
329 Masai giraffe artiodactyla Giraffa tippelskirchi
GCA_001651235.1_ASM165123v1 439328
330 Siberian musk deer artiodactyla Moschus moschiferus
GCA_004024705.1_MosMos_v1_BIUU 68415
331 water buffalo artiodactyla Bubalus bubalis
GCA_000471725.1_UMD_CASPUR_WB_2.0 89462
332 cow artiodactyla Bos taurus
GCA_000003205.6_Btau_5.0.1 9913
333 pronghorn artiodactyla Antilocapra americana
GCA_004027515.1_AntAmePen_v1_BIUU 9891
334 white-tailed deer artiodactyla Odocoileus virginianus
GCA_002102435.1_Ovir.te_1.0 9874
335 aoudad artiodactyla Ammotragus lervia
GCA_002201775.1_ALER1.0 9899
336 bighorn sheep artiodactyla Ovis canadensis
GCA_004026945.1_OviCan_v1_BIUU 37174
337 goat artiodactyla Capra hircus
GCA_001704415.1_ARS1 9925
338 Nilgiri tahr artiodactyla Hemitragus hylocrius
GCA_004026825.1_HemHyl_v1_BIUU 330464
339 hirola artiodactyla Beatragus hunteri
GCA_004027495.1_BeaHun_v1_BIUU 59527
340 wild yak artiodactyla Bos mutus
bosMut1 72004
341 American bison artiodactyla Bison bison
GCA_000754665.1_Bison_UMD1.0 9901
342 sheep artiodactyla Ovis aries
GCA_000298735.2_Oar_v4.0 9940
343 chiru artiodactyla Pantholops hodgsonii
GCA_000400835.1_PHO1.0 59538
344 wild goat artiodactyla Capra aegagrus
GCA_000978405.1_CapAeg_1.0 9923
345 Java mouse-deer artiodactyla Tragulus javanicus
GCA_004024965.1_TraJav_v1_BIUU 9849
346 pig artiodactyla Sus scrofa
susScr3 9823
347 zebu cattle artiodactyla Bos indicus
GCA_000247795.2_Bos_indicus_1.0 9915
348 common bottlenose dolphin artiodactyla Tursiops truncatus
GCA_001922835.1_NIST_Tur_tru_v1 9739
349 Saiga antelope artiodactyla Saiga tatarica
GCA_004024985.1_SaiTat_v1_BIUU 34875
350 Chinese rufous horseshoe bat chiroptera Rhinolophus sinicus
GCA_001888835.1_ASM188883v1 89399
351 black flying fox chiroptera Pteropus alecto
pteAle1 9402
352 Cantor's roundleaf bat chiroptera Hipposideros galeritus 58069
353 Egyptian rousette chiroptera Rousettus aegyptiacus
GCA_004024865.1_RouAeg_v1_BIUU 9407
354 long-tongued fruit bat chiroptera Macroglossus sobrinus 326083
355 large flying fox chiroptera Pteropus vampyrus
GCF_000151845.1_Pvam_2.0 132908
356 Brazilian free-tailed bat chiroptera Tadarida brasiliensis
GCA_004025005.1_TadBra_v1_BIUU 9438
357 great roundleaf bat chiroptera Hipposideros armiger
GCA_001890085.1_ASM189008v1 186990
358 straw-colored fruit bat chiroptera Eidolon helvum
eidHel1 77214
359 Antillean ghost-faced bat chiroptera Mormoops blainvillei
GCA_004026545.1_MorMeg_v1_BIUU 118852
360 tailed tailless bat chiroptera Anoura caudifer
GCA_004027475.1_AnoCau_v1_BIUU 27642
361 common vampire bat chiroptera Desmodus rotundus
GCA_002940915.2_ASM294091v2 9430
362 hairy big-eared bat chiroptera Micronycteris hirsuta
GCA_004026765.1_MicHir_v1_BIUU 148065
363 stripe-headed round-eared bat chiroptera Tonatia saurophila
GCA_004024845.1_TonSau_v1_BIUU 171122
364 Seba's short-tailed bat chiroptera Carollia perspicillata
GCA_004027735.1_CarPer_v1_BIUU 40233
365 Jamaican fruit-eating bat chiroptera Artibeus jamaicensis
GCA_004027435.1_ArtJam_v1_BIUU 9417
366 Indian false vampire chiroptera Megaderma lyra
GCA_004026885.1_MegLyr_v1_BIUU 9413
367 Schreibers' long-fingered bat chiroptera Miniopterus schreibersii
GCA_004026525.1_MinSch_v1_BIUU 9433
368 greater bulldog bat chiroptera Noctilio leporinus
GCA_004026585.1_NocLep_v1_BIUU 94963
369 Natal long-fingered bat chiroptera Miniopterus natalensis
GCF_001595765.1_Mnat.v1 291302
370 hog-nosed bat chiroptera Craseonycteris thonglongyai
GCA_004027555.1_CraTho_v1_BIUU 208972
371 Parnell's mustached bat chiroptera Pteronotus parnellii
ptePar1 59476
372 greater mouse-eared bat chiroptera Myotis myotis
GCA_004026985.1_MyoMyo_v1_BIUU 51298
373 Ashy-gray tube-nosed bat chiroptera Murina feae (Murina aurata feae)
GCA_004026665.1_MurFea_v1_BIUU 1453894
374 David's myotis chiroptera Myotis davidii
myoDav1 225400
375 Brandt's bat chiroptera Myotis brandtii
myoBra1 109478
376 big brown bat chiroptera Eptesicus fuscus
GCF_000308155.1_EptFus1.0 29078
377 red bat chiroptera Lasiurus borealis
GCA_004026805.1_LasBor_v1_BIUU 258930
378 little brown bat chiroptera Myotis lucifugus
myoLuc2 59463
379 common pipistrelle chiroptera Pipistrellus pipistrellus
GCA_004026625.1_PipPip_v1_BIUU 59474
380 African savanna elephant afrotheria Loxodonta africana
GCA_000001905.1_Loxafr3.0 9785
381 Florida manatee afrotheria Trichechus manatus
GCA_000243295.1_TriManLat1.0 9778
382 yellow-spotted hyrax afrotheria Heterohyrax brucei
GCA_004026845.1_HetBruBak_v1_BIUU 77598
383 Cape rock hyrax afrotheria Procavia capensis
GCA_004026925.1_ProCapCap_v1_BIUU 9813
384 aardvark afrotheria Orycteropus afer 9818
385 Cape golden mole afrotheria Chrysochloris asiatica
GCA_004027935.1_ChrAsi_v1_BIUU 185453
386 Cape elephant shrew afrotheria Elephantulus edwardii
eleEdw1 28737
387 Talazac's shrew tenrec afrotheria Microgale talazaci (Nesogale talazaci)
GCA_004026705.1_MicTal_v1_BIUU 2583312
388 small Madagascar hedgehog afrotheria Echinops telfairi
GCA_000313985.1_EchTel2.0 9371
389 Sunda flying lemur euarchontoglires Galeopterus variegatus
GCA_004027255.1_GalVar_v1_BIUU 482537
390 Chinese tree shrew euarchontoglires Tupaia chinensis
tupChi1 246437
391 South African ground squirrel euarchontoglires Xerus inauris
GCA_004024805.1_XerIna_v1_BIUU 234690
392 large tree shrew euarchontoglires Tupaia tana 70687
393 mountain beaver euarchontoglires Aplodontia rufa
GCA_004027875.1_AplRuf_v1_BIUU 51342
394 Alpine marmot euarchontoglires Marmota marmota
GCF_001458135.1_marMar2.1 9993
395 Daurian ground squirrel euarchontoglires Spermophilus dauricus
GCA_002406435.1_ASM240643v1 99837
396 crested porcupine euarchontoglires Hystrix cristata
GCA_004026905.1_HysCri_v1_BIUU 10137
397 thirteen-lined ground squirrel euarchontoglires Ictidomys tridecemlineatus
speTri2 43179
398 American beaver euarchontoglires Castor canadensis
GCA_004027675.1_CasCan_v1_BIUU 51338
399 long-tailed chinchilla euarchontoglires Chinchilla lanigera
chiLan1 34839
400 punctate agouti euarchontoglires Dasyprocta punctata 34846
401 pacarana euarchontoglires Dinomys branickii
GCA_004027595.1_DinBra_v1_BIUU 108858
402 fat dormouse euarchontoglires Glis glis
GCA_004027185.1_GliGli_v1_BIUU 41261
403 northern gundi euarchontoglires Ctenodactylus gundi
GCA_004027205.1_CteGun_v1_BIUU 10166
404 naked mole-rat euarchontoglires Heterocephalus glaber
GCA_000247695.1_HetGla_female_1.0 10181
405 Patagonian cavy euarchontoglires Dolichotis patagonum
GCA_004027295.1_DolPat_v1_BIUU 29091
406 capybara euarchontoglires Hydrochoerus hydrochaeris
GCA_004027455.1_HydHyd_v1_BIUU 10149
407 Montane guinea pig euarchontoglires Cavia tschudii
GCA_004027695.1_CavTsc_v1_BIUU 143287
408 domestic guinea pig euarchontoglires Cavia porcellus
GCA_000151735.1_Cavpor3.0 10141
409 degu euarchontoglires Octodon degus
GCA_000260255.1_OctDeg1.0 10160
410 lowland paca euarchontoglires Cuniculus paca 108852
411 social tuco-tuco euarchontoglires Ctenomys sociabilis
GCA_004027165.1_CteSoc_v1_BIUU 43321
412 Damara mole-rat euarchontoglires Fukomys damarensis
fukDam1 885580
413 woodland dormouse euarchontoglires Graphiurus murinus 51346
414 Desmarest's hutia euarchontoglires Capromys pilorides
GCA_004027915.1_CapPil_v1_BIUU 34842
415 Upper Galilee mountains blind mole rat euarchontoglires Nannospalax galili
GCA_000622305.1_S.galili_v1.0 1026970
416 nutria euarchontoglires Myocastor coypus
GCA_004027025.1_MyoCoy_v1_BIUU 10157
417 hazel dormouse euarchontoglires Muscardinus avellanarius
GCA_004027005.1_MusAve_v1_BIUU 39082
418 dassie-rat euarchontoglires Petromus typicus
GCA_004026965.1_PetTyp_v1_BIUU 10183
419 greater cane rat euarchontoglires Thryonomys swinderianus
GCA_004025085.1_ThrSwi_v1_BIUU 10169
420 snowshoe hare euarchontoglires Lepus americanus
GCA_004026855.1_LepAme_v1_BIUU 48086
421 Gambian giant pouched rat euarchontoglires Cricetomys gambianus
GCA_004027575.1_CriGam_v1_BIUU 10085
422 Prairie deer mouse euarchontoglires Peromyscus maniculatus
GCF_000500345.1_Pman_1.0 10042
423 southern grasshopper mouse euarchontoglires Onychomys torridus
GCA_004026725.1_OnyTor_v1_BIUU 38674
424 rabbit euarchontoglires Oryctolagus cuniculus
GCA_000003625.1_OryCun2.0 9986
425 muskrat euarchontoglires Ondatra zibethicus
GCA_004026605.1_OndZib_v1_BIUU 10060
426 northern mole vole euarchontoglires Ellobius talpinus
GCA_001685095.1_ETalpinus_0.1 329620
427 Mongolian gerbil euarchontoglires Meriones unguiculatus
GCA_004026785.1_MerUng_v1_BIUU 10047
428 fat sand rat euarchontoglires Psammomys obesus
GCA_002215935.1_ASM221593v1 48139
429 house mouse euarchontoglires Mus musculus
mm10 10090
430 Chinese hamster euarchontoglires Cricetulus griseus
GCA_900186095.1_CHOK1S_HZDv1 10029
431 Norway rat euarchontoglires Rattus norvegicus
GCF_000001895.5_Rnor_6.0 10116
432 western wild mouse euarchontoglires Mus spretus
GCA_001624865.1_SPRET_EiJ_v1 10096
433 meadow jumping mouse euarchontoglires Zapus hudsonius
GCA_004024765.1_ZapHud_v1_BIUU 160400
434 prairie vole euarchontoglires Microtus ochrogaster
micOch1 79684
435 Ryukyu mouse euarchontoglires Mus caroli
GCA_900094665.2_CAROLI_EIJ_v1.1 10089
436 Egyptian spiny mouse euarchontoglires Acomys cahirinus
GCA_004027535.1_AcoCah_v1_BIUU 10068
437 Gobi jerboa euarchontoglires Allactaga bullata (Orientallactaga bullata)
GCA_004027895.1_AllBul_v1_BIUU 1041416
438 shrew mouse euarchontoglires Mus pahari
GCF_900095145.1_PAHARI_EIJ_v1.1 10093
439 Transcaucasian mole vole euarchontoglires Ellobius lutescens
GCA_001685075.1_ASM168507v1 39086
440 hispid cotton rat euarchontoglires Sigmodon hispidus
GCA_004025045.1_SigHis_v1_BIUU 42415
441 lesser Egyptian jerboa euarchontoglires Jaculus jaculus
GCA_000280705.1_JacJac1.0 51337
442 Brazilian guinea pig euarchontoglires Cavia aperea
cavApe1 37548
443 golden hamster euarchontoglires Mesocricetus auratus
GCA_000349665.1_MesAur1.0 10036
444 Stephens's kangaroo rat euarchontoglires Dipodomys stephensi
GCA_004024685.1_DipSte_v1_BIUU 323379
445 American pika euarchontoglires Ochotona princeps
GCA_000292845.1_OchPri3.0 9978
446 Ord's kangaroo rat euarchontoglires Dipodomys ordii
dipOrd2 10020
447 little pocket mouse euarchontoglires Perognathus longimembris 38669

\ Table 1. Genome assemblies included in the 447-way Conservation track.\

\ \ \

References

\ compGeno 1 altColor 0,90,10\ bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus447way/hg38.cactus447way.bb\ color 0, 10, 100\ frames https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus447way/cactus447wayFrames.bb\ group compGeno\ irows on\ itemFirstCharCase noChange\ longLabel Cactus alignment on 447 mammal species, including Zoonomia genomes\ noInherit on\ parent cons447wayViewalign\ sGroup_Afrotheria Loxodonta_africana Trichechus_manatus Heterohyrax_brucei Procavia_capensis Orycteropus_afer Chrysochloris_asiatica Elephantulus_edwardii Microgale_talazaci Echinops_telfairi\ sGroup_Artiodactyla Eubalaena_japonica Eschrichtius_robustus Hippopotamus_amphibius Balaenoptera_acutorostrata Delphinapterus_leucas Balaenoptera_bonaerensis Inia_geoffrensis Phocoena_phocoena Monodon_monoceros Lipotes_vexillifer Orcinus_orca Platanista_gangetica Neophocaena_asiaeorientalis Mesoplodon_bidens Vicugna_pacos Ziphius_cavirostris Camelus_bactrianus Camelus_dromedarius Camelus_ferus Kogia_breviceps Catagonus_wagneri Rangifer_tarandus Elaphurus_davidianus Okapia_johnstoni Giraffa_tippelskirchi Moschus_moschiferus Bubalus_bubalis Bos_taurus Antilocapra_americana Odocoileus_virginianus Ammotragus_lervia Ovis_canadensis Capra_hircus Hemitragus_hylocrius Beatragus_hunteri Bos_mutus Bison_bison Ovis_aries Pantholops_hodgsonii Capra_aegagrus Tragulus_javanicus Sus_scrofa Bos_indicus Tursiops_truncatus Saiga_tatarica\ sGroup_Carnivora Panthera_onca Panthera_pardus Ailuropoda_melanoleuca Neomonachus_schauinslandi Zalophus_californianus Canis_lupus_orion Odobenus_rosmarus Felis_catus_fca126 Mirounga_angustirostris Felis_catus Canis_lupus_VD CanFam4 Canis_lupus_dingo Nyctereutes_procyonoides Cryptoprocta_ferox Ursus_maritimus Paradoxurus_hermaphroditus Lycaon_pictus Vulpes_lagopus Canis_lupus_familiaris Hyaena_hyaena Acinonyx_jubatus Panthera_tigris Enhydra_lutris Pteronura_brasiliensis Otocyon_megalotis Leptonychotes_weddellii Ailurus_fulgens Mellivora_capensis Mungos_mungo Helogale_parvula Suricata_suricatta Puma_concolor Felis_nigripes Mustela_putorius Spilogale_gracilis\ sGroup_Chiroptera Rhinolophus_sinicus Pteropus_alecto Hipposideros_galeritus Rousettus_aegyptiacus Macroglossus_sobrinus Pteropus_vampyrus Tadarida_brasiliensis Hipposideros_armiger Eidolon_helvum Mormoops_blainvillei Anoura_caudifer Desmodus_rotundus Micronycteris_hirsuta Tonatia_saurophila Carollia_perspicillata Artibeus_jamaicensis Megaderma_lyra Miniopterus_schreibersii Noctilio_leporinus Miniopterus_natalensis Craseonycteris_thonglongyai Pteronotus_parnellii Myotis_myotis Murina_feae Myotis_davidii Myotis_brandtii Eptesicus_fuscus Lasiurus_borealis Myotis_lucifugus Pipistrellus_pipistrellus\ sGroup_Euarchontoglires Galeopterus_variegatus Tupaia_chinensis Xerus_inauris Tupaia_tana Aplodontia_rufa Marmota_marmota Spermophilus_dauricus Hystrix_cristata Ictidomys_tridecemlineatus Castor_canadensis Chinchilla_lanigera Dasyprocta_punctata Dinomys_branickii Glis_glis Ctenodactylus_gundi Heterocephalus_glaber Dolichotis_patagonum Hydrochoerus_hydrochaeris Cavia_tschudii Cavia_porcellus Octodon_degus Cuniculus_paca Ctenomys_sociabilis Fukomys_damarensis Graphiurus_murinus Capromys_pilorides Nannospalax_galili Myocastor_coypus Muscardinus_avellanarius Petromus_typicus Thryonomys_swinderianus Lepus_americanus Cricetomys_gambianus Peromyscus_maniculatus Onychomys_torridus Oryctolagus_cuniculus Ondatra_zibethicus Ellobius_talpinus Meriones_unguiculatus Psammomys_obesus Mus_musculus Cricetulus_griseus Rattus_norvegicus Mus_spretus Zapus_hudsonius Microtus_ochrogaster Mus_caroli Acomys_cahirinus Allactaga_bullata Mus_pahari Ellobius_lutescens Sigmodon_hispidus Jaculus_jaculus Cavia_aperea Mesocricetus_auratus Dipodomys_stephensi Ochotona_princeps Dipodomys_ordii Perognathus_longimembris\ sGroup_Laurasiatheria Dicerorhinus_sumatrensis Diceros_bicornis Tapirus_indicus Tapirus_terrestris Ceratotherium_simum_cottoni Equus_asinus Ceratotherium_simum Equus_przewalskii Equus_caballus Manis_javanica Manis_pentadactyla Solenodon_paradoxus Scalopus_aquaticus Uropsilus_gracilis Condylura_cristata Erinaceus_europaeus Sorex_araneus Crocidura_indochinensis\ sGroup_Primates_catarrhini Pan_troglodytes Gorilla_gorilla Gorilla_beringei Pongo_abelii Pongo_pygmaeus Macaca_mulatta Theropithecus_gelada Macaca_arctoides Miopithecus_ogouensis Macaca_fascicularis Allenopithecus_nigroviridis Symphalangus_syndactylus Lophocebus_aterrimus Mandrillus_leucophaeus Macaca_radiata Cercocebus_torquatus Cercocebus_chrysogaster Cercopithecus_hamlyni Macaca_siberu Macaca_nemestrina Cercocebus_lunulatus Macaca_tonkeana Cercopithecus_diana Erythrocebus_patas Macaca_leonina Macaca_maura Papio_papio Papio_hamadryas Macaca_silenus Papio_anubis Cercopithecus_roloway Papio_kindae Papio_ursinus Allochrocebus_solatus Rhinopithecus_roxellana Chlorocebus_pygerythrus Cercocebus_atys Chlorocebus_sabaeus Cercopithecus_neglectus Papio_cynocephalus Macaca_nigra Nasalis_larvatus Allochrocebus_preussi Cercopithecus_nictitans Presbytis_comata Cercopithecus_albogularis Allochrocebus_lhoesti Cercopithecus_pogonias Presbytis_mitrata Pygathrix_cinerea Cercopithecus_mona Cercopithecus_petaurista Chlorocebus_aethiops Cercopithecus_lowei Nomascus_annamensis Nomascus_gabriellae Macaca_fuscata Piliocolobus_badius Nomascus_siki_a Nomascus_siki_b Macaca_cyclopis Pygathrix_nigripes_a Pygathrix_nigripes_b Colobus_polykomos Nomascus_concolor Piliocolobus_gordonorum Trachypithecus_geei Hylobates_klossii Trachypithecus_obscurus Piliocolobus_kirkii Trachypithecus_germaini Trachypithecus_hatinhensis Cercopithecus_cephus Trachypithecus_laotum Trachypithecus_francoisi Semnopithecus_vetulus Trachypithecus_pileatus Piliocolobus_tephrosceles Trachypithecus_auratus Cercopithecus_ascanius Trachypithecus_cristatus Semnopithecus_johnii Trachypithecus_crepusculus Trachypithecus_leucocephalus Pan_paniscus Hylobates_agilis Trachypithecus_melamera Semnopithecus_schistaceus Hylobates_abbotti Hylobates_muelleri Semnopithecus_priam Semnopithecus_hypoleucos Colobus_guereza Semnopithecus_entellus Hylobates_pileatus_a Hylobates_pileatus_b Rhinopithecus_bieti Rhinopithecus_strykeri Colobus_angolensis Macaca_thibetana Trachypithecus_phayrei Macaca_assamensis Hoolock_leuconedys Mandrillus_sphinx\ sGroup_Primates_platyrrhini Pithecia_chrysocephala Pithecia_hirsuta Pithecia_pithecia Pithecia_mittermeieri Pithecia_albicans Pithecia_pissinattii Pithecia_vanzolinii Cacajao_calvus Cacajao_ayresi Cacajao_melanocephalus Cacajao_hosomi Chiropotes_sagulatus Chiropotes_israelita Cheracebus_lugens Plecturocebus_brunneus Plecturocebus_hoffmannsi Plecturocebus_miltoni Cheracebus_torquatus Plecturocebus_cinerascens Plecturocebus_bernhardi Cheracebus_lucifer Plecturocebus_cupreus Plecturocebus_caligatus Plecturocebus_dubius Plecturocebus_moloch Plecturocebus_grovesi Ateles_geoffroyi_a Atele_geoffroyi_b Cheracebus_regulus Ateles_paniscus Ateles_chamek Ateles_marginatus Ateles_belzebuth Lagothrix_lagothricha Sapajus_macrocephalus Cebus_unicolor Cebus_olivaceus Alouatta_palliata Cebus_albifrons Aotus_trivirgatus Aotus_griseimembra Alouatta_caraya Aotus_vociferans Alouatta_belzebul Alouatta_discolor Aotus_azarae Alouatta_puruensis Alouatta_nigerrima Alouatta_macconnelli Alouatta_juara Alouatta_seniculus Sapajus_apella Aotus_nancymaae Saimiri_boliviensis Chiropotes_albinasus Leontocebus_nigricollis Leontocebus_fuscicollis Leontocebus_illigeri Saguinus_oedipus Saguinus_bicolor Saguinus_geoffroyi Saguinus_inustus Saguinus_mystax Saguinus_imperator Saimiri_sciureus Saguinus_labiatus Callimico_goeldii Saimiri_oerstedii Leontopithecus_chrysomelas Leontopithecus_rosalia Saimiri_cassiquiarensis Saimiri_ustus Saimiri_macrodon Callithrix_jacchus Cebuella_niveiventris Cebuella_pygmaea Mico_humeralifer Callibella_humilis Mico_spnv Mico_argentatus Saguinus_midas Callithrix_kuhlii Callithrix_geoffroyi\ sGroup_Primates_strepsirrhini Daubentonia_madagascariensis Propithecus_coronatus Propithecus_perrieri Varecia_variegata Propithecus_diadema Propithecus_edwardsi Indri_indri Propithecus_tattersalli Avahi_laniger Propithecus_verreauxi Avahi_peyrierasi Varecia_rubra Prolemur_simus Eulemur_rubriventer Eulemur_mongoz Cheirogaleus_major Eulemur_coronatus Eulemur_macaco Cheirogaleus_medius Eulemur_flavifrons Propithecus_coquerelli Eulemur_collaris Lepilemur_ruficaudatus Eulemur_rufus Eulemur_sanfordi Eulemur_albifrons Lepilemur_dorsalis Eulemur_fulvus Lepilemur_septentrionalis Hapalemur_occidentalis Hapalemur_alaotrensis Hapalemur_griseus Lepilemur_ankaranensis Lemur_catta Hapalemur_gilberti Hapalemur_meridionalis Galagoides_demidoff Mirza_zaza Microcebus_murinus Otolemur_garnettii Galago_senegalensis Otolemur_crassicaudatus Loris_lydekkerianus Loris_tardigradus Perodicticus_potto Perodicticus_ibeanus Galago_moholi Nycticebus_pygmaeus Nycticebus_bengalensis Arctocebus_calabarensis Nycticebus_coucang\ sGroup_Primates_tarsiidae Cephalopachus_bancanus Carlito_syrichta Tarsius_lariang Tarsius_wallacei\ sGroup_Xenarthra Choloepus_hoffmanni Dasypus_novemcinctus Myrmecophaga_tridactyla Tamandua_tetradactyla Tolypeutes_matacus Choloepus_didactylus Chaetophractus_vellerosus\ shortLabel Cactus 447-way\ speciesCodonDefault hg38\ speciesDefaultOff Pongo_abelii Gorilla_beringei Pan_troglodytes Pongo_pygmaeus Macaca_mulatta Theropithecus_gelada Macaca_arctoides Miopithecus_ogouensis Macaca_fascicularis Allenopithecus_nigroviridis Symphalangus_syndactylus Lophocebus_aterrimus Mandrillus_leucophaeus Macaca_radiata Cercocebus_torquatus Cercocebus_chrysogaster Cercopithecus_hamlyni Macaca_siberu Macaca_nemestrina Cercocebus_lunulatus Macaca_tonkeana Cercopithecus_diana Erythrocebus_patas Macaca_leonina Macaca_maura Papio_papio Papio_hamadryas Macaca_silenus Papio_anubis Cercopithecus_roloway Papio_kindae Papio_ursinus Allochrocebus_solatus Rhinopithecus_roxellana Chlorocebus_pygerythrus Cercocebus_atys Chlorocebus_sabaeus Cercopithecus_neglectus Papio_cynocephalus Macaca_nigra Nasalis_larvatus Allochrocebus_preussi Cercopithecus_nictitans Presbytis_comata Cercopithecus_albogularis Allochrocebus_lhoesti Cercopithecus_pogonias Presbytis_mitrata Pygathrix_cinerea Cercopithecus_mona Cercopithecus_petaurista Chlorocebus_aethiops Cercopithecus_lowei Nomascus_annamensis Nomascus_gabriellae Macaca_fuscata Piliocolobus_badius Nomascus_siki_a Nomascus_siki_b Macaca_cyclopis Pygathrix_nigripes_a Pygathrix_nigripes_b Colobus_polykomos Nomascus_concolor Piliocolobus_gordonorum Trachypithecus_geei Hylobates_klossii Trachypithecus_obscurus Piliocolobus_kirkii Trachypithecus_germaini Trachypithecus_hatinhensis Cercopithecus_cephus Trachypithecus_laotum Trachypithecus_francoisi Semnopithecus_vetulus Trachypithecus_pileatus Piliocolobus_tephrosceles Trachypithecus_auratus Cercopithecus_ascanius Trachypithecus_cristatus Semnopithecus_johnii Trachypithecus_crepusculus Trachypithecus_leucocephalus Pan_paniscus Hylobates_agilis Semnopithecus_schistaceus Hylobates_abbotti Hylobates_muelleri Trachypithecus_melamera Semnopithecus_priam Semnopithecus_hypoleucos Colobus_guereza Semnopithecus_entellus Hylobates_pileatus_a Hylobates_pileatus_b Rhinopithecus_bieti Rhinopithecus_strykeri Colobus_angolensis Macaca_thibetana Trachypithecus_phayrei Macaca_assamensis Pithecia_chrysocephala Pithecia_hirsuta Pithecia_pithecia Pithecia_mittermeieri Pithecia_albicans Hoolock_leuconedys Pithecia_pissinattii Pithecia_vanzolinii Cacajao_calvus Cacajao_ayresi Cacajao_melanocephalus Cacajao_hosomi Chiropotes_sagulatus Chiropotes_israelita Cheracebus_lugens Plecturocebus_brunneus Plecturocebus_hoffmannsi Plecturocebus_miltoni Cheracebus_torquatus Plecturocebus_cinerascens Plecturocebus_bernhardi Cheracebus_lucifer Plecturocebus_cupreus Plecturocebus_caligatus Plecturocebus_dubius Plecturocebus_moloch Plecturocebus_grovesi Ateles_geoffroyi_a Cheracebus_regulus Ateles_paniscus Ateles_chamek Ateles_marginatus Ateles_belzebuth Lagothrix_lagothricha Sapajus_macrocephalus Cebus_unicolor Cebus_olivaceus Alouatta_palliata Cebus_albifrons Aotus_trivirgatus Aotus_griseimembra Alouatta_caraya Aotus_vociferans Alouatta_belzebul Alouatta_discolor Aotus_azarae Alouatta_puruensis Alouatta_nigerrima Alouatta_macconnelli Alouatta_juara Alouatta_seniculus Sapajus_apella Aotus_nancymaae Saimiri_boliviensis Chiropotes_albinasus Leontocebus_nigricollis Leontocebus_fuscicollis Leontocebus_illigeri Saguinus_oedipus Saguinus_bicolor Saguinus_geoffroyi Saguinus_inustus Saguinus_mystax Saguinus_imperator Saimiri_sciureus Saguinus_labiatus Callimico_goeldii Saimiri_oerstedii Leontopithecus_chrysomelas Leontopithecus_rosalia Saimiri_cassiquiarensis Saimiri_ustus Saimiri_macrodon Callithrix_jacchus Cebuella_niveiventris Cebuella_pygmaea Mico_humeralifer Callibella_humilis Mico_spnv Mico_argentatus Saguinus_midas Callithrix_kuhlii Callithrix_geoffroyi Daubentonia_madagascariensis Cephalopachus_bancanus Carlito_syrichta Mandrillus_sphinx Galeopterus_variegatus Tarsius_lariang Propithecus_coronatus Propithecus_perrieri Varecia_variegata Propithecus_diadema Propithecus_edwardsi Indri_indri Propithecus_tattersalli Avahi_laniger Propithecus_verreauxi Tarsius_wallacei Avahi_peyrierasi Varecia_rubra Prolemur_simus Eulemur_rubriventer Eulemur_mongoz Cheirogaleus_major Eulemur_coronatus Eulemur_macaco Cheirogaleus_medius Eulemur_flavifrons Propithecus_coquerelli Eulemur_collaris Lepilemur_ruficaudatus Eulemur_rufus Eulemur_sanfordi Eulemur_albifrons Lepilemur_dorsalis Eulemur_fulvus Lepilemur_septentrionalis Hapalemur_occidentalis Hapalemur_alaotrensis Hapalemur_griseus Lepilemur_ankaranensis Lemur_catta Hapalemur_gilberti Hapalemur_meridionalis Galagoides_demidoff Mirza_zaza Microcebus_murinus Otolemur_garnettii Galago_senegalensis Otolemur_crassicaudatus Loris_lydekkerianus Loris_tardigradus Perodicticus_potto Perodicticus_ibeanus Galago_moholi Nycticebus_pygmaeus Nycticebus_bengalensis Arctocebus_calabarensis Nycticebus_coucang Dicerorhinus_sumatrensis Diceros_bicornis Tapirus_indicus Tapirus_terrestris Ceratotherium_simum_cottoni Equus_asinus Ceratotherium_simum Equus_przewalskii Equus_caballus Panthera_onca Panthera_pardus Ailuropoda_melanoleuca Neomonachus_schauinslandi Zalophus_californianus Canis_lupus_orion Odobenus_rosmarus Felis_catus_fca126 Mirounga_angustirostris Felis_catus Canis_lupus_VD CanFam4 Canis_lupus_dingo Nyctereutes_procyonoides Cryptoprocta_ferox Ursus_maritimus Paradoxurus_hermaphroditus Lycaon_pictus Vulpes_lagopus Canis_lupus_familiaris Hyaena_hyaena Acinonyx_jubatus Panthera_tigris Eubalaena_japonica Enhydra_lutris Eschrichtius_robustus Pteronura_brasiliensis Otocyon_megalotis Leptonychotes_weddellii Hippopotamus_amphibius Ailurus_fulgens Mellivora_capensis Rhinolophus_sinicus Pteropus_alecto Mungos_mungo Helogale_parvula Suricata_suricatta Puma_concolor Manis_javanica Balaenoptera_acutorostrata Felis_nigripes Mustela_putorius Hipposideros_galeritus Delphinapterus_leucas Rousettus_aegyptiacus Balaenoptera_bonaerensis Inia_geoffrensis Phocoena_phocoena Monodon_monoceros Lipotes_vexillifer Orcinus_orca Platanista_gangetica Macroglossus_sobrinus Neophocaena_asiaeorientalis Pteropus_vampyrus Mesoplodon_bidens Spilogale_gracilis Vicugna_pacos Ziphius_cavirostris Tupaia_chinensis Tadarida_brasiliensis Hipposideros_armiger Camelus_bactrianus Xerus_inauris Camelus_dromedarius Eidolon_helvum Choloepus_hoffmanni Camelus_ferus Kogia_breviceps Tupaia_tana Dasypus_novemcinctus Manis_pentadactyla Loxodonta_africana Trichechus_manatus Myrmecophaga_tridactyla Tamandua_tetradactyla Aplodontia_rufa Tolypeutes_matacus Choloepus_didactylus Catagonus_wagneri Marmota_marmota Spermophilus_dauricus Solenodon_paradoxus Mormoops_blainvillei Hystrix_cristata Anoura_caudifer Heterohyrax_brucei Procavia_capensis Desmodus_rotundus Micronycteris_hirsuta Orycteropus_afer Rangifer_tarandus Tonatia_saurophila Elaphurus_davidianus Okapia_johnstoni Giraffa_tippelskirchi Moschus_moschiferus Ictidomys_tridecemlineatus Bubalus_bubalis Bos_taurus Antilocapra_americana Odocoileus_virginianus Ammotragus_lervia Ovis_canadensis Castor_canadensis Capra_hircus Hemitragus_hylocrius Beatragus_hunteri Bos_mutus Carollia_perspicillata Artibeus_jamaicensis Chinchilla_lanigera Bison_bison Dasyprocta_punctata Dinomys_branickii Ovis_aries Megaderma_lyra Pantholops_hodgsonii Glis_glis Miniopterus_schreibersii Ctenodactylus_gundi Noctilio_leporinus Miniopterus_natalensis Heterocephalus_glaber Dolichotis_patagonum Capra_aegagrus Tragulus_javanicus Hydrochoerus_hydrochaeris Cavia_tschudii Cavia_porcellus Sus_scrofa Octodon_degus Craseonycteris_thonglongyai Cuniculus_paca Ctenomys_sociabilis Chaetophractus_vellerosus Fukomys_damarensis Graphiurus_murinus Capromys_pilorides Nannospalax_galili Bos_indicus Tursiops_truncatus Myocastor_coypus Muscardinus_avellanarius Saiga_tatarica Pteronotus_parnellii Petromus_typicus Myotis_myotis Thryonomys_swinderianus Murina_feae Lepus_americanus Myotis_davidii Myotis_brandtii Cricetomys_gambianus Eptesicus_fuscus Peromyscus_maniculatus Onychomys_torridus Oryctolagus_cuniculus Scalopus_aquaticus Ondatra_zibethicus Lasiurus_borealis Ellobius_talpinus Meriones_unguiculatus Psammomys_obesus Mus_musculus Cricetulus_griseus Rattus_norvegicus Mus_spretus Zapus_hudsonius Chrysochloris_asiatica Microtus_ochrogaster Mus_caroli Acomys_cahirinus Allactaga_bullata Mus_pahari Ellobius_lutescens Sigmodon_hispidus Uropsilus_gracilis Jaculus_jaculus Myotis_lucifugus Cavia_aperea Pipistrellus_pipistrellus Mesocricetus_auratus Elephantulus_edwardii Dipodomys_stephensi Ochotona_princeps Dipodomys_ordii Perognathus_longimembris Condylura_cristata Microgale_talazaci Echinops_telfairi Erinaceus_europaeus Sorex_araneus\ speciesDefaultOn Gorilla_gorilla Pongo_abelii Pithecia_chrysocephala Pithecia_hirsuta Cephalopachus_bancanus Carlito_syrichta Daubentonia_madagascariensis Propithecus_coronatus Panthera_onca Panthera_pardus Dicerorhinus_sumatrensis Diceros_bicornis Choloepus_hoffmanni Dasypus_novemcinctus Eubalaena_japonica Eschrichtius_robustus Rhinolophus_sinicus Pteropus_alecto Loxodonta_africana Trichechus_manatus Galeopterus_variegatus Tupaia_chinensis Dipodomys_ordii Perognathus_longimembris\ speciesGroups Primates_catarrhini Primates_platyrrhini Primates_tarsiidae Primates_strepsirrhini Carnivora Laurasiatheria Xenarthra Artiodactyla Chiroptera Afrotheria Euarchontoglires\ speciesLabels Acinonyx_jubatus="cheetah" Acomys_cahirinus="Egyptian spiny mouse" Ailuropoda_melanoleuca="giant panda" Ailurus_fulgens="Lesser panda" Allactaga_bullata="Gobi jerboa" Allenopithecus_nigroviridis="Allen's swamp monkey" Allochrocebus_lhoesti="L'Hoest's monkey" Allochrocebus_preussi="Preuss's monkey" Allochrocebus_solatus="Sun-tailed monkey" Alouatta_palliata="mantled howler" Alouatta_belzebul="Eastern Red-handed howler" Alouatta_caraya="black-and-gold howler" Alouatta_discolor="Spix's Red-handed howler" Alouatta_juara="Jurua red howler monkey" Alouatta_macconnelli="Guianan red howler" Alouatta_nigerrima="Amazon black howler" Alouatta_puruensis="Purús red howler monkey" Alouatta_seniculus="Colombian red howler" Ammotragus_lervia="aoudad" Anoura_caudifer="tailed tailless bat" Antilocapra_americana="pronghorn" Aotus_nancymaae="Ma's night monkey" Aotus_azarae="Azara's night monkey" Aotus_griseimembra="Gray-legged Night monkey" Aotus_trivirgatus="Humboldt's night monkey" Aotus_vociferans="Spix's night monkey" Aplodontia_rufa="mountain beaver" Arctocebus_calabarensis="Calabar Angwantibo" Artibeus_jamaicensis="Jamaican fruit-eating bat" Ateles_geoffroyi="Central American spider monkey" Ateles_belzebuth="white-bellied spider monkey" Ateles_chamek="black spider monkey" Ateles_marginatus="white-whiskered spider monkey" Ateles_paniscus="Red-faced black spider monkey" Avahi_laniger="Eastern Woolly lemur" Avahi_peyrierasi="Peyrieras's Woolly lemur" Balaenoptera_bonaerensis="Antarctic minke whale" Balaenoptera_acutorostrata="Minke whale" Beatragus_hunteri="hirola" Bison_bison="American bison" Bos_indicus="zebu cattle" Bos_mutus="wild yak" Bos_taurus="cow" Bubalus_bubalis="water buffalo" Cacajao_ayresi="Araca Uakari" Cacajao_calvus="Bald Uakari" Cacajao_hosomi="Neblina black Uakari" Cacajao_melanocephalus="Golden-brown Uakari" Callibella_humilis="black-crowned Dwarf Marmoset" Callimico_goeldii="Goeldi's monkey" Callithrix_jacchus="common marmoset" Callithrix_geoffroyi="Geoffroy's tufted-ear marmoset" Callithrix_kuhlii="Wied's Marmoset" Camelus_bactrianus="Bactrian camel" Camelus_dromedarius="Arabian camel" Camelus_ferus="wild Bactrian camel" CanFam4="German Shepherd dog (Mischka)" Canis_lupus_dingo="dingo" Canis_lupus_familiaris="dog" Canis_lupus_VD="domestic dog (BS72/Village Dog)" Canis_lupus_orion="Greenland wolf" Capra_aegagrus="wild goat" Capra_hircus="goat" Capromys_pilorides="Desmarest's hutia" Carlito_syrichta="Philippine tarsier" Carollia_perspicillata="Seba's short-tailed bat" Castor_canadensis="American beaver" Catagonus_wagneri="Chacoan peccary" Cavia_aperea="Brazilian guinea pig" Cavia_porcellus="domestic guinea pig" Cavia_tschudii="Montane guinea pig" Cebuella_niveiventris="Southern Pygmy Marmoset" Cebuella_pygmaea="Northern Pygmy Marmoset" Cebus_albifrons="white-fronted capuchin" Cebus_olivaceus="Guinan Weeper capuchin" Cebus_unicolor="Spix's white-fronted capuchin" Cephalopachus_bancanus="Western tarsier" Ceratotherium_simum_cottoni="northern white rhinoceros" Ceratotherium_simum="Southern white rhinoceros" Cercocebus_atys="sooty mangabey" Cercocebus_chrysogaster="Golden-bellied Mangabey" Cercocebus_lunulatus="white-naped Mangabey" Cercocebus_torquatus="Red-capped Mangabey" Cercopithecus_mona="Mona monkey" Cercopithecus_neglectus="De Brazza's monkey" Cercopithecus_ascanius="Red-tailed monkey" Cercopithecus_cephus="Mustached monkey" Cercopithecus_diana="Diana monkey" Cercopithecus_hamlyni="Owl-faced monkey" Cercopithecus_lowei="Lowe's monkey" Cercopithecus_albogularis="Sykes' monkey" Cercopithecus_nictitans="Putty-nosed monkey" Cercopithecus_petaurista="Spot-nosed monkey" Cercopithecus_pogonias="Crowned monkey" Cercopithecus_roloway="Roloway monkey" Chaetophractus_vellerosus="screaming hairy armadillo" Cheirogaleus_medius="fat-tailed dwarf lemur" Cheirogaleus_major="Greater Dwarf lemur" Cheracebus_lucifer="Yellow-handed Titi" Cheracebus_lugens="white-chested Titi" Cheracebus_regulus="Rio Jurua Collared Titi" Cheracebus_torquatus="white-collared Titi" Chinchilla_lanigera="long-tailed chinchilla" Chiropotes_albinasus="Red-nosed Bearded saki" Chiropotes_israelita="Spix's Bearded saki" Chiropotes_sagulatus="Guianan Bearded saki" Chlorocebus_aethiops="grivet monkey" Chlorocebus_sabaeus="green monkey" Chlorocebus_pygerythrus="Vervet monkey" Choloepus_didactylus="southern two-toed sloth" Choloepus_hoffmanni="Hoffmann's two-fingered sloth" Chrysochloris_asiatica="Cape golden mole" Colobus_guereza="guereza" Colobus_angolensis="Angolan colobus" Colobus_polykomos="King Colobus" Condylura_cristata="star-nosed mole" Craseonycteris_thonglongyai="hog-nosed bat" Cricetomys_gambianus="Gambian giant pouched rat" Cricetulus_griseus="Chinese hamster" Crocidura_indochinensis="Indochinese shrew" Cryptoprocta_ferox="fossa" Ctenodactylus_gundi="northern gundi" Ctenomys_sociabilis="social tuco-tuco" Cuniculus_paca="lowland paca" Dasyprocta_punctata="punctate agouti" Dasypus_novemcinctus="nine-banded armadillo" Daubentonia_madagascariensis="aye-aye" Delphinapterus_leucas="beluga whale" Desmodus_rotundus="common vampire bat" Dicerorhinus_sumatrensis="Sumatran rhinoceros" Diceros_bicornis="black rhinoceros" Dinomys_branickii="pacarana" Dipodomys_ordii="Ord's kangaroo rat" Dipodomys_stephensi="Stephens's kangaroo rat" Dolichotis_patagonum="Patagonian cavy" Echinops_telfairi="small Madagascar hedgehog" Eidolon_helvum="straw-colored fruit bat" Elaphurus_davidianus="Pere David's deer" Elephantulus_edwardii="Cape elephant shrew" Ellobius_lutescens="Transcaucasian mole vole" Ellobius_talpinus="northern mole vole" Enhydra_lutris="Sea otter" Eptesicus_fuscus="big brown bat" Equus_asinus="ass" Equus_caballus="horse" Equus_przewalskii="Przewalski's horse" Erinaceus_europaeus="western European hedgehog" Erythrocebus_patas="common Patas monkey" Eschrichtius_robustus="grey whale" Eubalaena_japonica="North Pacific right whale" Eulemur_flavifrons="blue-eyed black lemur" Eulemur_fulvus="brown lemur" Eulemur_macaco="black lemur" Eulemur_mongoz="mongoose lemur" Eulemur_albifrons="white-fronted brown lemur" Eulemur_collaris="Red-collared brown lemur" Eulemur_coronatus="Crowned lemur" Eulemur_rubriventer="Red-bellied lemur" Eulemur_rufus="Rufous brown lemur" Eulemur_sanfordi="Sanford's brown lemur" Felis_catus="domestic cat" Felis_nigripes="black-footed cat" Felis_catus_fca126="domestic cat (Fca126)" Fukomys_damarensis="Damara mole-rat" Galago_moholi="southern leser galago" Galago_senegalensis="Northern Lesser Galago" Galagoides_demidoff="Demidoff's Dwarf Galago" Galeopterus_variegatus="Sunda flying lemur" Giraffa_tippelskirchi="Masai giraffe" Glis_glis="fat dormouse" Gorilla_gorilla="western gorilla" Gorilla_beringei="Eastern Gorilla" Graphiurus_murinus="woodland dormouse" Hapalemur_alaotrensis="Lac Alaotra Bamboo lemur" Hapalemur_gilberti="Gilbert's Gray Bamboo lemur" Hapalemur_griseus="Common Gray Bamboo lemur" Hapalemur_meridionalis="Southern Bamboo lemur" Hapalemur_occidentalis="Northern Bamboo lemur" Helogale_parvula="dwarf mongoose" Hemitragus_hylocrius="Nilgiri tahr" Heterocephalus_glaber="naked mole-rat" Heterohyrax_brucei="yellow-spotted hyrax" Hippopotamus_amphibius="hippopotamus" Hipposideros_armiger="great roundleaf bat" Hipposideros_galeritus="Cantor's roundleaf bat" Hoolock_leuconedys="Eastern hoolock Gibbon" Hyaena_hyaena="striped hyena" Hydrochoerus_hydrochaeris="capybara" Hylobates_pileatus_a="pileated gibbon" Hylobates_pileatus_b="pileated gibbon" Hylobates_abbotti="Western gray gibbon" Hylobates_agilis="agile gibbon" Hylobates_klossii="Kloss's gibbon" Hylobates_muelleri="Southern gray gibbon" Hystrix_cristata="crested porcupine" Ictidomys_tridecemlineatus="thirteen-lined ground squirrel" Indri_indri="indri" Inia_geoffrensis="boutu" Jaculus_jaculus="lesser Egyptian jerboa" Kogia_breviceps="pygmy sperm whale" Lagothrix_lagothricha="Common Woolly monkey" Lasiurus_borealis="red bat" Lemur_catta="ring-tailed lemur" Leontocebus_fuscicollis="Spix's Saddle-back tamarin" Leontocebus_illigeri="Illiger's Saddle-back tamarin" Leontocebus_nigricollis="black-mantled tamarin" Leontopithecus_rosalia="golden lion tamarin" Leontopithecus_chrysomelas="Golden-headed Lion tamarin" Lepilemur_ankaranensis="Ankarana sportive lemur" Lepilemur_dorsalis="Gray's sportive lemur" Lepilemur_ruficaudatus="Red-tailed sportive lemur" Lepilemur_septentrionalis="Sahafary sportive lemur" Leptonychotes_weddellii="Weddell seal" Lepus_americanus="snowshoe hare" Lipotes_vexillifer="Yangtze River dolphin" Lophocebus_aterrimus="black crested mangabey" Loris_tardigradus="red slender loris" Loris_lydekkerianus="Gray Slender Loris" Loxodonta_africana="African savanna elephant" Lycaon_pictus="African hunting dog" Macaca_arctoides="stump-tailed macaque" Macaca_assamensis="Assamese macaque" Macaca_cyclopis="Taiwanexe macaque" Macaca_fascicularis="long-tailed macaque" Macaca_mulatta="Rhesus macaque" Macaca_nemestrina="southern pig-tailed macaque" Macaca_nigra="crested macaque" Macaca_silenus="lion-tailed macaque" Macaca_fuscata="Japanese macaque" Macaca_leonina="Northern Pig-tailed Macaque" Macaca_maura="Moor Macaque" Macaca_radiata="Bonnet Macaque" Macaca_siberu="Siberut Macaque" Macaca_thibetana="Tibetan Macaque" Macaca_tonkeana="Tonkean Macaque" Macroglossus_sobrinus="long-tongued fruit bat" Mandrillus_leucophaeus="drill" Mandrillus_sphinx="mandrill" Manis_javanica="Malayan pangolin" Manis_pentadactyla="Chinese pangolin" Marmota_marmota="Alpine marmot" Megaderma_lyra="Indian false vampire" Mellivora_capensis="ratel" Meriones_unguiculatus="Mongolian gerbil" Mesocricetus_auratus="golden hamster" Mesoplodon_bidens="Sowerby's beaked whale" Mico_argentatus="silvery marmoset" Mico_humeralifer="Santarem marmoset" Mico_spnv="Schneider's marmoset" Microcebus_murinus="gray mouse lemur" Microgale_talazaci="Talazac's shrew tenrec" Micronycteris_hirsuta="hairy big-eared bat" Microtus_ochrogaster="prairie vole" Miniopterus_natalensis="Natal long-fingered bat" Miniopterus_schreibersii="Schreibers' long-fingered bat" Miopithecus_ogouensis="Northern Talapoin monkey" Mirounga_angustirostris="northern elephant seal" Mirza_zaza="northern giant mouse lemur" Monodon_monoceros="narwhal" Mormoops_blainvillei="Antillean ghost-faced bat" Moschus_moschiferus="Siberian musk deer" Mungos_mungo="banded mongoose" Murina_feae="Ashy-gray tube-nosed bat" Mus_caroli="Ryukyu mouse" Mus_musculus="house mouse" Mus_pahari="shrew mouse" Mus_spretus="western wild mouse" Muscardinus_avellanarius="hazel dormouse" Mustela_putorius="European polecat" Myocastor_coypus="nutria" Myotis_brandtii="Brandt's bat" Myotis_davidii="David's myotis" Myotis_lucifugus="little brown bat" Myotis_myotis="greater mouse-eared bat" Myrmecophaga_tridactyla="giant anteater" Nannospalax_galili="Upper Galilee mountains blind mole rat" Nasalis_larvatus="proboscis monkey" Neomonachus_schauinslandi="Hawaiian monk seal" Neophocaena_asiaeorientalis="Yangtze finless porpoise" Noctilio_leporinus="greater bulldog bat" Nomascus_siki_a="southern white-cheeked crested gibbon" Nomascus_siki_b="southern white-cheeked crested gibbon" Nomascus_annamensis="Northern yellow-cheeked crested gibbon" Nomascus_concolor="Western black crested gibbon" Nomascus_gabriellae="Southern yellow-cheeked crested gibbon" Nyctereutes_procyonoides="raccoon dog" Nycticebus_bengalensis="Bengal slow loris" Nycticebus_coucang="Malaysian slow loris" Nycticebus_pygmaeus="Pygmy Slow Loris" Ochotona_princeps="American pika" Octodon_degus="degu" Odobenus_rosmarus="Pacific walrus" Odocoileus_virginianus="white-tailed deer" Okapia_johnstoni="okapi" Ondatra_zibethicus="muskrat" Onychomys_torridus="southern grasshopper mouse" Orcinus_orca="killer whale" Orycteropus_afer="aardvark" Oryctolagus_cuniculus="rabbit" Otocyon_megalotis="bat-eared fox" Otolemur_garnettii="Garnetts greater galago" Otolemur_crassicaudatus="Thick-tailed Greater Galago" Ovis_aries="sheep" Ovis_canadensis="bighorn sheep" Pan_paniscus="bonobo" Pan_troglodytes="chimpanzee" Panthera_onca="jaguar" Panthera_pardus="leopard" Panthera_tigris="tiger" Pantholops_hodgsonii="chiru" Papio_anubis="olive baboon" Papio_hamadryas="hamadryas baboon" Papio_cynocephalus="Yellow Baboon" Papio_kindae="Kinda Baboon" Papio_papio="Guinea Baboon" Papio_ursinus="Chacma Baboon" Paradoxurus_hermaphroditus="Asian palm civet" Perodicticus_ibeanus="East African Potto" Perodicticus_potto="West African Potto" Perognathus_longimembris="little pocket mouse" Peromyscus_maniculatus="Prairie deer mouse" Petromus_typicus="dassie-rat" Phocoena_phocoena="harbor porpoise" Piliocolobus_tephrosceles="Ashy red Colobus" Piliocolobus_badius="Upper Guinea red Colobus" Piliocolobus_gordonorum="Udzungwa red Colobus" Piliocolobus_kirkii="Zanzibar red Colobus" Pipistrellus_pipistrellus="common pipistrelle" Pithecia_pithecia="white-faced saki" Pithecia_albicans="Buffy saki" Pithecia_chrysocephala="Golden-faced saki" Pithecia_hirsuta="Hairy saki" Pithecia_mittermeieri="Mittermeier's saki" Pithecia_pissinattii="Pissinatti's saki" Pithecia_vanzolinii="Vanzolini's bald-faced saki" Platanista_gangetica="Ganges River dolphin" Plecturocebus_bernhardi="Prince Bernhard's Titi" Plecturocebus_brunneus="brown Titi" Plecturocebus_caligatus="Chestnut-bellied Titi" Plecturocebus_cinerascens="Ashy Titi" Plecturocebus_cupreus="Coppery Titi" Plecturocebus_dubius="Hershkovitzs Titi" Plecturocebus_grovesi="Groves's Titi" Plecturocebus_hoffmannsi="Hoffmanns's Titi" Plecturocebus_miltoni="Milton's Titi" Plecturocebus_moloch="Red-bellied Titi" Pongo_abelii="Sumatran orangutan" Pongo_pygmaeus="Bornean orangutan" Presbytis_comata="Javan langur" Presbytis_mitrata="Mitered langur" Procavia_capensis="Cape rock hyrax" Prolemur_simus="greater bamboo lemur" Propithecus_coquerelli="Coquerel's Sifaka" Propithecus_coronatus="Crowned Sifaka" Propithecus_diadema="Diademed Sifaka" Propithecus_edwardsi="Milne-Edward's Sifaka" Propithecus_perrieri="Perrier's Sifaka" Propithecus_tattersalli="Tattersall's Sifaka" Propithecus_verreauxi="Verreaux's Sifaka" Psammomys_obesus="fat sand rat" Pteronotus_parnellii="Parnell's mustached bat" Pteronura_brasiliensis="giant otter" Pteropus_alecto="black flying fox" Pteropus_vampyrus="large flying fox" Puma_concolor="puma" Pygathrix_nigripes_a="black-shanked douc" Pygathrix_nigripes_b="black-shanked douc" Pygathrix_cinerea="gray-shanked douc" Rangifer_tarandus="reindeer" Rattus_norvegicus="Norway rat" Rhinolophus_sinicus="Chinese rufous horseshoe bat" Rhinopithecus_bieti="Yunnan snub-nosed monkey" Rhinopithecus_roxellana="golden snub-nosed monkey" Rhinopithecus_strykeri="Stryker's snub-nosed monkey" Rousettus_aegyptiacus="Egyptian rousette" Saguinus_imperator="Emperor tamarin" Saguinus_midas="Midas tamarin" Saguinus_bicolor="Pied Bare-faced tamarin" Saguinus_geoffroyi="Geoffroy's tamarin" Saguinus_inustus="Mottled-face tamarin" Saguinus_labiatus="Red-bellied tamarin" Saguinus_mystax="Mustached tamarin" Saguinus_oedipus="Cotton-top tamarin" Saiga_tatarica="Saiga antelope" Saimiri_boliviensis="black-capped squirrel monkey" Saimiri_cassiquiarensis="Humboldt's squirrel monkey" Saimiri_macrodon="Ecuadorian squirrel monkey" Saimiri_oerstedii="Central American squirrel monkey" Saimiri_sciureus="Guianan squirrel monkey" Saimiri_ustus="Golden-backed squirrel monkey" Sapajus_apella="brown capuchin" Sapajus_macrocephalus="large-headed capuchin" Scalopus_aquaticus="eastern mole" Semnopithecus_entellus="Bengal sacred langur" Semnopithecus_hypoleucos="Malabar Sacred langur" Semnopithecus_johnii="Nilgiri langur" Semnopithecus_priam="Tufted Gray langur" Semnopithecus_schistaceus="Nepal Sacred langur" Semnopithecus_vetulus="Purple-faced langur" Sigmodon_hispidus="hispid cotton rat" Solenodon_paradoxus="Hispaniolan solenodon" Sorex_araneus="European shrew" Spermophilus_dauricus="Daurian ground squirrel" Spilogale_gracilis="western spotted skunk" Suricata_suricatta="meerkat" Sus_scrofa="pig" Symphalangus_syndactylus="siamang" Tadarida_brasiliensis="Brazilian free-tailed bat" Tamandua_tetradactyla="southern tamandua" Tapirus_indicus="Asiatic tapir" Tapirus_terrestris="Brazilian tapir" Tarsius_lariang="Lariang tarsier" Tarsius_wallacei="Wallace's tarsier" Theropithecus_gelada="gelada" Thryonomys_swinderianus="greater cane rat" Tolypeutes_matacus="placentals" Tonatia_saurophila="stripe-headed round-eared bat" Trachypithecus_francoisi="Francois's langur" Trachypithecus_auratus="East Javan Langur" Trachypithecus_crepusculus="Indochinese Gray Langur" Trachypithecus_cristatus="Sunda Silvery Langur" Trachypithecus_geei="Golden langur" Trachypithecus_germaini="Germain's langur" Trachypithecus_hatinhensis="Hatinh langur" Trachypithecus_laotum="Laos langur" Trachypithecus_leucocephalus="white-headed langur" Trachypithecus_melamera="Shan langur" Trachypithecus_obscurus="Dusky langur" Trachypithecus_phayrei="Phayre's langur" Trachypithecus_pileatus="capped langur" Tragulus_javanicus="Java mouse-deer" Trichechus_manatus="Florida manatee" Tupaia_chinensis="Chinese tree shrew" Tupaia_tana="large tree shrew" Tursiops_truncatus="common bottlenose dolphin" Uropsilus_gracilis="gracile shrew mole" Ursus_maritimus="polar bear" Varecia_variegata="black-and-white ruffed lemur" Varecia_rubra="red ruffed lemur" Vicugna_pacos="alpaca" Vulpes_lagopus="Arctic fox" Xerus_inauris="South African ground squirrel" Zalophus_californianus="California sea lion" Zapus_hudsonius="meadow jumping mouse" Ziphius_cavirostris="Cuvier's beaked whale"\ subGroups view=align\ summary https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus447way/cactus447waySummary.bb\ track cactus447way\ treeImage phylo/hg38_447way.png\ type bigMaf\ viewUi on\ caddSuper CADD 1.6 bed CADD 1.6 Score for all single-basepair mutations and selected insertions/deletions 0 100 100 130 160 177 192 207 0 0 0

Description

\ \

This track collection shows Combined Annotation Dependent Depletion scores.\ CADD is a tool for scoring the deleteriousness of single nucleotide variants as\ well as insertion/deletion variants in the human genome.

\ \

\ Some mutation annotations\ tend to exploit a single information type (e.g., phastCons or phyloP for\ conservation) and/or are restricted in scope (e.g., to missense changes). Thus,\ a broadly applicable metric that objectively weights and integrates diverse\ information is needed. Combined Annotation Dependent Depletion (CADD) is a\ framework that integrates multiple annotations into one metric by contrasting\ variants that survived natural selection with simulated mutations.\

\ \

\ CADD scores strongly correlate with allelic diversity, pathogenicity of both\ coding and non-coding variants, experimentally measured regulatory effects,\ and also rank causal variants within individual genome sequences with a higher\ value than non-causal variants. \ Finally, CADD scores of complex trait-associated variants from genome-wide\ association studies (GWAS) are significantly higher than matched controls and\ correlate with study sample size, likely reflecting the increased accuracy of\ larger GWAS.\

\ \

\ A CADD score represents a ranking not a prediction, and no threshold is defined\ for a specific purpose. Higher scores are more likely to be deleterious: \ Scores are \ \

  10 * -log of the rank

\ \ so that variants with scores above 20 are \ predicted to be among the 1.0% most deleterious possible substitutions in \ the human genome. We recommend thinking carefully about what threshold is \ appropriate for your application.\

\ \

Display Conventions and Configuration

\ There are six subtracks of this track: four for single-nucleotide mutations,\ one for each base, showing all possible substitutions, \ one for insertions and one for deletions. All subtracks show the CADD Phred\ score on mouseover. Zooming in shows the exact score on mouseover, same\ basepair = score 0.0.

\ PHRED-scaled scores are normalized to all potential ~9 billion SNVs, and\ thereby provide an externally comparable unit for analysis. For example, a\ scaled score of 10 or greater indicates a raw score in the top 10% of all\ possible reference genome SNVs, and a score of 20 or greater indicates a raw\ score in the top 1%, regardless of the details of the annotation set, model\ parameters, etc.\

\ The four single-nucleotide mutation tracks have a default viewing range of\ score 10 to 50. As explained in the paragraph above, that results in\ slightly less than 10% of the data displayed. The \ deletion and insertion tracks have a default filter of 10-100, because they\ display discrete items and not graphical data.\

\ \

\ Single nucleotide variants (SNV): For SNVs, at every\ genome position, there are three values per position, one for every possible\ nucleotide mutation. The fourth value, "no mutation", representing \ the reference allele, e.g., A to A, is always set to zero.\

\ When using this track, zoom in until you can see every basepair at the\ top of the display. Otherwise, there are several nucleotides per pixel under \ your mouse cursor and instead of an actual score, the tooltip text will show\ the average score of all nucleotides under the cursor. This is indicated by\ the prefix "~" in the mouseover. Averages of scores are not useful for any\ application of CADD.\

\ \

Insertions and deletions: Scores are also shown on mouseover for a\ set of insertions and deletions. On hg38, the set has been obtained from\ gnomAD3. On hg19, the set of indels has been obtained from various sources\ (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest\ is not in the track, you will need to use CADD's\ online scoring tool\ to obtain them.

\ \

Data access

\ CADD scores are freely available for all non-commercial applications from\ the CADD website.\ For commercial applications, see\ the license instructions there.\

\ \

\ The CADD data on the UCSC Genome Browser can be explored interactively with the\ Table Browser or the\ Data Integrator.\ For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed\ files that can be downloaded from\ our download server.\ The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual\ regions or the whole genome annotation can be obtained using our tools bigWigToWig\ or bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\
\ bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd/a.bw stdout\
\ or\
\ bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd/ins.bb stdout

\ \

Methods

\ \

\ Data were converted from the files provided on\ the CADD Downloads website,\ provided by the Kircher lab, using\ \ custom Python scripts, \ documented in our \ makeDoc files.\

\ \

Credits

\ Thanks to the CADD development team for providing precomputed data as simple tab-separated files.\

\ \

References

\ Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J.\ \ A general framework for estimating the relative pathogenicity of human genetic variants.\ Nat Genet. 2014 Mar;46(3):310-5.\ PMID: 24487276;\ PMC: PMC3992975\

\ \

\ Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M.\ \ CADD: predicting the deleteriousness of variants throughout the human genome.\ Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894.\ PMID: 30371827;\ PMC: PMC6323892\

\ phenDis 1 color 100,130,160\ group phenDis\ html caddSuper.html\ longLabel CADD 1.6 Score for all single-basepair mutations and selected insertions/deletions\ shortLabel CADD 1.6\ superTrack on hide\ track caddSuper\ type bed\ visibility hide\ cadd CADD 1.6 bigWig CADD 1.6 Score for all possible single-basepair mutations (zoom in for scores) 1 100 100 130 160 177 192 207 0 0 0

Description

\ \

\ A CADD score represents a ranking not a prediction, and no threshold is defined\ for a specific purpose. Higher scores are more likely to be deleterious: \ Scores are \ \

  10 * -log of the rank

\ \

Display Conventions and Configuration

\ \

Data access

\ CADD scores are freely available for all non-commercial applications from\ the CADD website.\ For commercial applications, see\ the license instructions there.\

\ \

Methods

\ \

\ Data were converted from the files provided on\ the CADD Downloads website,\ provided by the Kircher lab, using\ \ custom Python scripts, \ documented in our \ makeDoc files.\

\ \

Credits

\ Thanks to the CADD development team for providing precomputed data as simple tab-separated files.\

\ \

References

\ \

\ phenDis 0 color 100,130,160\ compositeTrack on\ group phenDis\ html caddSuper\ longLabel CADD 1.6 Score for all possible single-basepair mutations (zoom in for scores)\ maxWindowToDraw 10000000\ mouseOverFunction noAverage\ parent caddSuper\ shortLabel CADD 1.6\ track cadd\ type bigWig\ visibility dense\ caddDel CADD 1.6 Del bigBed 9 + CADD 1.6 Score: Deletions - label is length of deletion 1 100 100 130 160 177 192 207 0 0 0

Description

\ \

\ A CADD score represents a ranking not a prediction, and no threshold is defined\ for a specific purpose. Higher scores are more likely to be deleterious: \ Scores are \ \

  10 * -log of the rank

\ \

Display Conventions and Configuration

\ \

Data access

\ CADD scores are freely available for all non-commercial applications from\ the CADD website.\ For commercial applications, see\ the license instructions there.\

\ \

Methods

\ \

\ Data were converted from the files provided on\ the CADD Downloads website,\ provided by the Kircher lab, using\ \ custom Python scripts, \ documented in our \ makeDoc files.\

\ \

Credits

\ Thanks to the CADD development team for providing precomputed data as simple tab-separated files.\

\ \

References

\ \

\ phenDis 1 bigDataUrl /gbdb/hg38/cadd/del.bb\ filter.score 10:100\ filterByRange.score on\ filterLabel.score Show only items with PHRED scale score of\ filterLimits.score 0:100\ html caddSuper\ longLabel CADD 1.6 Score: Deletions - label is length of deletion\ mouseOver Mutation: $change CADD Phred score: $phred\ parent caddSuper\ shortLabel CADD 1.6 Del\ track caddDel\ type bigBed 9 +\ visibility dense\ caddIns CADD 1.6 Ins bigBed 9 + CADD 1.6 Score: Insertions - label is length of insertion 1 100 100 130 160 177 192 207 0 0 0

Description

\ \

\ A CADD score represents a ranking not a prediction, and no threshold is defined\ for a specific purpose. Higher scores are more likely to be deleterious: \ Scores are \ \

  10 * -log of the rank

\ \

Display Conventions and Configuration

\ \

Data access

\ CADD scores are freely available for all non-commercial applications from\ the CADD website.\ For commercial applications, see\ the license instructions there.\

\ \

Methods

\ \

\ Data were converted from the files provided on\ the CADD Downloads website,\ provided by the Kircher lab, using\ \ custom Python scripts, \ documented in our \ makeDoc files.\

\ \

Credits

\ Thanks to the CADD development team for providing precomputed data as simple tab-separated files.\

\ \

References

\ \

\ phenDis 1 bigDataUrl /gbdb/hg38/cadd/ins.bb\ filter.score 10:100\ filterByRange.score on\ filterLabel.score Show only items with PHRED scale score of\ filterLimits.score 0:100\ html caddSuper\ longLabel CADD 1.6 Score: Insertions - label is length of insertion\ mouseOver Mutation: $change CADD Phred score: $phred\ parent caddSuper\ shortLabel CADD 1.6 Ins\ track caddIns\ type bigBed 9 +\ visibility dense\ caddSuper1_7 CADD 1.7 bed CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions 0 100 100 130 160 177 192 207 0 0 0

Description

\ \

\ A CADD score represents a ranking not a prediction, and no threshold is defined\ for a specific purpose. Higher scores are more likely to be deleterious: \ Scores are \ \

  10 * -log of the rank

\ \

Display Conventions and Configuration

\ \

Methods

\ \

\ In CADD version 1.7, new features have been added to improve CADD scores for certain variant\ effects, boosting the overall performance of CADD and bringing new developments to the community.\ CADD v1.7 integrates annotations from recent efforts to assess variant effects, along with new\ conservation and mutation scores.

\ CADD v1.7 supports only the major chromosomes of the hg38/GRCh38 reference genome (chromosomes 1-22,\ X, and Y) and may be the last version to support the hg19/GRCh37 human reference genome.

\ This version includes scores derived from Evolutionary Scale Modeling (ESM) for assessing variants\ in protein-coding regions, along with scores from a convolutional neural network (CNN) trained on\ open chromatin sequences, used as a proxy for regulatory regions in the genome. The previously\ included conservation scores have been updated with data from the Zoonomia project. New annotations\ have also been added for 3' Untranslated Regions (3' UTRs), along with models of genome-wide\ mutational rates. The gene and transcript models have been updated by advancing from Ensembl version\ 95 to version 110, and the Ensembl Variant Effect Predictor (VEP) has been upgraded accordingly.

\ The models in CADD v1.7 have been trained similarly to the version 1.6 release. The logistic\ regression uses an L2 penalty with C = 1, and training was completed after thirteen L-BFGS\ iterations using the sklearn library The new models exhibit a high degree of similarity to the\ previous release, with a Spearman correlation of 0.946 for CADD scores calculated for 100,000\ randomly selected variants between CADD GRCh38-v1.6 and CADD GRCh38-v1.7. The v1.7 models perform\ comparably to earlier versions in distinguishing known pathogenic variants (ClinVar) from common\ variants (gnomAD) across the genome. Improvements in CADD v1.7 are particularly evident when\ focusing on specific variant categories, such as missense or 3' UTR variants, where the latest\ release includes updated annotations.

\ More information can be found at the\ CADD site\ and the Schubach et al., Nucleic Acids Res, 2024 publication.\ \ \ Data were converted from the files provided on\ the CADD Downloads website,\ provided by the Kircher lab, using\ \ custom Python scripts,\ documented in our \ makeDoc files.\

\ \ \

Data access

\ CADD scores are freely available for all non-commercial applications from\ the CADD website.\ For commercial applications, see\ the license instructions there.\

\ \

\ The CADD data on the UCSC Genome Browser can be explored interactively with the\ Table Browser or the\ Data Integrator.\ For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed\ files that can be downloaded from\ our download server.\ The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual\ regions or the whole genome annotation can be obtained using our tools bigWigToWig\ or bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\
\ bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd1.7/a.bw stdout\
\ or\
\ bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd1.7/ins.bb stdout

\ \ \

Credits

\ Thanks to the CADD development team for providing precomputed data as simple tab-separated files.\

\ \

References

\ \

\ Schubach M, Maass T, Nazaretyan L, Röner S, Kircher M.\ \ CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to\ improve genome-wide variant predictions.\ Nucleic Acids Res. 2024 Jan 5;52(D1):D1143-D1154.\ PMID: 38183205; PMC: PMC10767851\

\ phenDis 1 color 100,130,160\ group phenDis\ html caddSuper1_7\ longLabel CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions\ pennantIcon New red ../goldenPath/newsarch.html#100924 "October 9, 2024"\ shortLabel CADD 1.7\ superTrack on hide\ track caddSuper1_7\ type bed\ visibility hide\ cadd1_7 CADD 1.7 bigWig CADD 1.7 Score for all possible single-basepair mutations (zoom in for scores) 1 100 100 130 160 177 192 207 0 0 0

Description

\ \

\ A CADD score represents a ranking not a prediction, and no threshold is defined\ for a specific purpose. Higher scores are more likely to be deleterious: \ Scores are \ \

  10 * -log of the rank

\ \

Display Conventions and Configuration

\ \

Methods

\ \

\ CADD v1.7 supports only the major chromosomes of the hg38/GRCh38 reference genome (chromosomes 1-22,\ X, and Y) and may be the last version to support the hg19/GRCh37 human reference genome.

\ \ \

Data access

\ CADD scores are freely available for all non-commercial applications from\ the CADD website.\ For commercial applications, see\ the license instructions there.\

\ \

\ The CADD data on the UCSC Genome Browser can be explored interactively with the\ Table Browser or the\ Data Integrator.\ For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed\ files that can be downloaded from\ our download server.\ The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual\ regions or the whole genome annotation can be obtained using our tools bigWigToWig\ or bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\
\ bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd1.7/a.bw stdout\
\ or\
\ bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd1.7/ins.bb stdout

\ \ \

Credits

\ Thanks to the CADD development team for providing precomputed data as simple tab-separated files.\

\ \

References

\ \

\ phenDis 0 color 100,130,160\ compositeTrack on\ group phenDis\ html caddSuper1_7\ longLabel CADD 1.7 Score for all possible single-basepair mutations (zoom in for scores)\ maxWindowToDraw 10000000\ mouseOverFunction noAverage\ parent caddSuper1_7\ pennantIcon New red ../goldenPath/newsarch.html#100924 "October 9, 2024"\ shortLabel CADD 1.7\ track cadd1_7\ type bigWig\ visibility dense\ cadd1_7_Del CADD 1.7 Del bigBed 9 + CADD 1.7 Score: Deletions - label is length of deletion 1 100 100 130 160 177 192 207 0 0 0

Description

\ \

\ A CADD score represents a ranking not a prediction, and no threshold is defined\ for a specific purpose. Higher scores are more likely to be deleterious: \ Scores are \ \

  10 * -log of the rank

\ \

Display Conventions and Configuration

\ \

Methods

\ \

\ CADD v1.7 supports only the major chromosomes of the hg38/GRCh38 reference genome (chromosomes 1-22,\ X, and Y) and may be the last version to support the hg19/GRCh37 human reference genome.

\ \ \

Data access

\ CADD scores are freely available for all non-commercial applications from\ the CADD website.\ For commercial applications, see\ the license instructions there.\

\ \

\ The CADD data on the UCSC Genome Browser can be explored interactively with the\ Table Browser or the\ Data Integrator.\ For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed\ files that can be downloaded from\ our download server.\ The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual\ regions or the whole genome annotation can be obtained using our tools bigWigToWig\ or bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\
\ bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd1.7/a.bw stdout\
\ or\
\ bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd1.7/ins.bb stdout

\ \ \

Credits

\ Thanks to the CADD development team for providing precomputed data as simple tab-separated files.\

\ \

References

\ \

\ phenDis 1 bigDataUrl /gbdb/hg38/cadd1.7/del.bb\ filter.score 10:100\ filterByRange.score on\ filterLabel.score Show only items with PHRED scale score of\ filterLimits.score 0:100\ html caddSuper1_7\ longLabel CADD 1.7 Score: Deletions - label is length of deletion\ mouseOver Mutation: $change CADD Phred score: $phred\ parent caddSuper1_7 on\ pennantIcon New red ../goldenPath/newsarch.html#100924 "October 9, 2024"\ shortLabel CADD 1.7 Del\ track cadd1_7_Del\ type bigBed 9 +\ visibility dense\ cadd1_7_Ins CADD 1.7 Ins bigBed 9 + CADD 1.7 Score: Insertions - label is length of insertion 1 100 100 130 160 177 192 207 0 0 0

Description

\ \

\ A CADD score represents a ranking not a prediction, and no threshold is defined\ for a specific purpose. Higher scores are more likely to be deleterious: \ Scores are \ \

  10 * -log of the rank

\ \

Display Conventions and Configuration

\ \

Methods

\ \

\ CADD v1.7 supports only the major chromosomes of the hg38/GRCh38 reference genome (chromosomes 1-22,\ X, and Y) and may be the last version to support the hg19/GRCh37 human reference genome.

\ \ \

Data access

\ CADD scores are freely available for all non-commercial applications from\ the CADD website.\ For commercial applications, see\ the license instructions there.\

\ \

\ The CADD data on the UCSC Genome Browser can be explored interactively with the\ Table Browser or the\ Data Integrator.\ For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed\ files that can be downloaded from\ our download server.\ The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual\ regions or the whole genome annotation can be obtained using our tools bigWigToWig\ or bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\
\ bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd1.7/a.bw stdout\
\ or\
\ bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/cadd1.7/ins.bb stdout

\ \ \

Credits

\ Thanks to the CADD development team for providing precomputed data as simple tab-separated files.\

\ \

References

\ \

\ phenDis 1 bigDataUrl /gbdb/hg38/cadd1.7/ins.bb\ filter.score 10:100\ filterByRange.score on\ filterLabel.score Show only items with PHRED scale score of\ filterLimits.score 0:100\ html caddSuper1_7\ longLabel CADD 1.7 Score: Insertions - label is length of insertion\ mouseOver Mutation: $change CADD Phred score: $phred\ parent caddSuper1_7 on\ pennantIcon New red ../goldenPath/newsarch.html#100924 "October 9, 2024"\ shortLabel CADD 1.7 Ins\ track cadd1_7_Ins\ type bigBed 9 +\ visibility dense\ cancerExpr Cancer Gene Expr Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23) 0 100 0 0 0 127 127 127 0 0 0

Description

\ \ The Cancer Genome Atlas (TCGA), a collaboration between the\ National Cancer Institute (NCI)\ and \ National Human Genome Research Institute (NHGRI), has generated comprehensive,\ multi-dimensional maps of the key genomic changes in 33 types of cancer. The TCGA\ dataset, 2.5 petabytes of data describing tumor tissue and matched normal tissues from\ more than 11,000 patients, is publically available and has been used widely by the\ research community.

\ \

\ The Cancer Genome Atlas is a NIH-funded project to catalog genetic mutations\ responsible for cancer. The data shown here is RNA-seq expression data produced by the\ consortium.

\ \

For questions or feedback on the data, please contact \ TCGA.\

\ \

TCGA Gene Expression

\ The gene track shows RNA expression level for each TCGA tissue in GENCODE canonical\ genes. The gene scores are a total of all transcripts in that gene.

\ \

TCGA Transcript Expression

\ The transcript track shows RNA expression levels for each TCGA tissue using GENCODE v23\ transcripts.

\ \ \

Display Conventions

\ In Full and Pack display modes, expression for each genomic item (gene/transcript) is\ represented by a colored bar chart, where the height of each bar represents the median\ expression level across all samples for a tissue, and the bar color indicates the\ tissue.

\ The bar chart display has the same width and tissue order for all genomic items.\ Mouse hover over a bar will show the tissue and median expression levels.\ The Squish display mode draws a rectangle for each gene, colored to indicate the tissue\ with highest expression level if it contributes more than 10% to the overall expression\ (and colored black if no tissue predominates).\ In Dense mode, the darkness of the grayscale rectangle displayed for the gene reflects the total\ median expression level across all tissues.

\ \

\ This track was designed to be used in conjunction with the GTEx expression tracks that can act as a\ control.

\ \

\ The color of each cancer was derived by mapping the tissue of origin to the closest GTEx tissue,\ then taking the GTEx tissue's color. Five cancers did not have a matching GTEx tissue and were\ assigned a rainbow color scheme; these cancers are Cholangiocarcinoma, Esophageal carcinoma, Head\ and Neck squamous cell carcinoma, Sarcoma and Uveal Melanoma.

\ \

\ The ordering of the cancers is based on the alphabetical ordering of their GTEx tissues. The five\ cancers that did not match were ordered alphabetically.

\ \

Methods

\ \

TCGA chose cancers for study based on two broad criteria; poor prognosis/overall \ public health impact and availability of human tumor and matched normal tissue samples that meet \ TCGA\ standards.

\ \

\ RNA sequencing was performed using a polyA library and the Illumina HiSeq 2000 platform. All RNA\ sequencing was performed by UNC.

\ \

\ RNA sequencing was performed using a polyA library and the Illumina HiSeq 2000 platform. All RNA\ sequencing was performed by UNC.

\ \

Credits

References

\ J. Vivian et al., \ \ \ Rapid and efficient analysis of 20,000 RNA-seq samples with Toil\ bioRxiv bioRxiv, vol. 2, p. 62497, 2016.\

\ phenDis 1 barChartBars Adrenocortical_carcinoma Bladder_Urothelial_Carcinoma Brain_Lower_Grade_Glioma Breast_invasive_carcinoma Cervical_squamous_cell_carcinoma_and_endocervical_adenocarcinoma Colon_adenocarcinoma Glioblastoma_multiforme Kidney_Chromophobe Kidney_renal_clear_cell_carcinoma Kidney_renal_papillary_cell_carcinoma Liver_hepatocellular_carcinoma Lung_adenocarcinoma Lung_squamous_cell_carcinoma Lymphoid_Neoplasm_Diffuse_Large_B-cell_Lymphoma Mesothelioma Ovarian_serous_cystadenocarcinoma Pancreatic_adenocarcinoma Pheochromocytoma_and_Paraganglioma Prostate_adenocarcinoma Rectum_adenocarcinoma Skin_Cutaneous_Melanoma Stomach_adenocarcinoma Testicular_Germ_Cell_Tumors Thymoma Thyroid_carcinoma Uterine_Carcinosarcoma Uterine_Corpus_Endometrioid_Carcinoma Cholangiocarcinoma Esophageal_carcinoma Head_and_Neck_squamous_cell_carcinoma Sarcoma Uveal_Melanoma\ barChartColors \\#8FBC8F #8FBC8F #CDB79E #EEEE00 #EEEE00 #00CDCD #EED5D2 \\#CDB79E #CDB79E #CDB79E #CDB79E #CDB79E #CDB79E #9ACD32 #9ACD32 #9ACD32 \\#FFB6C1 #CD9B1D #D9D9D9 #1E90FF #CDB79E #FFD39B #A6A6A6 #008B45 #008B45 \\#EED5D2 #EED5D2 #ff0000 #ff8d00 #ffdb00 #00d619 #009fff\ barChartLabel Cancer types\ barChartMatrixUrl /gbdb/hgFixed/human/expMatrix/tcgaMatrix.tab\ barChartMetric median\ barChartSampleUrl /gbdb/hgFixed/human/expMatrix/tcgaLargeSamples.tab\ barChartUnit TPM\ bigDataUrl /gbdb/hg38/tcga/tcgaTranscExpr.bb\ defaultLabelFields name2\ group phenDis\ html tcgaExpr\ labelFields name2, name\ longLabel Transcript-level Expression in 33 TCGA Cancer Tissues (GENCODE v23)\ maxLimit 8000\ parent cancerExpr\ shortLabel Cancer Transc Expr\ track tcgaTranscExpr\ type bigBarChart\ visibility pack\ ccdsGene CCDS genePred Consensus CDS 0 100 12 120 12 133 187 133 0 0 0

Description

\ This track shows human genome high-confidence gene annotations from the\ Consensus \ Coding Sequence (CCDS) project. This project is a collaborative effort \ to identify a core set of \ human protein-coding regions that are consistently annotated and of high \ quality. The long-term goal is to support convergence towards a standard set \ of gene annotations on the human genome.\

Collaborators include:\

European Bioinformatics \ Institute (EBI)\
National Center for \ Biotechnology Information (NCBI)\
University of \ California, Santa Cruz (UCSC)\
Wellcome Trust Sanger \ Institute (WTSI)\

\ \

\ For more information on the different gene tracks, see our Genes FAQ.

\ \

Methods

\ CDS annotations of the human genome were obtained from two sources:\ NCBI \ RefSeq and a union of the gene annotations from \ Ensembl and \ Vega, collectively known \ as Hinxton.

\ Genes with identical CDS genomic coordinates in both sets become CCDS \ candidates. The genes undergo a quality evaluation, which must be approved by \ all collaborators. The following criteria are currently used to assess each\ gene: \

an initiating ATG (Exception: a non-ATG translation start codon is \ annotated if it has sufficient experimental support), a valid stop codon, and \ no in-frame stop codons (Exception: selenoproteins, which contain a TGA codon \ that is known to be translated to a selenocysteine instead of functioning as \ a stop codon) \
ability to be translated from the genome reference sequence without frameshifts\
recognizable splicing sites\
no intersection with putative pseudogene predictions\
supporting transcripts and protein homology\
conservation evidence with other species\

\ A unique CCDS ID is assigned to the CCDS, which links together all gene \ annotations with the same CDS. CCDS gene annotations are under continuous\ review, with periodic updates to this track.\

\ The sequences are generated based on second-order Markov models of monomer\ variants, and graphical models of larger scale higher order repeats.\ The graphical models are based on an analysis of Sanger reads from the\ HuRef sequencing project (Assembly\ GCA_000002125.1; BioProject\ PRJNA19621),\ and their local-ordering is supported by observed same-read monomer\ adjacencies. The Markov models are generated by the program linearSat, which\ was written for this project and that also generates a linear representation\ of monomer order. The software linearSat generates a second-order Markov\ chain to the size of a given array provided by sequence coverage normalization\ estimates. The sequence definitions of transposable element insertions are\ limited to the sequences directly adjacent to alpha satellite within the read\ database, and incomplete representations are noted with an adjacent\ 100 bp gap. In total, these sequences provide a more complete reference\ of sequence composition and higher order repeat variation inherent to a\ given alpha satellite array, used to assemble centromeric regions of the\ human chromosomes.\

\ \

Credits

\ The data for this track was supplied by\ Karen Miga.\

\ \

References

\ Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ.\ \ Centromere reference models for human chromosomes X and Y satellite arrays.\ Genome Res. 2014 Apr;24(4):697-707.\ PMID: 24501022; PMC: PMC3975068\

\ map 1 chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY\ color 255,0,0\ group map\ longLabel Centromere Locations\ shortLabel Centromeres\ track centromeres\ type bed 4 .\ url https://www.ncbi.nlm.nih.gov/nuccore/$$\ urlLabel NCBI accession record:\ visibility hide\ hprcChainNetViewchain Chains bed 3 Human Genomes, Chain/Net pairwise alignments, as mapped by the HPRC project 3 100 0 0 0 255 255 0 1 0 0 hprc 1 longLabel Human Genomes, Chain/Net pairwise alignments, as mapped by the HPRC project\ parent hprcChainNet\ shortLabel Chains\ spectrum on\ track hprcChainNetViewchain\ view chain\ visibility pack\ chm13LiftOver CHM13 alignments bigChain GCA_009914755.4 CHM13 (GCA_009914755.4) v1_nfLO liftOver alignments 0 100 120 20 0 187 137 127 0 0 0

Description

\ These tracks show the one-to-one v1_nfLO alignments of the GRCh38/hg38 to the\ T2T-CHM13 v2.0 assembly.\

\ \

Display Conventions

\ The track displays boxes joined together by either single or double lines,\ with the boxes represent aligning regions, single lines indicating gaps that\ are largely due to a deletion in the CHM13 v2.0 assembly or an insertion in\ the GRCh38/hg38, and double lines representing more complex gaps that involve\ substantial sequence in both assembly.\

\ \ \

Methods

GRCh38/hg38 pre-processing

\ To prevent ambiguous alignments, all false duplications, as determined by the Genome in a Bottle Consortium\ (GCA_000001405.15_GRCh38_GRC_exclusions_T2Tv2.bed), \ as well as the GRCh38 modeled centromeres,\ were masked from the GRCh38/hg38 primary assembly. In addition, unlocalized and unplaced (random) contigs were removed.\

\ \

Alignment and Chain Creation

\ For the minimap2-based pipeline, the initial chain file was generated using\ nf-LO v1.5.1 with\ minimap2 v2.24 alignments. These \ chains were then split at all locations that contained unaligned segments greater than 1kbp or \ gaps greater than 10kbp. Split chain files were then converted to PAF format\ with extended CIGAR strings using chaintools (v0.1),\ and alignments between nonhomologous chromosomes were removed. The trim-paf operation of\ rustybam (v0.1.29) \ was next used to remove overlapping alignments \ in the query sequence, and then the target sequence, to create 1:1 alignments. PAF alignments \ were converted back to the chain format with paf2chain commit f68eeca, and finally, \ chaintools was used to generate the inverted chain file.\

\ \

\ Full commands with parameters used were:\

\
    nextflow run main.nf --source GRCh38.fa --target chm13v2.0.fasta --outdir dir -profile local --aligner minimap2\
    python chaintools/src/split.py -c input.chain -o input-split.chain\
    python chaintools/src/to_paf.py -c input-split.chain -t target.fa -q query.fa -o input-split.paf\
    awk '$1==$6' input-split.paf | rb break-paf --max-size 10000  | rb trim-paf -r | rb invert | rb trim-paf -r | rb invert > out.paf\
    paf2chain -i out.paf > out.chain\
    python chaintools/src/invert.py -c out.chain -o out_inverted.chain\

\ \

\ The above process does not add chain ids or scores. The UCSC utilities\ chainMergeSort and chainScore are used to update the\ chains:\ \

\
    chainMergeSort out.chain | chainScore stdin chm13v2.0.2bit hg38.2bit chm13v2.0-hg38.chain\
    chainMergeSort out_inverted.chain | chainScore stdin hg38.2bit chm13v2.0.2bit hg38-chm13v2.0.chain\

\ \

\ Rustybam trim-paf\ uses dynamic programming and the CIGAR string to find an optimal\ splitting point between overlapping alignments in the query sequence. It\ starts its trimming with the largest overlap and then recursively trims\ smaller overlaps.\

\ \

\ Results were validated by using chaintools to confirm that there were no\ overlapping sequences with respect to both CHM13v2.0 and GRCh38 in the\ released chain file. In addition, trimmed alignments were visually inspected\ with SafFire to confirm their quality.\

\ \

\ \ map 1 group map\ longLabel Chromosome Bands Localized by FISH Mapping Clones\ shortLabel Chromosome Band\ track cytoBand\ type bed 4 +\ visibility hide\ cytoBandIdeo Chromosome Band (Ideogram) bed 4 + Chromosome Bands Localized by FISH Mapping Clones (for Ideogram) 1 100 0 0 0 127 127 127 0 0 0 map 1 group map\ longLabel Chromosome Bands Localized by FISH Mapping Clones (for Ideogram)\ shortLabel Chromosome Band (Ideogram)\ track cytoBandIdeo\ type bed 4 +\ visibility dense\ clinGenComp ClinGen bigBed 9 + ClinGen curation activities (Dosage Sensitivity and Gene-Disease Validity) 0 100 0 0 0 127 127 127 0 0 0

Description

\ \

NOTE:
\ These data are for research purposes only. While the ClinGen data are \ open to the public, users seeking information about a personal medical or \ genetic condition are urged to consult with a qualified physician for \ diagnosis and for answers to personal medical questions.\

\
\ UCSC presents these data for use by qualified professionals, and even \ such professionals should use caution in interpreting the significance of \ information found here. No single data point should be taken at face \ value and such data should always be used in conjunction with as much \ corroborating data as possible. No treatment protocols should be \ developed or patient advice given on the basis of these data without \ careful consideration of all possible sources of information.\
\
\ No attempt to identify individual patients should \ be undertaken. No one is authorized to attempt to identify patients \ by any means.\
\ \

\ \

\ The Clinical Genome Resource (ClinGen)\ tracks display data generated from several key curation activities related to gene-disease validity,\ dosage sensitivity, and variant pathogenicity.\ ClinGen is a National Institute of Health (NIH)-funded initiative dedicated to \ identifying clinically relevant genes and variants for use in precision medicine and research. \ This is accomplished by harnessing the data from both research efforts and clinical genetic \ testing and using it to propel expert and machine-driven curation activities. \ ClinGen works closely with the National Center for Biotechnology Information (NCBI) of the \ National Library of Medicine (NLM)\ which distributes part of this information through its ClinVar database.\

\ \

\ The available data tracks are:\

ClinGen Dosage Sensitivity Map -Haploinsufficiency (ClinGen \ Haploinsufficiency) and -Triplosensitivity (ClinGen Triplosensitivity) -\ Shows evidence supporting or refuting haploinsufficiency (loss) and triplosensitivity (gain) as \ mechanisms for disease at gene-level and larger genomic regions.\
ClinGen Gene-Disease Validity Classification (ClinGen Validity) -\ Provides a semi-qualitative measurement for the strength of evidence of a gene-disease relationship. \
Clingen CSPEC variant interpretation VCEP specifications -\ Identifies loci that have ClinGen criteria Specification (CSpec) \ information. This is used and \ applied by ClinGen Variant Curation Expert Panels (VCEPs) and biocurators in the classification of variants.\

\ A rating system is used to classify the evidence supporting or refuting dosage\ sensitivity for individual genes and regions, which takes in consideration the following criteria:\ number of causative variants reported, patterns of inheritance, consistency of phenotype, evidence\ from large-scale case-control studies, mutational mechanisms, data from public genome variation \ databases, and expert consensus opinion.\

\ The system is intended to be of a "dynamic nature", with regions being reevaluated periodically to \ incorporate emerging evidence. The evidence collected is displayed within a publicly available \ database. \ Evidence that haploinsufficiency or triplosensitivity of a gene is associated with a specific \ phenotype will aid in the interpretive assessment of CNVs including that gene or genomic region.\

\ Similarly, a qualitative classification system is used to correlate the evidence of \ a gene-disease relationship: "Definitive", "Strong", "Moderate", \ "Limited", "Animal Model Only", \ "No Known Disease Relationship", "Disputed", or "Refuted".\

\ \

Display Conventions

Haploinsufficiency/Triplosensitivity tracks

\ Items are shaded according to dosage sensitivity type, red \ for haploinsufficiency score 3, blue for triplosensitivity score 3, \ and grey for other evidence scores or \ not yet evaluated).\ Mouseover on items shows the supporting evidence of dosage sensitivity.\ Tracks can be filtered according to the supporting evidence of dosage sensitivity.\ \

\ Dosage Scores are used to classify the evidence of the supporting dosage sensitivity map:\

0 - no evidence available

1 - little evidence for dosage pathogenicity

2 - some evidence for dosage pathogenicity

3 - sufficient evidence for dosage pathogenicity

30 - gene associated with autosomal recessive phenotype

40 - dosage sensitivity unlikely

\ \

\ For more information on the use of the scores see the ClinGen\ FAQs.\

\ \

Gene-Disease Validity track

\ \

\ The gene-disease validity classifications are labeled with the disease entity and hovering \ over the features shows the associated gene. Items are color coded based on the strength of their \ classification as provided below:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

Color	Classifications
	Definitive: The role of this gene in this particular disease has been \ repeatedly demonstrated and has been upheld over time
	Strong: The role of this gene in disease has been independently\ demonstrated typically in at least two separate studies, including both strong variant-level\ evidence in unrelated probands and compelling gene-level evidence from experimental data
	Moderate: There is moderate evidence to support a causal role for this\ gene in this disease, typically including both several probands with variants and moderate \ experimental data supporting the gene-disease assertion
	Limited: There is limited evidence to support a causal role for this \ gene in this disease, such as few probands with variants and limited experimental data supporting \ the gene-disease assertion
	Animal Model Only: There are no published human probands with variants \ but there is animal model data supporting the gene-disease assertion
	No Known Disease Relationship: Evidence for a causal role in disease \ has not been reported
	Disputed: Conflicting evidence disputing a role for this gene in this \ disease has arisen since the initial report identifying an association between the gene and disease
	Refuted: Evidence refuting the role of the gene in the specified \ disease has been reported and significantly outweighs any evidence supporting the role

\ \

\ The version of the ClinGen Standard Operating Procedures (SOPs) that each gene-disease \ classification was performed with is provided as well. An older or newer SOP version does not \ necessarily mean the classification is any more or less valid but is provided for clarity. \ Each details page also contains a direct link to an evidence summary detailing the rationale behind\ the specific classification and information such as a breakdown of the semi-qualitative framework, \ relevant PubMed IDs, the type of data (Genetic vs Experimental Evidence), and a detailed summary.\

\ \

\ These tracks are multi-view composite tracks that contain multiple data types (views). Each view \ within a track has separate display controls, as described \ here.\

\ \

ClinGen VCEP Specifications track

\ \

\ \

\ Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E\ et al.\ \ Standards and guidelines for the interpretation of sequence variants: a joint consensus\ recommendation of the American College of Medical Genetics and Genomics and the Association for\ Molecular Pathology.\ Genet Med. 2015 May;17(5):405-24.\ PMID: 25741868; PMC: PMC4544753\

\ \

\ Riggs ER, Church DM, Hanson K, Horner VL, Kaminsky EB, Kuhn RM, Wain KE, Williams ES, Aradhya S,\ Kearney HM et al.\ \ Towards an evidence-based process for the clinical interpretation of copy number variation.\ Clin Genet. 2012 May;81(5):403-12.\ PMID: 22097934; PMC: PMC5008023\

\ \

\ Strande NT, Riggs ER, Buchanan AH, Ceyhan-Birsoy O, DiStefano M, Dwight SS, Goldstein J, Ghosh R,\ Seifert BA, Sneddon TP et al.\ \ Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed\ by the Clinical Genome Resource.\ Am J Hum Genet. 2017 Jun 1;100(6):895-906.\ PMID: 28552198; PMC: PMC5473734\

\ \ phenDis 1 compositeTrack on\ group phenDis\ html clinGen\ itemRgb on\ longLabel ClinGen curation activities (Dosage Sensitivity and Gene-Disease Validity)\ noParentConfig on\ pennantIcon New red ../goldenPath/newsarch.html#100924 "October 9, 2024"\ shortLabel ClinGen\ track clinGenComp\ type bigBed 9 +\ visibility hide\ iscaComposite ClinGen CNVs bed 3 Clinical Genome Resource (ClinGen) CNVs 0 100 0 0 0 127 127 127 0 0 0

\

The ClinGen CNVs track is no longer being updated. These data, along with updates,\ can be found in the \ ClinVar Copy Number Variants (ClinVar CNVs) track.

\
\ See our \ news archive for more information.
\

\ \

Description

NOTE:
\ These data are for research purposes only. While the ClinGen data are\ open to the public, users seeking information about a personal medical or\ genetic condition are urged to consult with a qualified physician for\ diagnosis and for answers to personal medical questions.\

\ \
UCSC presents these data for use by qualified professionals, and even\ such professionals should use caution in interpreting the significance of \ information found here. No single data point should be taken at face \ value and such data should always be used in conjunction with as much \ corroborating data as possible. No treatment protocols should be \ developed or patient advice given on the basis of these data without \ careful consideration of all possible sources of information.\
\ \
No attempt to identify individual patients should\ be undertaken. No one is authorized to attempt to identify patients \ by any means.\
\ \

\ \

\ The Clinical Genome Resource (ClinGen)\ is a National Institutes of Health (NIH)-funded program dedicated to building a genomic\ knowledge base to improve patient care. \ This will be accomplished by harnessing the data from both research efforts and clinical genetic\ testing, and using it to propel expert and machine-driven curation activities. \ By facilitating collaboration within the genomics community,\ we will all better understand the relationship between genomic variation and human health. \ ClinGen will work closely with the National\ Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM), \ which will distribute this information through its\ ClinVar database.\

\ \

\ The ClinGen dataset displays clinical microarray data submitted to dbGaP/dbVar at NCBI\ by ClinGen member laboratories (dbVar study\ nstd37),\ as well as clinical data reported in Kaminsky et al., 2011 (dbVar study\ ntsd101)\ (see reference below). This track shows copy number variants (CNVs) found in patients referred\ for genetic testing for indications such as intellectual disability, developmental delay,\ autism and congenital anomalies. Additionally, the ClinGen "Curated Pathogenic" and\ "Curated Benign" tracks represent genes/genomic regions reviewed for dosage sensitivity\ in an evidence-based manner by the ClinGen Structural Variation Working Group (dbVar study\ nstd45).\

\ \

The CNVs in this study have been reviewed for their clinical significance by\ the submitting ClinGen laboratory. Some of the deletions and duplications in the track\ have been reported as causative for a phenotype by the submitting clinical \ laboratory; this information was based on current knowledge at the time of submission.\ However, it should be noted that phenotype information is often vague and imprecise and\ should be used with caution. While all samples were submitted because of a phenotype in \ a patient, only 15% of patients had variants determined to be causal, \ and most patients will have additional variants that are not causal.\

\ \

CNVs are separated into subtracks and are labeled as:\

Pathogenic
Uncertain: Likely Pathogenic
Uncertain
Uncertain: Likely Benign
Benign

\ The user should be aware that some of the data were submitted using a 3-class\ system, with the two "Likely" categories omitted. \

\ \

Two subtracks, "Path Gain" and "Path Loss", are aggregate tracks\ showing graphically the accumulated level of gains and losses in the \ Pathogenic subtrack across the genome. Similarly, "Benign Gain" and\ "Benign Loss" show the accumulated level of gains and losses in the\ Benign subtrack. These tracks are collectively called "Coverage"\ tracks.\

\ \

Many samples have multiple variants, not all of which are causative \ of the phenotype. The CNVs in these samples have been decoupled, so it is not\ possible to connect multiple imbalances as coming from a single patient.\ It is therefore not possible to identify individuals via their genotype. \

\ \ \

Methods and Color Convention

\ The samples were analyzed by arrays from patients referred for \ cytogenetic testing due to clinical phenotypes. Samples were analyzed with a \ probe spacing of 20-75 kb. The minimum CNV breakpoints are shown; if available,\ the maximum CNV breakpoints are provided in the details page, but are not shown \ graphically on the Browser image.\

\ \

Data were submitted to \ dbGaP at NCBI and thence decoupled as described into\ dbVar for unrestricted release.\

\ \

\ The entries are colored red for loss and \ blue for gain. The names of items use the \ ClinVar convention of appending "_inheritance" indicating the mechanism of \ inheritance, if known: "_pat, _mat, _dnovo, _unk" as paternal, maternal, \ de novo and unknown, respectively. \

\ \

Verification

\ Most data were validated by the submitting laboratory using various methods, \ including FISH, G-banded karyotype, MLPA and qPCR.\

\ \

Credits

\ Thank you to ClinGen and NCBI for technical coordination and consultation, and to\ the UCSC Genome Browser staff for engineering the track display.\

\ \

References

\ Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler\ EE, Epstein CJ et al.\ \ Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals\ with developmental disabilities or congenital anomalies.\ Am J Hum Genet. 2010 May 14;86(5):749-64.\ PMID: 20466091; PMC: PMC2869000\

\ \

\ Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A,\ Mulle JG, Warren ST et al.\ \ An evidence-based approach to establish the functional and clinical significance of copy number\ variants in intellectual and developmental disabilities.\ Genet Med. 2011 Sep;13(9):777-84.\ PMID: 21844811; PMC: PMC3661946\

\ phenDis 1 compositeTrack on\ dimensions dimensionY=class dimensionX=level\ group phenDis\ longLabel Clinical Genome Resource (ClinGen) CNVs\ pennantIcon snowflake.png /goldenPath/newsarch.html#093020b "ClinGen CNV data are now updated on ClinVar Variants track. See news archive for details."\ shortLabel ClinGen CNVs\ sortOrder class=+ level=+ view=+\ subGroup1 view Views cov=Coverage cnv=CNVs dose=Dose\ subGroup2 class Class path=Pathogenic likP=Likely_Pathogenic unc=Uncertain likB=Likely_Benign ben=Benign\ subGroup3 level Evidence cur=Curated sub=Submitted\ track iscaComposite\ type bed 3\ visibility hide\ clinGenCspec ClinGen VCEP Specifications bigBed 9 + Clingen CSpec Variant Interpretation VCEP Specifications 3 100 0 0 0 127 127 127 0 0 0 phenDis 1 bigDataUrl /gbdb/hg38/bbi/clinGen/clinGenCspec.bb\ longLabel Clingen CSpec Variant Interpretation VCEP Specifications\ mouseOver Disease: $disease
Panel: $panel
Status: $status\ noScoreFilter on\ parent clinGenComp on\ pennantIcon New red ../goldenPath/newsarch.html#100924 "October 9, 2024"\ shortLabel ClinGen VCEP Specifications\ track clinGenCspec\ type bigBed 9 +\ visibility pack\ clinvarSubLolly ClinVar interp bigLolly ClinVar SNVs submitted interpretations and evidence 0 100 0 0 0 127 127 127 0 0 0 phenDis 1 bigDataUrl /gbdb/hg38/clinvarSubLolly/clinvarSubLolly.bb\ configurable off\ group phenDis\ lollyMaxSize 10\ lollyNoStems on\ lollySizeField 10\ longLabel ClinVar SNVs submitted interpretations and evidence\ mouseOverField _mouseOver\ parent clinvar\ shortLabel ClinVar interp\ skipFields reviewStatus\ track clinvarSubLolly\ type bigLolly\ urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"\ viewLimits 0:5\ xrefDataUrl /gbdb/hg38/clinvarSubLolly/clinvarSub.bb\ yAxisLabel.0 0 on 150,150,150 OTH\ yAxisLabel.1 1 on 150,150,150 B\ yAxisLabel.2 2 on 150,150,150 LB\ yAxisLabel.3 3 on 150,150,150 VUS\ yAxisLabel.4 4 on 150,150,150 LP\ yAxisLabel.5 5 on 150,150,150 P\ yAxisNumLabels off\ clinvar ClinVar Variants bed 12 + ClinVar Variants 0 100 0 0 0 127 127 127 0 0 0

Description

\ \

NOTE:
\ ClinVar is intended for use primarily by physicians and other\ professionals concerned with genetic disorders, by genetics researchers, and\ by advanced students in science and medicine. While the ClinVar database is\ open to all academic users, users seeking information about a personal medical\ or genetic condition are urged to consult with a qualified physician for\ diagnosis and for answers to personal questions.

\ \

\ These tracks show the genomic positions of variants in the\ ClinVar database. \ ClinVar is a free, public archive of reports\ of the relationships among human variations and phenotypes, with supporting\ evidence.

\ \

\ The ClinVar SNVs track displays substitutions and indels shorter than 50 bp and \ the ClinVar CNVs track displays copy number variants (CNVs) equal or larger than 50 bp.\ Until October 2017, all variants with the ClinVar types \ copy number gain/loss and DbVar "nsv" accessions were assigned in the CNV \ category. Because the ClinVar type no longer captures this information, any variation equal to or \ larger than 50 bp is now considered a CNV.\

\ \

\ The ClinVar Interpretations track displays the genomic positions of individual variant \ submissions and interpretations of the clinical significance and their relationship to disease in \ the ClinVar database.\

\ \

\ Note: The data in the track are obtained directly from ClinVar's FTP site.\ We display the data obtained from ClinVar as-is to avoid discrepancies between UCSC and NCBI. \ However, be aware that the ClinVar conventions are different from the VCF standard. \ Variants may be right-aligned or may contain additional context, e.g. for\ inserts. ExAC/gnomAD make available a converter\ to make ClinVar more comparable to VCF files.

\ \

Display Conventions and Configuration

\ \

\ Items can be filtered according to the size of the variant, variant type, clinical significance,\ allele origin, and molecular consequence, using the track Configure options.\ Each subtrack has separate display controls, as described\ here.\

\ \

\ Mouseover on the genomic locations of ClinVar variants shows variant details, clinical \ interpretation, and associated conditions. Further information on each variant is displayed on \ the details page by a click onto any variant. ClinVar is an archive for assertions of clinical \ significance made by the submitters. The level of review supporting the assertion of clinical \ significance for the variation is reported as the \ review status. \ Stars (0 to 4) provide a graphical representation of the aggregate review status. \

\ \

\ Entries in the ClinVar CNVs track are colored by type of variant, among others:\

red for loss
blue for gain
purple for inversion
orange for insertion

\ A light-to-dark color gradient indicates the clinical significance of each variant, with the \ lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the \ CNV color code is described \ here. \

\ \

\ Entries in the ClinVar SNVs and ClinVar Interpretations tracks are colored by clinical \ significance:\

red for pathogenic
dark blue for variant of uncertain significance
green for benign
dark grey for not provided
light blue for conflicting

\ \

\ The variants in the ClinVar Interpretations track are sorted by the variant \ classification of each submission:\

P: Pathogenic
LP: Likely Pathogenic
VUS: Variant of Unknown Significance
LB: Likely Benign
B: Benign
OTH: Others

\ The size of the bead represents \ the number of submissions at that genomic position. For track display clarity, these submission\ numbers are binned into three categories:\

Small-sized beads: 1-2 submissions
Medium-sized beads: 3-7 submissions
Large-sized beads: 8 or more submissions

\ Hovering on the track items shows the genomic variations which start at that position \ and the number of individual submissions with that classification. The details page lists all\ rated submissions from ClinVar, with specific details to the interpretation of the clinical or \ functional significance of each variant in relation to a condition. Interpretation is at \ variant-level, not at case (or patient-specific) level.\

\ \

\ More information about using and understanding the ClinVar data can be found \ here.\

\ \

\ For the human genome version hg19: the hg19 genome released by UCSC in 2009 had a \ mitochondrial genome "chrM" that was not the same as the one later used for most\ databases like ClinVar. As a result, we added the official mitochondrial genome\ in 2020 as "chrMT" and all mitochondrial annotations of ClinVar and most other\ databases are shown on the mitochondrial genome called "chrMT". For full description\ of the issue of the mitochondrial genome in hg19, please see the \ README file \ on our download site. \

\ \ \

\ Thanks to NCBI for making the ClinVar data available on their FTP site as a tab-separated file.\

\ \

References

\ Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J\ et al.\ \ ClinVar: public archive of interpretations of clinically relevant variants.\ Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8.\ PMID: 26582918; PMC: PMC4702865\

\ \

\ Azzariti DR, Riggs ER, Niehaus A, Rodriguez LL, Ramos EM, Kattman B, Landrum MJ, Martin CL, Rehm HL.\ \ Points to consider for sharing variant-level information from clinical genetic testing with\ ClinVar.\ Cold Spring Harb Mol Case Stud. 2018 Feb;4(1).\ PMID: 29437798; PMC: PMC5793773\

\ \ phenDis 1 compositeTrack on\ dataVersion /gbdb/$D/bbi/clinvarAlpha/version.txt\ group phenDis\ itemRgb on\ longLabel ClinVar Variants\ noParentConfig on\ scoreLabel ClinVar Star-Rating (0-4)\ shortLabel ClinVar Variants\ track clinvar\ type bed 12 +\ urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"\ visibility hide\ cloneEndSuper Clone Ends bed 3 Mapping of clone libraries end placements 0 100 0 0 0 127 127 127 0 0 0

Description

\ This track shows the NCBI clone end mappings from the\ NCBI Clone DB database. Libraries with more than\ 30,000 clones are included in this track display.

\ Bacterial artificial chromosomes (BACs) are a key part of many\ large-scale sequencing projects. A BAC typically consists of 50 - 300 kb of\ DNA. During the early phase of a sequencing project, it is common\ to sequence a single read (approximately 500 bases) off each end of\ a large number of BACs. Later on in the project, these BAC end reads\ can be mapped to the genome sequence.

\ These BAC end pairs can be useful for validating the assembly over\ relatively long ranges. In some cases, the BACs are useful biological\ reagents. This track can also be used for determining which BAC\ contains a given gene, useful information for certain wet lab experiments.

\ The scoring scheme used for this annotation assigns 1000 to an alignment\ when the BAC end pair aligns to only one location in the genome (after\ filtering). When a BAC end pair or clone aligns to multiple locations, the\ score is calculated as 1500/(number of alignments).

\ \

Display Conventions and Configuration

\ \

\ Items in this track are colored according to their strand orientation. Blue indicates alignment to the forward strand, \ and green indicates alignment to the negative strand.\

\ \ \

Methods

\ The mappings of these BAC end sequences are taken directly from the\ NCBI Clone DB FTP site\ ftp.ncbi.nih.gov/repository/clone/reports/Homo_sapiens/\ *.GCF_000001405.26.106.*.gff files.

\ UCSC filtered the NCBI Clone DB mapped ends to drop ends that mapped to a\ region that was three times longer than the median size of the clones in\ the library. Only libraries with more than\ 30,000 clones are included in this track display.

\ Click through on displayed items to the Clone DB database information,\ including\ Clone DB distributor references.

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

clone information from NCBI Clone DB and UCSC mapping statistics
ABC8	2,007,047	3,888,476	1,205,466	1,192,784	12,682	% 1.05
WI2	1,122,564	2,298,885	589,547	582,843	6,704	% 1.14
ABC12	1,120,939	2,169,280	778,216	771,827	6,389	0.82
ABC7	1,116,966	2,152,975	650,329	644,071	6,258	0.96
ABC9	1,065,503	2,084,892	757,644	750,648	6,996	0.92
ABC10	1,062,082	2,121,489	788,344	781,331	7,013	0.89
ABC14	1,042,929	2,089,193	846,055	839,126	6,929	0.82
ABC13	1,009,643	2,057,345	811,829	803,589	8,240	1.01
ABC11	998,880	1,966,644	730,565	724,864	5,701	0.78
ABC23	942,133	1,535,766	437,098	433,896	3,202	0.73
ABC16	907,948	1,534,288	452,316	449,101	3,215	0.71
ABC24	835,600	1,383,475	399,056	395,776	3,280	0.82
ABC27	768,336	1,229,804	334,232	331,822	2,410	0.72
ABC18	743,640	1,204,811	325,150	322,904	2,246	0.69
COR2A	723,569	1,441,881	583,327	578,578	4,749	0.81
ABC22	519,274	780,151	189,988	188,743	1,245	0.66
ABC21	436,930	680,160	182,214	180,973	1,241	0.68
RP11	292,975	394,813	86,875	85,903	972	1.12
COR02	272,396	546,984	208,377	206,782	1,595	0.77
CTD	226,848	403,688	96,594	94,941	1,653	1.71
CH17	176,209	325,659	105,805	105,060	745	0.70
ABC20	49,132	80,350	24,720	24,474	246	1.00
UCSC dropped	152,979	n/a	n/a	n/a	n/a	n/a
multiple mappings	775,629	n/a	n/a	n/a	n/a	n/a

\ \

Credits

\ Additional information about the clone, including how it\ can be obtained, may be found at the\ NCBI Clone Registry. To view the registry entry for a\ specific clone, open the details page for the clone and click on its name at\ the top of the page.

\ map 1 compositeTrack on\ dimensions dimensionX=source\ dragAndDrop on\ group map\ longLabel Mapping of clone libraries end placements\ noInherit on\ shortLabel Clone Ends\ sortOrder source=+\ subGroup1 source Source agencourt=Agencourt chori=Chori corielle=Coriell caltech=CalTech rpci=RPCI wibr=WIBR placements=Placements\ track cloneEndSuper\ type bed 3\ visibility hide\ ghClusteredInteraction Clustered Interactions bigInteract GeneHancer Regulatory Elements and Gene Interactions 3 100 0 0 0 127 127 127 0 0 0 https://www.genecards.org/cgi-bin/carddisp.pl?gene=$&keywords=$&prefilter=enhancers#enhancers regulation 1 interactDirectional clusterTarget\ interactMultiRegion on\ longLabel GeneHancer Regulatory Elements and Gene Interactions\ parent geneHancer\ shortLabel Clustered Interactions\ track ghClusteredInteraction\ type bigInteract\ url https://www.genecards.org/cgi-bin/carddisp.pl?gene=$&keywords=$&prefilter=enhancers#enhancers\ urlLabel Interaction in GeneCards\ view d_I\ visibility pack\ iscaViewDetail CNVs gvf Clinical Genome Resource (ClinGen) CNVs 3 100 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/dbvar/?term=$$ phenDis 1 longLabel Clinical Genome Resource (ClinGen) CNVs\ noScoreFilter .\ parent iscaComposite\ shortLabel CNVs\ track iscaViewDetail\ type gvf\ url https://www.ncbi.nlm.nih.gov/dbvar/?term=$$\ urlLabel ClinGen details:\ view cnv\ visibility pack\ colonWangCellType Colon Cells bigBarChart Colon cells binned by cell type from Wang et al 2020 3 100 0 0 0 127 127 127 0 0 0 https://cells.ucsc.edu/?ds=human-intestine+colon&gene=$$

Description

\ This track shows data from Single-cell transcriptome analysis reveals differential\ nutrient absorption functions in human intestine. Droplet-based\ single-cell RNA sequencing (scRNA-seq) was used to survey gene expression\ profiles of the epithelium in the human ileum, colon, and rectum. A total of 7\ cell clusters were identified: enterocytes (EC), goblet cells (G), paneth-like\ cells (PLC), enteroendocrine cells (EEC), progenitor cells (PRO),\ transient-amplifying cells (TA) and stem cells (SC).

\ \

\ This track collection contains two bar chart tracks of RNA expression in colon\ cells where cells are grouped by cell type \ (Colon Cells) or donor \ (Colon Donor). The default track \ displayed is Colon Cells.

\ \

Display Conventions

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \
Color Cell classification
epithelial
secretory
stem cell
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated \ with those classes. Note that the Colon Donor track \ is colored by donor for improved clarity.

\ \

Method

\ Using scRNA-seq, RNA profiles of intestinal epithelial cells were obtained for \ 4,472 cells from two human colon samples. Tissue samples belonged to a male \ donor age 54 (Colon-1) and a female donor age 67 (Colon-2) both diagnosed with \ Adenocarcinoma. The healthy intestinal mucous membranes used for each sample \ were cut away from the tumor border in surgically removed ascending colon tissue. \ Additionally, the intestinal tissues were washed in Hank's balanced salt solution \ (HBSS) to remove mucus, blood cells, and muscle tissue. The sample was enriched \ for epithelial cells through centrifugation before being dissociated with Tryple \ to obtain single-cell suspensions. RNA-seq libraries were prepared using 10x \ Genomics 3' v2 kit and sequenced on an Illumina Hiseq X Ten PE150.

\ \

The cell/gene matrix and cell-level metadata was downloaded from the UCSC Cell Browser.\ The UCSC command line utility matrixClusterColumns, matrixToBarChart, and bedToBigBed were used \ to transform these into a bar chart format bigBed file that can be visualized. The coloring \ was done by defining colors for the broad level cell classes and then using another UCSC utility,\ hcaColorCells, to interpolate the colors across all cell types. The UCSC utilities can be found on \ our download server.

\ \

Data Access

\ The raw bar chart data can be\ explored interactively with the Table\ Browser, or the Data Integrator. For\ automated analysis, the data may be queried from our REST API. Please refer to our mailing\ list archives for questions, or our Data Access FAQ for more\ information.

\ \

Credit

\ Thanks to Yalong Wang, Wanlu Song, and to the many authors who worked on\ producing and publishing this data set. The data were integrated into the UCSC\ Genome Browser by Jim Kent and Brittney Wick then reviewed by Luis Nassar. The\ UCSC work was paid for by the Chan Zuckerberg Initiative.

\ \

References

\ Wang Y, Song W, Wang J, Wang T, Xiong X, Qi Z, Fu W, Yang X, Chen YG.\ \ Single-cell transcriptome analysis reveals differential nutrient absorption functions in human\ intestine.\ J Exp Med. 2020 Feb 3;217(2).\ PMID: 31753849; PMC: PMC7041720

\ \ \ singleCell 1 barChartBars enteroendocrine_cell enterocyte goblet_cell paneth-like_cell progenitor_cell stem_cell transit-amplifying_cell\ barChartColors #c7d2e5 #0198c0 #0251fc #7197d7 #4d689b #9e9fa2 #949dae\ barChartLimit 1.6\ barChartMetric mean\ barChartStatsUrl /gbdb/hg38/bbi/colonWang/cell_type.stats\ barChartUnit UMI/cell\ bigDataUrl /gbdb/hg38/bbi/colonWang/cell_type.bb\ defaultLabelFields name\ html colonWang\ labelFields name,name2\ longLabel Colon cells binned by cell type from Wang et al 2020\ parent colonWang\ shortLabel Colon Cells\ track colonWangCellType\ transformFunc NONE\ type bigBarChart\ url https://cells.ucsc.edu/?ds=human-intestine+colon&gene=$$\ urlLabel View on the UCSC Cell Browser:\ visibility pack\ colonWangDonor Colon Donor bigBarChart Colon cells binned by organ donor from Wang et al 2020 0 100 0 0 0 127 127 127 0 0 0 https://cells.ucsc.edu/?ds=human-intestine+colon&gene=$$

Description

\ \

Display Conventions

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \
Color Cell classification
epithelial
secretory
stem cell
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated \ with those classes. Note that the Colon Donor track \ is colored by donor for improved clarity.

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \
Color Cell classification
epithelial
secretory
stem cell
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated \ with those classes. Note that the Colon Donor track \ is colored by donor for improved clarity.

\ \ \ \ \ \ \ \ \ \
Percentile JARVIS score threshold
99th 0.9998
95th 0.9826
90th 0.7338
\

HMC

\ Scores were downloaded and converted to .bedGraph files with a custom Python \ script. The bedGraph files were then converted to bigWig files, as documented in our \ makeDoc hg19 build log.

\ \

\ Approximately 1000 samples from the Chromosomal Aberrations and Heritable\ Diseases collections of the NIGMS Repository were genotyped on the Affymetrix\ Genome-Wide Human SNP 6.0 Array and analyzed for CNVs at the Coriell Institute\ for Medical Research. Genotyping data for many of these samples is available\ through dbGaP.\

\ \

\ The genotyped samples represent a diverse set of copy-number variants. The\ selection was weighted to over-sample commonly manifested types of aberrations.\ Karyotyping was performed on all NIGMS Repository cell lines that were\ submitted with reported chromosome abnormalities. When available, the ISCN\ description of the sample, based on G-banding and FISH analysis, is included\ in the phenotypic data. Karyotypes for these cells can be viewed in the\ online Repository catalog.\

\ \

\ Field definitions for an item description:\

CN State: Copy Number of the imbalance. Note that all CNVs with\ a copy number of 2 are colored neutral (black) and occur on the sex\ chromosomes, where a CN State of 2 should not be interpreted\ as normal, as it would be on an autosome.
Cell Type: Type of cell culture; one of the following:\ B Lymphocyte, Fibroblast, Amniotic fluid-derived cell line or\ Chorionic villus-derived cell line.
Description (Diagnosis): May be a medical diagnosis,\ such as "albinism" or a chromosomal phenotype, such as\ "translocation" or other description.
ISCN nomenclature: A description of the chromosomal\ karyotype in formal ISCN nomenclature.

\ \

\ CN State item coloring:\

CN State 0 == score 0
CN State 1 == score 100
CN State 2 == score 200
CN State 3 == score 300
CN State 4 == score 400

\ \ Use the score filter limits on the configuration page\ to select desired CN States.\

\ \

Credits

\ We thank Dorit Berlin and Zhenya Tang of the NIGMS Human Genetic Cell\ Repository at the\ Coriell Institute for Medical\ Research for these data.\

\ \

References

\ NCBI dbGaP:\ \ Genotyping NIGMS Chromosomal Aberration and Inherited Disorder Samples.\ \
\ NIGMS Human Genetic Cell Repository\ online catalog at the Coriell Institute for Medical Research.\ \

\ phenDis 1 exonArrows off\ group phenDis\ itemRgb on\ longLabel Coriell Cell Line Copy Number Variants\ origAssembly hg19\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ scoreFilterByRange on\ shortLabel Coriell CNVs\ track coriellDelDup\ type bed 9 +\ url http://ccr.coriell.org/Sections/Search/Search.aspx?q=$$\ urlLabel Coriell details:\ visibility hide\ cortexVelmeshevCellType Cortex Cells bigBarChart Cerebral cortex RNA binned by cell type from Velmeshev et al 2019 3 100 0 0 0 127 127 127 0 0 0 https://cells.ucsc.edu/?ds=autism&gene=$$

Description

\ This track displays data from Single-cell genomics identifies cell type-specific\ molecular changes in autism. Single-nucleus RNA sequencing (snRNA-seq)\ was performed on post-mortem cortical tissue samples from patients with autism\ spectrum disorder (ASD) as well as control donors. A total of 17 cell clusters\ were identified using known cell type markers found in Velmeshev et\ al., 2019.

\ \

\ This track collection contains five bar chart tracks of RNA expression in the human\ cerebral cortex where cells are grouped by cell type \ (Cortex Cells), diagnosis\ (Cortex Diagnosis), donor \ (Cortex Donor), sample \ (Cortex Sample), and sex\ (Cortex Sex). \ The default track displayed is Cortex Cells.

\ \

Display Conventions

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \ \
Color Cell classification
neural
immune
endothelial
glia
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes. The colors will be purest in the \ Cortex Cells subtrack, where\ the bars represent relatively pure cell types. They can give an overview of the\ cell composition within other categories in other subtracks as well.

\ \

Method

\ Healthy cortical samples were taken from 16 controls (ages 4-22) without \ neurological disorders and 15 ASD patients (ages 7-21). A total of 41 post-mortem\ tissue samples were obtained from both the prefrontal cortex (PFC) and anterior\ cingulate cortex (ACC). When present, subcortical white matter was removed\ prior to collection from cortical samples containing all layers of cortical\ grey matter. ASD and control samples were matched for sex and age and processed\ together to minimize batch effects. Nuclei were isolated from brain tissue\ using a glass dounce homogenizer in lysis buffer and then filtered twice\ through a 30 µm cell strainer. Next, samples were processed\ using 10x Genomics 3' library kit and the resulting single-nucleus libraries\ were pooled together and sequenced on an Illumina NovaSeq 6000. This process\ generated 104,559 single-nuclei gene expression profiles in total.

\ \

\ The cell/gene matrix and cell-level metadata was downloaded from the UCSC Cell Browser. The\ UCSC command line utility matrixClusterColumns, matrixToBarChart, and bedToBigBed\ were used to transform these into a bar chart format bigBed file that can be\ visualized. The coloring was done by defining colors for the broad level cell\ classes and then using another UCSC utility, hcaColorCells, to interpolate the\ colors across all cell types. The UCSC utilities can be found on \ our download server.

\ \

Data Access

\ \ \

Credit

\ Thanks to Dmitry Velmeshev and to the many authors who worked on\ producing and publishing this data set. The data were integrated into the UCSC\ Genome Browser by Jim Kent and Brittney Wick then reviewed by by Daniel Schmelter. \ The UCSC work was paid for by the Chan Zuckerberg Initiative.

\ \

References

\ Velmeshev D, Schirmer L, Jung D, Haeussler M, Perez Y, Mayer S, Bhaduri A, Goyal N, Rowitch DH,\ Kriegstein AR.\ \ Single-cell genomics identifies cell type-specific molecular changes in autism.\ Science. 2019 May 17;364(6441):685-689.\ PMID: 31097668; PMC: PMC7678724\

\ singleCell 1 barChartBars astrocyte_(fibrous) astrocyte_(protoplasmic) endothelial_cell interneuron_PVALB+ interneuron_SST+ interneuron_SV2C+ interneuron_VIP+ neuron_L2/3_cortex neuron_L4_cortex neuron_L5/6_corticofugal neuron_L5/6_cortico-cortical microglial_cell neuron_NRGN+_I neuron_NRGN+_II neuron_maturing oligodendrocyte_precursor oligodendrocyte\ barChartColors #81ce00 #81cd00 #01c000 #ebbf00 #ebbf00 #eabe00 #ebbf00 #ecbf00 #ecbf00 #ecbf00 #edbf00 #ef1211 #c8b701 #c5b701 #ebbf00 #c5be01 #86c601\ barChartLimit 4\ barChartMetric mean\ barChartStatsUrl /gbdb/hg38/bbi/cortexVelmeshev/cell_type.stats\ barChartUnit UMI/cell\ bigDataUrl /gbdb/hg38/bbi/cortexVelmeshev/cell_type.bb\ defaultLabelFields name2\ html cortexVelmeshev\ labelFields name,name2\ longLabel Cerebral cortex RNA binned by cell type from Velmeshev et al 2019\ parent cortexVelmeshev\ shortLabel Cortex Cells\ track cortexVelmeshevCellType\ transformFunc NONE\ type bigBarChart\ url https://cells.ucsc.edu/?ds=autism&gene=$$\ urlLabel View on the UCSC Cell Browser:\ visibility pack\ cortexVelmeshevDiagnosis Cortex Diagnosis bigBarChart Cerebral cortex RNA binned by ASD/control diagnosis from Velmeshev et al 2019 0 100 0 0 0 127 127 127 0 0 0 https://cells.ucsc.edu/?ds=autism&gene=$$

Description

\ \

Display Conventions

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \ \
Color Cell classification
neural
immune
endothelial
glia
\

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \ \
Color Cell classification
neural
immune
endothelial
glia
\

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \ \
Color Cell classification
neural
immune
endothelial
glia
\

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \ \
Color Cell classification
neural
immune
endothelial
glia
\

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \ \
Color Cell classification
neural
immune
endothelial
glia
\

Methods

The data in COSMIC are curated from a number of high-quality sources and combined into a single\ resource. The sources include:

\ \

Peer-reviewed journal articles
\ CGP laboratories at the Sanger Institute, UK
TCGA data portal
The ICGC data portal
IARC p53 database

\ \

Information on known cancer genes, selected from the \ Cancer Gene Census is curated manually to maximize its descriptive content. \ \

\ UCSC was provided with the COSMIC annotations directly. The columns were reconfigured to match\ our BED format, and 35 mutations were removed as they had illegal coordinates (start>stop).\ The resulting file was converted to a bigBed for display using the bedToBigBed utility.\

\ \

Display

Dense - Indicate the positions where COSMIC mutations have been annotated in a single horizontal\ track.
Squish - Indicate each mutation, in vertical pileups where appropriate, while minimizing \ screen space used.
Pack - Indicate each mutation with Genomic Mutation ID (COSVnnnnn).
Full - Show each mutation in detail, one per line, with Genomic Mutation ID (COSVnnnnn).

\ Clicking into any item also displays the reference allele, alternate allele, and the\ Cosmic legacy mutation identifier (COSNnnnnn). Outlinks can also be found directly to COSMIC\ for additional information.\

\ \

Data Access

\ The limited data available to UCSC can be explored interactively \ with the Table Browser,\ or the Data Integrator. For automated analysis, the data may be\ queried from our REST API. Please refer to our\ mailing list archives\ for questions, or our Data Access FAQ for more\ information.

\ The complete data can be explored and downloaded via the COSMIC \ website.\

\ \

Contacts

For further information on COSMIC, or for help with the information provided, please contact\ \ cosmic@sanger.\ ac.\ uk.\

Dense - Indicate the positions where COSMIC mutations have been annotated in a single horizontal\ track.
Squish - Indicate each mutation, in vertical pileups where appropriate, while minimizing \ screen space used.
Pack - Indicate each mutation with COSMIC identifier (COSMnnnnn).
Full - Show each mutation in detail, one per line, with COSM identifier (COSMnnnnn).

\ \

Data Access

\ Due to licensed material, we do not allow downloads or Table Browser access for the bigBed data. The\ raw data underlying this track can be explored and downloaded via the COSMIC \ website. The\ CosmicMutantExport.tsv.gz file was converted to a BED file using the cosmicToBed\ utility, and then converted into a bigBed file using the bedToBigBed utility. You can\ download these tools from the\ utilities directory.\

\ \

Contacts

For further information on COSMIC, or for help with the information provided, please contact\ \ cosmic@sanger.\ ac.\ uk.\

\ \

References

\ phenDis 1 bigDataUrl /gbdb/hg38/cosmic/cosMutHg38V82.bb\ color 200, 0, 0\ group phenDis\ html cosmicRegions\ labelFields cosmLabel\ longLabel Catalogue of Somatic Mutations in Cancer V82\ mouseOverField _mouseOver\ noScoreFilter on\ pennantIcon snowflake.png ../goldenPath/newsarch.html#091523 "COSMIC data is now updated on the COSMIC track (not COSMIC Regions). See news archive for details."\ searchIndex name,cosmLabel\ shortLabel COSMIC Regions\ tableBrowser off\ track cosmicRegions\ type bigBed 8 +\ url http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=$$\ urlLabel COSMIC ID:\ iscaViewTotal Coverage (Graphical) bedGraph 4 Clinical Genome Resource (ClinGen) CNVs 2 100 0 0 0 127 127 127 0 0 0 phenDis 0 alwaysZero on\ longLabel Clinical Genome Resource (ClinGen) CNVs\ maxHeightPixels 128:57:16\ parent iscaComposite\ shortLabel Coverage (Graphical)\ track iscaViewTotal\ type bedGraph 4\ view cov\ viewLimits 0:100\ viewUi on\ visibility full\ covid COVID Data Container of SARS-CoV-2 data 0 100 0 0 0 127 127 127 0 0 0

Description

\ This is a container track for all data related to SARS-CoV-2 for hg38 \ in the UCSC Genome Browser. Click into any of the sub-tracks to see information\ details on the specific annotations.

\ phenDis 0 cartVersion 4\ group phenDis\ longLabel Container of SARS-CoV-2 data\ shortLabel COVID Data\ superTrack on\ track covid\ cpgIslandSuper CpG Islands bed 4 + CpG Islands (Islands < 300 Bases are Light Green) 0 100 0 100 0 128 228 128 0 0 0

Description

\ \

\ The unmasked version of the track displays potential CpG islands\ that exist in repeat regions and would otherwise not be visible\ in the repeat masked version.\

\ \

\ By default, only the masked version of the track is displayed. To view the\ unmasked version, change the visibility settings in the track controls at\ the top of this page.\

\ \

Methods

\ \

GC content of 50% or greater
length greater than 200 bp
ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the \ \ basis of the number of Gs and Cs in the segment

\ \

    Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)

\ \ where N = length of sequence.

\ The calculation of the track data is performed by the following command sequence:\

\
twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\\
  | cpg_lh /dev/stdin 2> cpg_lh.err \\\
    |  awk '{$2 = $2 - 1; width = $3 - $2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\\
     | sort -k1,1 -k2,2n > cpgIsland.bed\

\ The unmasked track data is constructed from\ twoBitToFa -noMask output for the twoBitToFa command.\

\ \

\ The track "CRISPR Targets" shows all potential -NGG target sites across the genome.\ The target sequence of the guide is shown with a thick (exon) bar. The PAM\ motif match (NGG) is shown with a thinner bar. Guides\ are colored to reflect both predicted specificity and efficiency. Specificity\ reflects the "uniqueness" of a 20mer sequence in the genome; the less unique a\ sequence is, the more likely it is to cleave other locations of the genome\ (off-target effects). Efficiency is the frequency of cleavage at the target\ site (on-target efficiency).

\ \

Shades of gray stand for sites that are hard to target specifically, as the\ 20mer is not very unique in the genome:

\ \ \ \ \

	impossible to target: target site has at least one identical copy in the genome and was not scored
	hard to target: many similar sequences in the genome that alignment stopped, repeat?
	hard to target: target site was aligned but results in a low specificity score <= 50 (see below)

\ \

Colors highlight targets that are specific in the genome (MIT specificity > 50) but have different predicted efficiencies:

\ \ \ \ \ \

	unable to calculate Doench/Fusi 2016 efficiency score
	low predicted cleavage: Doench/Fusi 2016 Efficiency percentile <= 30
	medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile > 30 and < 55
	high predicted cleavage: Doench/Fusi 2016 Efficiency > 55

\ \

\ Mouse-over a target site to show predicted specificity and efficiency scores:
\

The MIT Specificity score summarizes all off-targets into a single number from\ 0-100. The higher the number, the fewer off-target effects are expected. We\ recommend guides with an MIT specificity > 50.
The efficiency score tries to predict if a guide leads to rather strong or\ weak cleavage. According to (Haeussler et al. 2016), the \ Doench 2016 Efficiency score should be used to select the guide with the highest\ cleavage efficiency when expressing guides from RNA PolIII Promoters such as\ U6. Scores are given as percentiles, e.g. "70%" means that 70% of mammalian\ guides have a score equal or lower than this guide. The raw score number is\ also shown in parentheses after the percentile.
The Moreno-Mateos 2015 Efficiency\ score should be used instead of the Doench 2016 score when transcribing the\ guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or\ Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses,\ see the note above.

\ \

Click onto features to show all scores and predicted off-targets with up to\ four mismatches. The Out-of-Frame score by Bae et al. 2014\ is correlated with\ the probability that mutations induced by the guide RNA will disrupt the open\ reading frame. The authors recommend out-of-frame scores > 66 to create\ knock-outs with a single guide efficiently.

\ \

Off-target sites are sorted by the CFD (Cutting Frequency Determination)\ score (Doench et al. 2016).\ The higher the CFD score, the more likely there is off-target cleavage at that site.\ Off-targets with a CFD score < 0.023 are not shown on this page, but are available when\ following the link to the external CRISPOR tool.\ When compared against experimentally validated off-targets by\ Haeussler et al. 2016, the large majority of predicted\ off-targets with CFD scores < 0.023 were false-positives. For storage and performance\ reasons, on the level of individual off-targets, only CFD scores are available.

\ \

Methods

\ \

Relationship between predictions and experimental data

\ \

\ Like most algorithms, the MIT specificity score is not always a perfect\ predictor of off-target effects. Despite low scores, many tested guides\ caused few and/or weak off-target cleavage when tested with whole-genome assays\ (Figure 2 from Haeussler\ et al. 2016), as shown below, and the published data contains few data points\ with high specificity scores. Overall though, the assays showed that the higher\ the specificity score, the lower the off-target effects.

\ \

Similarly, efficiency scoring is not very accurate: guides with low\ scores can be efficient and vice versa. As a general rule, however, the higher\ the score, the less likely that a guide is very inefficient. The\ following histograms illustrate, for each type of score, how the share of\ inefficient guides drops with increasing efficiency scores:\

\ \

When reading this plot, keep in mind that both scores were evaluated on\ their own training data. Especially for the Moreno-Mateos score, the\ results are too optimistic, due to overfitting. When evaluated on independent\ datasets, the correlation of the prediction with other assays was around 25%\ lower, see Haeussler et al. 2016. At the time of\ writing, there is no independent dataset available yet to determine the\ Moreno-Mateos accuracy for each score percentile range.

\ \

Track methods

\ The entire human (hg38) genome was scanned for the -NGG motif. Flanking 20mer\ guide sequences were\ aligned to the genome with BWA and scored with MIT Specificity scores using the\ command-line version of crispor.org. Non-unique guide sequences were skipped.\ Flanking sequences were extracted from the genome and input for Crispor\ efficiency scoring, available from the Crispor downloads page, which\ includes the Doench 2016, Moreno-Mateos 2015 and Bae\ 2014 algorithms, among others.

\ Note that the Doench 2016 scores were updated by\ the Broad institute in 2017 ("Azimuth" update). As a result, earlier versions of\ the track show the old Doench 2016 scores and this version of the track shows new\ Doench 2016 scores. Old and new scores are almost identical, they are\ correlated to 0.99 and for more than 80% of the guides the difference is below 0.02.\ However, for very few guides, the difference can be bigger. In case of doubt, we recommend\ the new scores. Crispor.org can display both\ scores and many more with the "Show all scores" link.

\ \

Data Access

\ Positional data can be explored interactively with the \ Table\ Browser or the Data Integrator.\ For small programmatic positional queries, the track can be accessed using our \ REST API. For genome-wide data or \ automated analysis, CRISPR genome annotations can be downloaded from\ our download server\ as a bigBedFile.

\ The files for this track are called crispr.bb, which lists positions and\ scores, and crisprDetails.tab, which has information about off-target matches. Individual\ regions or whole genome annotations can be obtained using our tool bigBedToBed,\ which can be compiled from the source code or downloaded as a pre-compiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here. The tool\ can also be used to obtain only features within a given range, e.g.

\ bigBedToBed\ http://hgdownload.soe.ucsc.edu/gbdb/hg38/crisprAllTargets/crispr.bb -chrom=chr21\ -start=0 -end=1000000 stdout

\ \

Credits

\ \

\ Track created by Maximilian Haeussler, with helpful input\ from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU).\

\ \

References

\ \

\ Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S,\ Shkumatava A, Teboul L, Kent J et al.\ Evaluation of off-target and on-target scoring algorithms and integration into the\ guide RNA selection tool CRISPOR.\ Genome Biol. 2016 Jul 5;17(1):148.\ PMID: 27380939; PMC: PMC4934014\

\ \

\ Bae S, Kweon J, Kim HS, Kim JS.\ \ Microhomology-based choice of Cas9 nuclease target sites.\ Nat Methods. 2014 Jul;11(7):705-6.\ PMID: 24972169\

\ \

\ Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C,\ Orchard R et al.\ \ Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.\ Nat Biotechnol. 2016 Feb;34(2):184-91.\ PMID: 26780180; PMC: PMC4744125\

\ \

\ Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O\ et al.\ \ DNA targeting specificity of RNA-guided Cas9 nucleases.\ Nat Biotechnol. 2013 Sep;31(9):827-32.\ PMID: 23873081; PMC: PMC3969858\

\ \

\ Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ.\ \ CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.\ Nat Methods. 2015 Oct;12(10):982-8.\ PMID: 26322839; PMC: PMC4589495\

\ genes 1 bigDataUrl /gbdb/hg38/crisprAll/crispr.bb\ denseCoverage 0\ detailsTabUrls _offset=/gbdb/$db/crisprAll/crisprDetails.tab\ group genes\ html crisprAll\ itemRgb on\ longLabel CRISPR/Cas9 -NGG Targets, whole genome\ mouseOverField _mouseOver\ noGenomeReason This track is too big for whole-genome Table Browser access, it would lead to a timeout in your internet browser. Small regional queries can work, but large regions, such as entire chromosomes, will fail. Please see the CRISPR Track documentation, the section "Data Access", for bulk-download options and remote access via the bedToBigBed tool. API access should always work. Contact us if you encounter difficulties with accessing the data.\ scoreFilterMax 100\ scoreLabel MIT Guide Specificity Score\ shortLabel CRISPR Targets\ tableBrowser tbNoGenome\ track crisprAllTargets\ type bigBed 9 +\ url http://crispor.tefor.net/crispor.py?org=$D&pos=$S:${&pam=NGG\ urlLabel Click here to show this guide on Crispor.org, with expression oligos, validation primers and more\ visibility hide\ crossTissueMaps Cross Tissue Nuclei Single Nuclei sequenced across many tissues 0 100 0 0 0 127 127 127 0 0 0

\ Description

\ \

\ Please see the\ GTEx portal\ for further interactive displays and additional data.

\ \

Display Conventions and Configuration

\ Tissue-cell type combinations in the Full and Combined tracks are\ colored by which cell type they belong to in the below table:\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Color Cell Type
Endothelial
Epithelial
Glia
Immune
Neuron
Stromal
Other
\

\ \

Methods

\ \

\ For detailed methods, please refer to Eraslan et al, or the\ \ GTEx portal website.\

\ \

UCSC Methods

\ \

Data Access

\ \

Credits

Thanks to the GTEx Consortium for creating and analyzing these data.

\ \

References

\ singleCell 0 configureByPopup off\ group singleCell\ longLabel Single Nuclei sequenced across many tissues\ shortLabel Cross Tissue Nuclei\ superTrack on\ track crossTissueMaps\ visibility hide\ dbSnpArchive dbSNP Archive bed 6 + dbSNP Track Archive 0 100 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$

Description

\ \

\ This composite track contains information about single nucleotide polymorphisms (SNPs)\ and small insertions and deletions (indels) — collectively Simple\ Nucleotide Polymorphisms — from\ dbSNP, available from\ ftp.ncbi.nih.gov/snp.\ You can click into each track for a version/subset-specific description.

\ This collection includes numbered versions of the entire dbSNP datasets\ (All SNP) as well as three tracks with subsets of the items in that version. \ Here is information on each of the subsets:\

dbSNP 153: The dbSNP build 153 is composed of 5 subtracks. Click the track for\ a description of the subtracks.
Common SNPs: SNPs that have a minor allele frequency\ of at least 1% and are mapped to a single location in the reference\ genome assembly. Frequency data are not available for all SNPs,\ so this subset is incomplete.
Flagged SNPs: SNPs flagged as clinically associated by dbSNP, \ mapped to a single location in the reference genome assembly, and \ not known to have a minor allele frequency of at least 1%.\ Frequency data are not available for all SNPs, so this subset may\ include some SNPs whose true minor allele frequency is 1% or greater.
Mult. SNPs: SNPs that have been mapped to multiple locations\ in the reference genome assembly.

\ The default maximum weight for this track is 1, so unless\ the setting is changed in the track controls, SNPs that map to multiple genomic \ locations will be omitted from display. When a SNP's flanking sequences \ map to multiple locations in the reference genome, it calls into question \ whether there is true variation at those sites, or whether the sequences\ at those sites are merely highly similar but not identical.\

\ \

Interpreting and Configuring the Graphical Display

\ Variants are shown as single tick marks at most zoom levels.\ When viewing the track at or near base-level resolution, the displayed\ width of the SNP corresponds to the width of the variant in the reference\ sequence. Insertions are indicated by a single tick mark displayed between\ two nucleotides, single nucleotide polymorphisms are displayed as the width \ of a single base, and multiple nucleotide variants are represented by a \ block that spans two or more bases.\

\ \

\ On the track controls page, SNPs can be colored and/or filtered from the \ display according to several attributes:\

\ \ Class: Describes the observed alleles
\
- Single - single nucleotide variation: all observed alleles are single nucleotides\ \ (can have 2, 3 or 4 alleles)
- In-del - insertion/deletion
- Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
- Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats
- Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/-
- No Variation - the submission reports an invariant region in the surveyed sequence
- Mixed - the cluster contains submissions from multiple classes
- Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length > 1
- Insertion - the polymorphism is an insertion relative to the reference assembly
- Deletion - the polymorphism is a deletion relative to the reference assembly
- Unknown - no classification provided by data contributor
\
\ \ Validation: Method used to validate\ \ the variant (each variant may be validated by more than one method)
\
- By Frequency - at least one submitted SNP in cluster has frequency data submitted
- By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
- By Submitter - at least one submitter SNP in cluster was validated by independent assay
- By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
- By HapMap (human only) - submitted by\ HapMap project
- By 1000Genomes (human only) - submitted by\ \ 1000Genomes project
- Unknown - no validation has been reported for this variant
\
\ \ Function: dbSNP's predicted functional effect of variant on RefSeq transcripts,\ both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\ not shown in UCSC Genome Browser.\ A variant may have more than one functional role if it overlaps\ multiple transcripts.\ These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the\ MISO Sequence Ontology Browser.
\
- Unknown - no functional classification provided (possibly intergenic)
- synonymous_variant -\ \ A sequence variant where there is no resulting change to the encoded amino acid\ \ (dbSNP term: coding-synon)
- intron_variant -\ \ A transcript variant occurring within an intron\ \ (dbSNP term: intron)
- downstream_gene_variant -\ \ A sequence variant located 3' of a gene\ \ (dbSNP term: near-gene-3)
- upstream_gene_variant -\ \ A sequence variant located 5' of a gene\ \ (dbSNP term: near-gene-5)
- nc_transcript_variant -\ \ A transcript variant of a non coding RNA gene\ \ (dbSNP term: ncRNA)
- stop_gained -\ \ A sequence variant whereby at least one base of a codon is changed, resulting in\ \ a premature stop codon, leading to a shortened transcript\ \ (dbSNP term: nonsense)
- missense_variant -\ \ A sequence variant, where the change may be longer than 3 bases, and at least\ \ one base of a codon is changed resulting in a codon that encodes for a\ \ different amino acid\ \ (dbSNP term: missense)
- stop_lost -\ \ A sequence variant where at least one base of the terminator codon (stop)\ \ is changed, resulting in an elongated transcript\ \ (dbSNP term: stop-loss)
- frameshift_variant -\ \ A sequence variant which causes a disruption of the translational reading frame,\ \ because the number of nucleotides inserted or deleted is not a multiple of three\ \ (dbSNP term: frameshift)
- inframe_indel -\ \ A coding sequence variant where the change does not alter the frame\ \ of the transcript\ \ (dbSNP term: cds-indel)
- 3_prime_UTR_variant -\ \ A UTR variant of the 3' UTR\ \ (dbSNP term: untranslated-3)
- 5_prime_UTR_variant -\ \ A UTR variant of the 5' UTR\ \ (dbSNP term: untranslated-5)
- splice_acceptor_variant -\ \ A splice variant that changes the 2 base region at the 3' end of an intron\ \ (dbSNP term: splice-3)
- splice_donor_variant -\ \ A splice variant that changes the 2 base region at the 5' end of an intron\ \ (dbSNP term: splice-5)
\ In the Coloring Options section of the track controls page,\ function terms are grouped into several categories, shown here with default colors:\
- Locus:\ \ downstream_gene_variant,\ \ upstream_gene_variant
- Coding - Synonymous:\ \ synonymous_variant\ \
- Coding - Non-Synonymous:\ \ stop_gained,\ \ missense_variant,\ \ stop_lost,\ \ frameshift_variant,\ \ inframe_indel
- Untranslated:\ \ 5_prime_UTR_variant,\ \ 3_prime_UTR_variant
- Intron:\ \ intron_variant
- Splice Site:\ \ splice_acceptor_variant,\ \ splice_donor_variant\
\
\ \ Molecule Type: Sample used to find this variant
\
- Genomic - variant discovered using a genomic template
- cDNA - variant discovered using a cDNA template
- Unknown - sample type not known
\
\ \ Unusual Conditions (UCSC): UCSC checks for several anomalies \ that may indicate a problem with the mapping, and reports them in the \ Annotations section of the SNP details page if found:\
- AlleleFreqSumNot1 - Allele frequencies do not sum\ to 1.0 (+-0.01). This SNP's allele frequency data are\ \ probably incomplete.
- DuplicateObserved,\ MixedObserved - Multiple distinct insertion SNPs have \ \ been mapped to this location, with either the same inserted \ \ sequence (Duplicate) or different inserted sequence (Mixed).
- FlankMismatchGenomeEqual,\ \ FlankMismatchGenomeLonger,\ \ FlankMismatchGenomeShorter - NCBI's alignment of\ the flanking sequences had at least one mismatch or gap\ \ near the mapped SNP position.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- MultipleAlignments - This SNP's flanking sequences \ align to more than one location in the reference assembly.
- NamedDeletionZeroSpan - A deletion (from the\ genome) was observed but the annotation spans 0 bases.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- NamedInsertionNonzeroSpan - An insertion (into the\ genome) was observed but the annotation spans more than 0\ bases. (UCSC's re-alignment of flanking sequences to the\ genome may be informative.)
- NonIntegerChromCount - At least one allele\ frequency corresponds to a non-integer (+-0.010000) count of\ chromosomes on which the allele was observed. The reported\ total sample count for this SNP is probably incorrect.
- ObservedContainsIupac - At least one observed allele \ from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N).
- ObservedMismatch - UCSC reference allele does not\ match any observed allele from dbSNP. This is tested only\ \ for SNPs whose class is single, in-del, insertion, deletion,\ \ mnp or mixed.
- ObservedTooLong - Observed allele not given (length\ too long).
- ObservedWrongFormat - Observed allele(s) from dbSNP\ have unexpected format for the given class.
- RefAlleleMismatch - The reference allele from dbSNP\ does not match the UCSC reference allele, i.e., the bases in\ \ the mapped position range.
- RefAlleleRevComp - The reference allele from dbSNP\ matches the reverse complement of the UCSC reference\ allele.
- SingleClassLongerSpan - All observed alleles are\ single-base, but the annotation spans more than 1 base.\ (UCSC's re-alignment of flanking sequences to the genome may\ be informative.)
- SingleClassZeroSpan - All observed alleles are\ single-base, but the annotation spans 0 bases. (UCSC's\ re-alignment of flanking sequences to the genome may be\ informative.)
\ Another condition, which does not necessarily imply any problem,\ is noted:\
- SingleClassTriAllelic, SingleClassQuadAllelic - \ Class is single and three or four different bases have been\ \ observed (usually there are only two).
\
\ \ Miscellaneous Attributes (dbSNP): several properties extracted\ from dbSNP's SNP_bitfield table\ (see dbSNP_BitField_v5.pdf for details)\
- Clinically Associated (human only) - SNP is in OMIM and/or at \ \ least one submitter is a Locus-Specific Database. This does\ \ not necessarily imply that the variant causes any disease,\ \ only that it has been observed in clinical studies.
- Appears in OMIM/OMIA - SNP is mentioned in \ \ Online Mendelian Inheritance in Man for \ \ human SNPs, or Online Mendelian Inheritance in Animals for \ \ non-human animal SNPs. Some of these SNPs are quite common,\ \ others are known to cause disease; see OMIM/OMIA for more\ \ information.
- Has Microattribution/Third-Party Annotation - At least\ \ one of the SNP's submitters studied this SNP in a biomedical\ \ setting, but is not a Locus-Specific Database or OMIM/OMIA.
- Submitted by Locus-Specific Database - At least one of\ \ the SNP's submitters is associated with a database of variants\ \ associated with a particular gene. These variants may or may\ \ not be known to be causative.
- MAF >= 5% in Some Population - Minor Allele Frequency is \ \ at least 5% in at least one population assayed.
- MAF >= 5% in All Populations - Minor Allele Frequency is \ \ at least 5% in all populations assayed.
- Genotype Conflict - Quality check: different genotypes \ \ have been submitted for the same individual.
- Ref SNP Cluster has Non-overlapping Alleles - Quality\ \ check: this reference SNP was clustered from submitted SNPs\ \ with non-overlapping sets of observed alleles.
- Some Assembly's Allele Does Not Match Observed - \ \ Quality check: at least one assembly mapped by dbSNP has an allele\ at the mapped position that is not present in this SNP's observed\ alleles.
\

\ Several other properties do not have coloring options, but do have \ some filtering options:\

\ \ Average heterozygosity: Calculated by dbSNP as described in \ \ Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters.\
- Average heterozygosity should not exceed 0.5 for bi-allelic \ single-base substitutions.
\
\ \ Weight: Alignment quality assigned by dbSNP
\
- Weight can be 0, 1, 2, 3 or 10.
- Weight = 1 are the highest quality alignments.
- Weight = 0 and weight = 10 are excluded from the data set.
- A filter on maximum weight value is supported, which defaults to 1\ on all tracks except the Mult. SNPs track, which defaults to 3.
\
\ \ Submitter handles: These are short, single-word identifiers of\ labs or consortia that submitted SNPs that were clustered into this\ reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs\ have been observed by many different submitters, and some by only a\ single submitter (although that single submitter may have tested a\ large number of samples).\
\ \ AlleleFrequencies: Some submissions to dbSNP include \ allele frequencies and the study's sample size \ (i.e., the number of distinct chromosomes, which is two times the\ number of individuals assayed, a.k.a. 2N). dbSNP combines all\ available frequencies and counts from submitted SNPs that are \ clustered together into a reference SNP.\

\ \

\ You can configure this track such that the details page displays\ the function and coding differences relative to \ particular gene sets. Choose the gene sets from the list on the SNP \ configuration page displayed beneath this heading: On details page,\ show function and coding differences relative to. \ When one or more gene tracks are selected, the SNP details page \ lists all genes that the SNP hits (or is close to), with the same keywords \ used in the function category. The function usually \ agrees with NCBI's function, except when NCBI's functional annotation is \ relative to an XM_* predicted RefSeq (not included in the UCSC Genome \ Browser's RefSeq Genes track) and/or UCSC's functional annotation is \ relative to a transcript that is not in RefSeq.\

\ \

Insertions/Deletions

\ \

UCSC Re-alignment of flanking sequences

\ dbSNP determines the genomic locations of SNPs by aligning their flanking \ sequences to the genome.\ UCSC displays SNPs in the locations determined by dbSNP, but does not\ have access to the alignments on which dbSNP based its mappings.\ Instead, UCSC re-aligns the flanking sequences \ to the neighboring genomic sequence for display on SNP details pages. \ While the recomputed alignments may differ from dbSNP's alignments,\ they often are informative when UCSC has annotated an unusual condition.\

\ Non-repetitive genomic sequence is shown in upper case like the flanking \ sequence, and a "|" indicates each match between genomic and flanking bases.\ Repetitive genomic sequence (annotated by RepeatMasker and/or the\ Tandem Repeats Finder with period <= 12) is shown in lower case, and matching\ bases are indicated by a "+".\

\ \

Data Sources and Methods

\ \

\ The data that comprise this track were extracted from database dump files \ and headers of fasta files downloaded from NCBI. \ The database dump files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/database/\ (for human, organism_tax_id = human_9606;\ for mouse, organism_tax_id = mouse_10090).\ The fasta files were downloaded from \ ftp://ftp.ncbi.nih.gov/snp/organisms/\ organism_tax_id/rs_fasta/\

Coordinates, orientation, location type and dbSNP reference allele data\ were obtained from files like b138_SNPContigLoc.bcp.gz and \ b138_ContigInfo.bcp.gz.
b138_SNPMapInfo.bcp.gz provides the alignment weights.\
Functional classification was obtained from files like \ b138_SNPContigLocusId.bcp.gz. The internal database representation\ uses dbSNP's function terms, but for display in SNP details pages,\ these are translated into\ Sequence Ontology terms.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies.\ For the human assembly, allele frequencies were also taken from\ SNPAlleleFreq_TGP.bcp.gz .
Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and \ SNPSubSNPLink.bcp.gz.
SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP,\ such as clinically-associated. See the document \ dbSNP_BitField_v5.pdf for details.
The header lines in the rs_fasta files were used for molecule type,\ class and observed polymorphism.

\ \

Data Access

\ Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies,\ and more information about how to convert SNPs between assemblies can be found on the following\ FAQ entry.

\ The raw data can be explored interactively with the \ Table Browser,\ Data Integrator, or \ Variant Annotation Integrator.\ For automated analysis, the genome annotation files can be downloaded in their entirety for \ hg38,\ hg19, \ and mm10 as\ (snp*.txt.gz). \ You can also make queries using the UCSC Genome Browser \ JSON API or \ public MySQL server. Please refer to our \ mailing list archives\ for questions and example queries, or our \ Data Access FAQ for more information.\

\ \

Orthologous Alleles (human assemblies only)

\ For the human assembly, we provide a related table that contains\ orthologous alleles in the chimpanzee, orangutan and rhesus macaque\ reference genome assemblies. \ We use our liftOver utility to identify the orthologous alleles. \ The candidate human SNPs are a filtered list that meet the criteria:\

class = 'single'
mapped position in the human reference genome is one base long
aligned to only one location in the human reference genome
not aligned to a chrN_random chrom
biallelic (not tri- or quad-allelic)

\ \ In some cases the orthologous allele is unknown; these are set to 'N'.\ If a lift was not possible, we set the orthologous allele to '?' and the \ orthologous start and end position to 0 (zero).\ \

Masked FASTA Files (human assemblies only)

\ \ FASTA files that have been modified to use \ IUPAC\ ambiguous nucleotide characters at\ each base covered by a single-base substitution are available for download in the\ genome's snp*Mask folder.\ Note that only single-base substitutions (no insertions or deletions) were used\ to mask the sequence, and these were filtered to exlcude problematic SNPs.\ \

References

\ Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \ dbSNP: the NCBI database of genetic variation.\ Nucleic Acids Res. 2001 Jan 1;29(1):308-11.\ PMID: 11125122; PMC: PMC29783\

\ varRep 1 cartVersion 3\ group varRep\ html ../../dbSnpArchive\ longLabel dbSNP Track Archive\ maxWindowToDraw 10000000\ shortLabel dbSNP Archive\ superTrack on\ track dbSnpArchive\ type bed 6 +\ url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$\ urlLabel dbSNP:\ dbVarSv dbVar Common Struct Var NCBI Curated Common Structural Variants from dbVar 0 100 0 0 0 127 127 127 0 0 0

Description

\ The tracks listed here contain data from the\ \ nstd186 (NCBI Curated Common Structural Variants) study. This is a collection of structural\ variants (SV) originally submitted to dbVar which are part of a study with at least 100 samples and\ have an allele frequency of >=0.01 in at least one population. The complete dataset is imported\ from these common-population studies:\

\ \

\ gnomAD Structural Variants\ (nstd166):\ Catalog of SVs detected from the sequencing of the complete genome of 10,847 unrelated\ individuals from the GnomAD v2.1 release.

\ 1000 Genomes Consortium Phase 3 Integrated SV\ (estd219):\ Structural variants of the 1000 Genomes project Phase 3 as reported in a separate article\ specifically dedicated to the analysis of SVs. Many of these data are identical to those reported\ in the estd214 study.

\ DECIPHER Common CNVs\ (nstd183):\ Consensus set of common population CNVs selected from high-resolution controls sets where frequency\ information is available.\

\ \

\ There are two tracks in this collection:\

\ NCBI dbVar Curated Common Structural Variants (dbVar Common SV): Shows copy number\ variants calls (variants >=50 nucleotides) from the nstd186 study.
\ NCBI dbVar Curated Conflict Variants (dbVar Conflict SV): Shows copy number\ variants from nstd186\ (NCBI Curated Common Structural Variants) that overlap with\ nstd102 (Clinical\ Structural Variants).

\ It only includes copy number gain, copy number loss, copy number variation, duplications, and\ deletions (including mobile element deletions), that are part of a study with at least 100 samples,\ include allele frequency data, and have an allele frequency of >=0.01 in at least one population.\

\ \

\ For more information on the number of variant calls and latest statistics for nstd186 see\ Summary of nstd186\ (NCBI Curated Common Structural Variants).\

\ \

\ There are six subtracks in this track set:\

\ \

NCBI Curated Common SVs: African - \ Variants with AF >= 0.01 for \ African Population.
NCBI Curated Common SVs: European -\ Variants with AF >= 0.01 for \ European Population.
NCBI Curated Common SVs: all populations -\ Variants with AF >= 0.01 for \ Global Population.
NCBI Curated Common SVs: all populations from gnomAD - \ Variants with AF >= 0.01 from \ gnomAD Structural Variants.
NCBI Curated Common SVs: all populations from 1000 Genomes - \ Variants with AF >= 0.01 from \ 1000 Genomes Consortium Phase 3 Integrated SV.
NCBI Curated Common SVs: all populations from DECIPHER -\ Variants with AF >= 0.01 from \ DECIPHER Consensus CNVs.

\ \

Display Conventions and Configuration

\ Items in all subtracks follow the same conventions: items are colored by variant type, and are \ based on the dbVar colors described in the \ dbVar Overview page. \ Red for copy number loss or deletion,\ blue for copy number gain or duplication, and\ violet for copy number variation. \

\ \

\ Mouseover on items indicates genes affected, size, variant type, and allele frequencies (AF). \ All tracks can be filtered according to the Variant Size and Variant Type.\

\ \

Data Access

\ The raw data can be explored interactively with the\ Table Browser, or the\ Data Integrator. For automated analysis,\ the data may be queried from our\ REST API. \

\ \ \

Credits

\ Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical \ coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter, of \ the Genome Browser team for engineering the track display. \

\ \

References

\ \ \ varRep 1 compositeTrack on\ filterLabel.length Variant Size\ filterLabel.type Variant Type\ filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB\ filterValues.type alu deletion,copy number gain,copy number loss,copy number variation,deletion,duplication,herv deletion,line1 deletion,sva deletion\ group varRep\ html dbVarCommon\ itemRgb on\ longLabel NCBI dbVar Curated Common Structural Variants\ mouseOverField label\ searchIndex name\ shortLabel dbVar Common SV\ superTrack dbVarSv pack\ track dbVar_common\ type bigBed 9 + .\ visibility pack\ dbVar_conflict dbVar Conflict SV bigBed 9 + . NCBI dbVar Curated Conflict Variants 3 100 0 0 0 127 127 127 0 0 0

Description

\ The track NCBI dbVar Curated Common SVs: Conflicts with Pathogenic highlights loci where\ common copy number variants from\ nstd186 (NCBI Curated \ Common Structural Variants) overlap with structural Variants with clinical assertions,\ submitted to ClinVar by external labs (Clinical Structural \ Variants - nstd102).\

\ \

\ Overlap in the track refers to reciprocal overlap between variants in the common\ (NCBI Curated Common Structural Variants) versus clinical (ClinVar Long Variants)\ tracks. Reciprocal overlap values can be anywhere from 10% to 100%.\

\ \

\ For more information on the number of variant calls and latest statistics for nstd186 see\ Summary of nstd186\ (NCBI Curated Common Structural Variants).\

\ \

Display Conventions and Configuration

\ \

\ Items in all subtracks follow the same conventions: items are colored by variant type, and are\ based on the dbVar colors described in the\ dbVar Overview page.\ Red for copy number loss or deletion,\ blue for copy number gain or duplication, and\ violet for copy number variation. \

\ \

\ Mouseover on items indicates genes affected, size, variant type, and allele frequencies (AF). \ All tracks can be filtered according to the variant length, variant type and \ variant overlap. This last filter defines four bins within that range from which the \ user can choose.\

\ \ \

Data Access

\ The raw data can be explored interactively with the\ Table Browser, or the\ Data Integrator. For automated analysis,\ the data may be queried from our\ REST API.

\ \

\ The data can also be found directly from the dbVar \ nstd186 data access, as well as in the\ \ dbVar Track Hub, where additional subtracks are included. For questions about\ dbVar track data, please contact \ dbvar@ncbi.\ nlm.\ nih.\ gov.\ \

\ \ Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical \ coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter of \ the Genome Browser team for engineering the track display.\

\ \

References

\ \ varRep 1 compositeTrack on\ filterLabel.length Variant Length\ filterLabel.overlap Variant Overlap\ filterLabel.type Variant Type\ filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB\ filterValues.overlap 10 to 25,25 to 50,50 to 75,75 to 90,90 to 100\ filterValues.type alu deletion,copy number gain,copy number loss,copy number variation,deletion,duplication,herv deletion,line1 deletion,sva deletion\ html dbVarConflict\ itemRgb on\ longLabel NCBI dbVar Curated Conflict Variants\ mouseOverField label\ searchIndex name\ shortLabel dbVar Conflict SV\ superTrack dbVarSv pack\ track dbVar_conflict\ type bigBed 9 + .\ visibility pack\ decipher DECIPHER CNVs bigBed 9 + DECIPHER CNVs 0 100 0 0 0 127 127 127 0 0 0 https://www.deciphergenomics.org/patient/$$

Description

\ \

NOTE:
\ While the DECIPHER database is \ open to the public, users seeking information about a personal medical or\ genetic condition are urged to consult with a qualified physician for\ diagnosis and for answers to personal questions.\

Because the UCSC Genes mappings for CNVs are based on associations from\ RefSeq and UniProt, they are dependent on any interpretations from those\ sources. Furthermore, because many DECIPHER records refer to multiple gene\ names, or syndromes not tightly mapped to individual genes, the associations\ in this track should be treated with skepticism and any conclusions\ based on them should be carefully scrutinized using independent\ resources.\

Data Display Agreement Notice
\ These data are only available for display in the Browser, and not for bulk\ download. Access to bulk data may be obtained directly from DECIPHER\ (https://www.deciphergenomics.org/about/data-sharing) and is subject to a\ Data Access Agreement, in which the user certifies that no attempt to\ identify individual patients will be undertaken. The same restrictions\ apply to the public data displayed at UCSC in the UCSC Genome Browser;\ no one is authorized to attempt to identify patients by any means.\

These data are made available as soon as possible and may be a\ pre-publication release. For information on the proper use of DECIPHER\ data, please see https://www.deciphergenomics.org/about/data-sharing.\

The DECIPHER consortium provides these data in good faith as a research\ tool, but without verifying the accuracy, clinical validity, or utility of\ the data. The DECIPHER consortium makes no warranty, express or implied,\ nor assumes any legal liability or responsibility for any purpose for\ which the data are used.\

\ \

\ The \ DECIPHER\ database of submicroscopic chromosomal imbalance \ collects clinical information about chromosomal \ microdeletions/duplications/insertions, translocations and inversions, \ and displays this information on the human genome map.\

\ This track shows genomic regions of reported cases and their \ associated phenotype information. All data have passed the strict\ consent requirements of the DECIPHER project and are approved for\ unrestricted public release. Clicking the Patient View ID link\ brings up a more detailed informational page on the patient at the \ DECIPHER web site. \ \

Display Conventions and Configuration

\ The genomic locations of DECIPHER variants are labeled with the DECIPHER variant descriptions. \ Mouseover on items shows variant details, clinical interpretation, and associated conditions. \ Further information on each variant is displayed on the details page by a click onto any variant. \

\ \

\ For the CNVs track, the entries are colored by the type of variant:\

red for loss
blue for gain
grey for amplification

\ \

\ A light-to-dark color gradient indicates the clinical significance of each variant, with \ the lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the \ CNV color code is described here.\ Items can be filtered according to the size of the variant, variant type, and clinical significance \ using the track Configure options.\

\ \

\ For the SNVs track, the entries are colored according to the estimated clinical significance \ of the variant:\

black for likely or definitely pathogenic
dark grey for uncertain or unknown
light grey for likely or definitely benign

\ \

Method

\ Data provided by the DECIPHER project group are imported and processed\ to create a simple BED track to annotate the genomic regions associated\ with individual patients.\

\ \ \

Contact

\ For more information on DECIPHER, please contact\ \ contact@deciphergenomics.\ org\

\ \

References

\ Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM,\ Carter NP.\ \ DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.\ Am J Hum Genet. 2009 Apr;84(4):524-33.\ PMID: 19344873; PMC: PMC2667985\

\ phenDis 1 bigDataUrl /gbdb/hg38/decipher/decipherCnv.bb\ filter.size 0\ filterByRange.size on\ filterLimits.size 2:170487333\ filterValues.pathogenicity Benign,Likely Benign,Likely Pathogenic,Pathogenic,Uncertain,Unknown\ filterValues.variant_class Amplification,Copy-Number Gain,Deletion,Duplication,Duplication/Trip\ group phenDis\ html decipher\ itemRgb on\ longLabel DECIPHER CNVs\ mergeSpannedItems on\ mouseOverField _mouseOvera\ searchIndex name\ shortLabel DECIPHER CNVs\ tableBrowser off knownCanonToDecipher knownToDecipher decipherRaw\ track decipher\ type bigBed 9 +\ url https://www.deciphergenomics.org/patient/$$\ urlLabel Decipher Patient View:\ visibility hide\ decipherSnvs DECIPHER SNVs bed 4 DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs) 0 100 0 0 0 127 127 127 0 0 0

Description

\ \

Display Conventions and Configuration

\ \

\ For the CNVs track, the entries are colored by the type of variant:\

red for loss
blue for gain
grey for amplification

\ \

\ For the SNVs track, the entries are colored according to the estimated clinical significance \ of the variant:\

black for likely or definitely pathogenic
dark grey for uncertain or unknown
light grey for likely or definitely benign

\ \

Method

\ Data provided by the DECIPHER project group are imported and processed\ to create a simple BED track to annotate the genomic regions associated\ with individual patients.\

\ \ \

Contact

\ The samples were analyzed using nine different CGH platforms with initial CNV calls filtered as\ described in Coe et al. (2014).\

\ \

\ Final CNV calls were decoupled from identifying information and submitted to dbVar as\ nstd54 and\ nstd100\ for unrestricted release.\

\ \

\ The 15,767 case individuals from the Cooper study comprise nstd54 sampleset 1, while the 8,329\ control individuals from the Cooper study comprise nstd54 samplesets 2-12. The 13,318 case\ individuals from the Coe study were combined with the Cooper case individuals to comprise nstd100\ sampleset 1. The 11,255 control individuals from the Coe study comprise nsdt100 samplesets 2 and 3.\

\ \

\ The Case subtrack was constructed using nstd100 sampleset 1. The Control subtrack was constructed by\ combining nstd100 samplesets 2 and 3 with nstd54 samplesets 2-12.\

\ \

Credits

\ \

\ We would like to thank Gregory Cooper, Brad Coe and the\ Eichler Lab at the University of\ Washington for providing the data for this track.\

\ \

References

\ \

\ Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C,\ Buono S, Vissers LE et al.\ \ Refining analyses of copy number variation identifies specific genes associated with developmental\ delay.\ Nat Genet. 2014 Oct;46(10):1063-71.\ PMID: 25217958; PMC: PMC4177294\

\ \

\ Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig\ V et al.\ \ A copy number variation morbidity map of developmental delay.\ Nat Genet. 2011 Aug 14;43(9):838-46.\ PMID: 21841781; PMC: PMC3171215\

\ phenDis 1 compositeTrack on\ group phenDis\ longLabel Copy Number Variation Morbidity Map of Developmental Delay\ noScoreFilter .\ shortLabel Development Delay\ track cnvDevDelay\ type gvf\ visibility hide\ dgvGold DGV Gold Standard bigBed 12 + Database of Genomic Variants: Gold Standard Variants 0 100 0 0 0 127 127 127 0 0 0 http://dgv.tcag.ca/gb2/gbrowse_details/dgv2_hg38?ref=$S;start=${;end=$};name=$$;class=Sequence varRep 1 bigDataUrl /gbdb/hg38/dgv/dgvGold.bb\ longLabel Database of Genomic Variants: Gold Standard Variants\ mouseOver ID:$name; Position; $chrom:${chromStart}-${chromEnd}; Type:$variant_sub_type; Frequency:$Frequency\ parent dgvPlus\ searchIndex name\ shortLabel DGV Gold Standard\ track dgvGold\ type bigBed 12 +\ url http://dgv.tcag.ca/gb2/gbrowse_details/dgv2_hg38?ref=$S;start=${;end=$};name=$$;class=Sequence\ dgvPlus DGV Struct Var bed 9 + Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del) 0 100 0 0 0 127 127 127 0 0 0 http://dgv.tcag.ca/dgv/app/variant?id=$$&ref=$D

Description

\ This track displays copy number variants (CNVs), insertions/deletions (InDels),\ inversions and inversion breakpoints annotated by the\ Database of Genomic Variants (DGV), which\ contains genomic variations observed in healthy individuals.\ DGV focuses on structural variation, defined as\ genomic alterations that involve segments of DNA that are larger than\ 1000 bp. Insertions/deletions of 50 bp or larger are also included.\

\ \

Display Conventions

\ This track contains three subtracks:\

Structural Variant Regions: annotations that have been generated from one or more reported\ structural variants at the same location.\
Supporting Structural Variants: the sample-level reported structural variants.\
Gold Standard Variants: curated variants from a selected number of studies in DGV.\

\ Color is used in both subtracks to indicate the type of variation:\

Inversions and\ inversion breakpoints are purple.\
CNVs and InDels are blue if there is a\ gain in size relative to the reference.\
CNVs and InDels are red if there is a\ loss in size relative to the reference.\
CNVs and InDels are brown if there are reports of\ both a loss and a gain in size\ relative to the reference.\

\ The DGV Gold Standard subtrack utilizes a boxplot-like display to represent the \ merging of records as explained in the Methods section below. In this track, the \ middle box (where applicable), represents the high confidence location of the CNV, \ while the thin lines and end boxes represent the possible range of the CNV.\

\ Clicking on a variant leads to a page with detailed information about the variant, \ such as the study reference and PubMed abstract link, the study's method and any\ genes overlapping the variant. Also listed, if available, are the sequencing or array platform\ used for the study, a sample cohort description, sample size, sample ID(s) in which\ the variant was observed, observed gains and observed losses.\ If the particular variant is a merged variant, links to genome browser views of \ the supporting variants are listed. If the particular variant is a supporting variant,\ a link to the genome browser view of its merged variant is displayed.\ A link to DGV's Variant Details page for each variant is also provided.\

\ For most variants, DGV uses accessions from peer archives of structural variation\ (dbVar\ at NCBI or DGVa at EBI).\ These accessions begin with either "essv",\ "esv", "nssv", or "nsv", followed by a number.\ Variant submissions processed by EBI begin with "e"\ and those processed by NCBI begin with "n".\

\ Accessions with ssv are for variant calls on a particular sample, and if they\ are copy number variants, they generally indicate whether the change is a gain\ or loss. \ In a few studies the ssv represents the variant called by a single\ algorithm. If multiple algorithms were used, overlapping ssv's from\ the same individual would be combined to generate a sample level\ sv. \

\ If there are many samples analyzed in a study, and if there are many\ samples which have the same variant, there will be multiple ssv's with\ the same start and end coordinates.\ These sample level variants are then merged and combined to form a\ representative variant that highlights the common variant found in\ that study. The result is called a structural variant (sv) record.\ Accessions with sv are for regions asserted by submitters to contain\ structural variants, and often span ssv elements for both losses and\ gains. dbVar and DGVa do not record numbers of losses and gains\ encompassed within sv regions.\

\ DGV merges clusters of variants that share at least 70% reciprocal\ overlap in size/location, and assigns an accession beginning with\ "dgv", followed by an internal variant serial number,\ followed by an abbreviated study id. For example,\ the first merged variant from the Shaikh et al. 2009 study (study\ accession=nstd21) would be dgv1n21. The second merged variant would be\ dgv2n21 and so forth.\ Since in this case there is an additional level of clustering,\ it is possible for an "sv" variant to be both a merged\ variant and a supporting variant.\

\ For most sv and dgv variants, DGV displays the total number of\ sample-level gains and/or losses at the bottom of their variant detail\ page. Since each ssv variant is for one sample, its total is 1.\

\ \

Methods

\ Published structural variants are imported from peer archives\ dbVar and\ DGVa.\ DGV then applies quality filters and merges overlapping variants.\

\ For data sets where the variation calls are reported at a\ sample-by-sample level, DGV merges calls with similar boundaries\ across the sample\ set. Only variants of the same type (i.e. CNVs, Indels, inversions)\ are merged, and gains and losses are merged separately.\ Sample level calls that overlap by ≥ 70% are merged in this\ process.\

\ The initial criteria for the Gold Standard set require that a variant \ is found in at least two different studies and found in at least two different \ samples. After filtering out low-quality variants, the remaining variants are \ clustered according to 50% minimum overlap, and then merged into a single \ record. Gains and losses are merged separately.

\ The highest ranking variant in the cluster defines the inner box, while the \ outer lines define the maximum possible start and stop coordinates of the CNV. \ In this way, the inner box forms a high-confidence CNV location and the \ thin connecting lines indicate confidence intervals for the location of CNV.

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser, or\ the Data Integrator. For automated access, this track, like all\ others, is available via our API. However, for bulk\ processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed\ file that can be downloaded from the\ download server.\ The exact filenames can be found in the track configuration file. Annotations can be converted to\ ASCII text by our tool bigBedToBed which can be compiled from the source code or\ downloaded as a precompiled binary for your system. Instructions for downloading source code and\ binaries can be found\ here. The tool can\ also be used to obtain only features within a given range, for example:

\ \

\
bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/hg38/dgv/dgvMerged.bb  -chrom=chr6 -start=0 -end=1000000 stdout\

\ \

Credits

\ Thanks to the Database of Genomic Variants for providing these data.\ In citing the Database of Genomic Variants please refer to MacDonald\ et al.\

\ \

References

\ Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C.\ \ Detection of large-scale variation in the human genome.\ Nat Genet. 2004 Sep;36(9):949-51.\ PMID: 15286789\

\ \

\ MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW.\ \ The Database of Genomic Variants: a curated collection of structural variation in the human\ genome.\ Nucleic Acids Res. 2014 Jan;42(Database issue):D986-92.\ PMID: 24174537; PMC: PMC3965079\

\ \

\ Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW.\ \ Development of bioinformatics resources for display and analysis of copy number and other structural\ variants in the human genome.\ Cytogenet Genome Res. 2006;115(3-4):205-14.\ PMID: 17124402\

\ \ varRep 1 compositeTrack on\ coriellUrlBase http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=\ dataVersion 2020-02-25\ exonArrows off\ exonNumbers off\ group varRep\ itemRgb on\ longLabel Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)\ noScoreFilter .\ shortLabel DGV Struct Var\ track dgvPlus\ type bed 9 +\ url http://dgv.tcag.ca/dgv/app/variant?id=$$&ref=$D\ urlLabel DGV Browser and Report:\ visibility hide\ dosageSensitivity Dosage Sensitivity bigBed 9 + 2 pHaplo and pTriplo dosage sensitivity map from Collins et al 2022 0 100 0 0 0 127 127 127 0 0 0

Description

\ \

\ This container track represents dosage sensitivity map data from Collins et al 2022. There are\ two tracks, one corresponding to the probability of haploinsufficiency (pHaplo) and \ one to the probability of triplosensitivity (pTriplo).

\ Rare copy-number variants (rCNVs) include deletions and duplications that occur \ infrequently in the global human population and can confer substantial risk for \ disease. Collins et al aimed to quantify the properties of haploinsufficiency (i.e., \ deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout \ the human genome by analyzing rCNVs from nearly one million individuals to construct a \ genome-wide catalog of dosage sensitivity across 54 disorders, which defined 163 dosage \ sensitive segments associated with at least one disorder. These segments were typically \ gene-dense and often harbored dominant dosage sensitive driver genes. An ensemble \ machine learning model was built to predict dosage sensitivity probabilities (pHaplo & \ pTriplo) for all autosomal genes, which identified 2,987 haploinsufficient and 1,559 \ triplosensitive genes, including 648 that were uniquely triplosensitive.\

\ \

Display Conventions and Configuration

\ \

\ Each of the tracks is displayed with a distinct item (bed track) covering the entire gene locus wherever \ a score was available. Clicking on an item provides a link to DECIPHER which contains the sensitivity scores as well as\ additional information. Mousing over the items will display the gene symbol, the ESNG ID for that gene, \ and the respective sensitivity score for the track rounded to two decimal places. Filters are \ also available to specify specific score thresholds to display for each of the tracks.

\ \

Coloring and Interpretation

\ \

\ Each of the tracks is colored based on standardized cutoffs for pHaplo and pTriplo as described by the\ authors:

\ pHaplo scores ≥0.86 indicate that the average effect sizes of deletions are as strong as \ the loss-of-function of genes known to be constrained against protein truncating variants (average OR≥2.7)\ (Karczewski et al., 2020). \ pHaplo scores ≥0.55 indicate an odds ratio ≥2.

\ pTriplo scores ≥0.94 indicate that the average effect sizes of deletions are as strong as\ the loss-of-function of genes known to be constrained against protein truncating variants (average OR≥2.7)\ (Karczewski et al., 2020).\ pHaplo scores ≥0.68 indicate an odds ratio ≥2.

\ Applying these cutoffs defined 2,987 haploinsufficient (pHaplo≥0.86) and 1,559\ triplosensitive (pTriplo≥0.94) genes with rCNV effect sizes comparable to loss-of-function\ of gold-standard PTV-constrained genes.

See below for a summary of the color scheme:

\ \

Dark red items - pHaplo ≥ 0.86
Bright red items - pHaplo < 0.86
Dark blue items - pTriplo ≥ 0.94
Bright blue items - pTriplo < 0.94

\ \

Methods

\ \

\ The data were downloaded from Zenodo which consisted of a 3-column file with\ gene symbols, pHaplo, and pTriplo scores. Since the data were created using\ GENCODEv19 models, the hg19 data was mapped using those coordinates by picking the earliest\ transcription start site of all of the respective gene transcripts and the furthest \ transcription end site. This leads to some gene boundaries that are not representative of a real\ transcript, but since the data are for gene loci annotations this maximum coverage was used.\ Finally, both scores were rounded to two decimal points for easier interpretation.

\ For hg38, we attempted to use updated gene positions using a few different datasets since \ gene symbols have been updated many times since GENCODEv19. A summary of the workflow\ can be seen below, with each subsequent step being used only for genes where mapping failed:

Gene symbols were mapped using MANE1.0. < 2000 items failed mapping here.
Mapping with GENCODEv45 was attempted.
Mapping with GENCODEv20 was attempted. At this point, 448 items were not mapped.
Finally, any missing items were lifted using the hg19 track. 19/448 items failed\ mapping due to their regions having been split from hg19 to hg38.

\ \

\ In summary, the hg19 track was mapped using the original GENCODEv19 mappings, and a series\ of steps were taken to map the hg38 gene symbols with updated coordinates. 19/18641 items\ could not be mapped and are missing from the hg38 tracks.

\ The complete \ makeDoc can be found online. This includes all of the track creation steps.

\ \

Data Access

\ \

\ For automated download and analysis, the genome annotation is stored at UCSC in bigBed\ files that can be downloaded from\ our download server.\ Individual regions or the whole genome annotation can be obtained using our tool \ bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\

\ bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/dosageSensitivityCollins2022/pHaploDosageSensitivity.bb stdout\
\

\ \

\ Please refer to our\ Data Access FAQ\ for more information.\

\ \

Credits

\ \

\ Thanks to DECIPHER for their support and assistance with the data. We would also like to \ thank Anna Benet-Pagès for suggesting and assisting in track development and interpretation.\

\ \

References

\ \

\ Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj LM,\ Ulirsch J et al.\ \ A cross-disorder dosage sensitivity map of the human genome.\ Cell. 2022 Aug 4;185(16):3041-3055.e25.\ PMID: 35917817; PMC: PMC9742861\

\ phenDis 1 compositeTrack on\ group phenDis\ html dosageSensitivityCollins2022\ itemRgb on\ longLabel pHaplo and pTriplo dosage sensitivity map from Collins et al 2022\ noParentConfig on\ shortLabel Dosage Sensitivity\ track dosageSensitivity\ type bigBed 9 + 2\ visibility hide\ cons470wayViewphastcons Element Conservation (phastCons) bed 4 Multiz Alignment & Conservation (470 mammals) 0 100 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Multiz Alignment & Conservation (470 mammals)\ parent cons470way\ shortLabel Element Conservation (phastCons)\ track cons470wayViewphastcons\ view phastcons\ visibility hide\ epdNew EPDnew Promoters bigBed 8 Promoters from EPDnew 0 100 0 0 0 127 127 127 0 0 0

Description

\ \

\ \

\ Items are shaded according to manufacturing company:\

IDT (Integrated DNA Technologies)
Twist Biosciences
MGI Tech (Beijing Genomics Institute)
Roche NimbleGen
Agilent Technologies
Illumina

\ \

\ Tracks labeled as Probes (P) indicate the footprint of the oligonucleotide probes\ mapped to the human genome. This is the technically relevant targeted region by the assay. However, \ the sequenced region will be bigger than this since flanking sequences are sequenced as well. \ Tracks labeled as Target Regions (T) indicate the genomic regions targeted by the\ assay. This is the biologically relevant target region. Not all targeted regions\ will necessarily be sequenced perfectly; there might be some capture bias at certain locations.\ The Target\ Regions are those normally used for coverage analysis. \

\ \

Note that most exome probesets are available on hg19 only. If you are working with hg38 and cannot find\ a particular probeset there, try to go to hg19, configure the same track, and\ see if it exists there. If you cannot find an array, do not hesitate to send us\ an email with the name of the manufacturer website with the probe file. If\ an array is available on hg19 but not on hg38 and you need it for your work, we\ can lift the locations. Our mailing list can be reached at genome@soe.ucsc.edu.\

\ \

Methods

\ \

\ The capture of the genomic regions of interest using in-solution capture, is achieved \ through the hybridization of a set of probes (oligonucleotides) with a sample of fragmented genomic \ DNA in a solution environment. The probes hybridize selectively to the genomic regions of interest \ which, after a process of exclusion of the non-selective DNA material, can be pulled down and \ sequenced, enabling selective DNA sequencing of the genomic regions of interest (e.g., exons).\ In-solution capture sequencing is a sensitive method to detect single nucleotide variants, \ insertions and deletions, and copy number variations.\

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
Kit Targeted Region Databases Used for Design Year of Release
IDT - xGen Exome Research Panel V1.0 39 Mb Coding sequences from RefSeq (19,396 genes) 2015
IDT - xGen Exome Research Panel V2.0 34 Mb Coding sequences from RefSeq 109 (19,433 genes) 2020
Twist - RefSeq Exome Panel 3.6 Mb Curated subset of protein coding genes from CCDS N/A
Twist - Core Exome Panel 33 Mb Protein coding genes from CCDS N/A
Twist - Comprehensive Exome Panel 36.8 Mb Protein coding genes from RefSeq, CCDS, and GENCODE 2020
Twist - Exome Panel 2.0 36.4 Mb Protein coding genes from RefSeq, CCDS, and GENCODE 2021
MGI - Easy Exome Capture V4 59 Mb CCDS, GENCODE, RefSeq, and miRBase N/A
MGI - Easy Exome Capture V5 69 Mb CCDS, GENCODE, RefSeq, miRBase, and MGI Clinical Database N/A
Agilent - SureSelect Clinical Research Exome 54 Mb Disease-associated regions from OMIM, HGMD, and ClinVar 2014
Agilent - SureSelect Clinical Research Exome V2 63.7 Mb Disease-associated regions from OMIM, HGMD, ClinVar, and ACMG 2017
Agilent - SureSelect Focused Exome 12 Mb Disease-associated regions from HGMD, OMIM and ClinVar 2016
Agilent - SureSelect All Exon V4 51 Mb Coding regions from CCDS, RefSeq, and GENCODE v6, miRBase v17, TCGA v6, and UCSC known genes 2011
Agilent - SureSelect All Exon V4 + UTRs 71 Mb Coding regions and 5' and 3' UTR sequences from CCDS, RefSeq, and GENCODE v6, regions from miRBase v17, TCGA v6, and UCSC known genes 2011
Agilent - SureSelect All Exon V5 50 Mb Coding regions from Refseq, GENCODE, UCSC, TCGA, CCDS, and miRBase (21.522 genes) 2012
Agilent - SureSelect All Exon V5 + UTRs 74 Mb Coding regions and 5' and 3' UTR sequences from Refseq, GENCODE, UCSC, TCGA, CCDS, and miRBase (21.522 genes) 2012
Agilent - SureSelect All Exon V6 r2 60 Mb Coding regions from RefSeq, CCDS, GENCODE, HGMD, and OMIM 2016
Agilent - SureSelect All Exon V6 + COSMIC r2 66 Mb Coding regions from RefSeq, CCDS, GENCODE, HGMD, and OMIM, and targets from both TCGA and COSMIC 2016
Agilent - SureSelect All Exon V6 + UTR r2 75 Mb Coding regions and 5' and 3' UTR sequences from RefSeq, GENCODE, CCDS, and UCSC known genes,and miRNAs and lncRNA sequences 2016
Agilent - SureSelect All Exon V7 35.7 Mb Coding regions from RefSeq, CCDS, GENCODE, and UCSC known genes 2018
Roche - KAPA HyperExome 43Mb Coding regions from CCDS, RefSeq, Ensembl, GENCODE,and variants from ClinVar 2020
Roche - SeqCap EZ Exome V3 64 Mb Coding regions from RefSeq RefGene CDS, CCDS, and miRBase v14 databases, plus coverage of 97% Vega, 97% Gencode, and 99% Ensembl 2018
Roche - SeqCap EZ Exome V3 + UTR 92 Mb Coding sequences from RefSeq RefGene, CCDS, and miRBase v14, plus coverage of 97% Vega, 97% Gencode, and 99% Ensembl and UTRs from RefSeq RefGene table from UCSC GRCh37/hg19 March 2012 and Ensembl (GRCh37 v64) 2018
Roche - SeqCap EZ MedExome 47 Mb Coding sequences from CCDS 17, RefSeq, Ensembl 76, VEGA 56, GENCODE 20, miRBase 21, and disease-associated regions from GeneTests, ClinVar, and based on customer input 2014
Roche - SeqCap EZ MedExome + Mito 47 Mb Coding sequences and mitochondrial genes from CCDS 17, RefSeq, Ensembl 76, VEGA 56, GENCODE 20 and miRBase 21, disease-associated regions from GeneTests, ClinVar, and based on customer input 2014
Illumina - Nextera DNA Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v19 2015
Illumina - Nextera Rapid Capture Exome 37 Mb 212,158 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19 2013
Illumina - Nextera Rapid Capture Exome V1.2 37 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v12 2014
Illumina - Nextera Rapid Capture Expanded Exome 66 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v12 2013
Illumina - TruSeq DNA Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, and Ensembl 2017
Illumina - TruSeq Rapid Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENECODE v19 2015
Illumina - TruSight ONE V1.1 12 Mb Coding regions of 6700 genes from HGMD, OMIM, and GeneTest 2017
Illumina - TruSight Exome 7 Mb Disease-causing mutations as curated by HGMD 2017
Illumina - AmpliSeq Exome Panel N/A CCDS coding regions 2019
\ \

Data Access

\ The raw data can be explored interactively with the Table Browser\ or cross-referenced with Data Integrator. The data can be\ accessed from scripts through our API, with track names\ found in the Table Schema page for each subtrack after "Primary Table:".\ \

\ For downloading the data, the annotations are stored in bigBed files that\ can be accessed at\ \ our download directory. \ Regional or the whole genome text annotations can be obtained using our utility \ bigBedToBed. Instructions for downloading utilities can be found\ here.\

\ \

Credits

\ \

\ Thanks to Illumina (U.S.), Roche NimbleGen, Inc. (U.S.), Agilent Technologies (U.S.), MGI Tech\ (Beijing Genomics Institute, China), Twist Bioscience (U.S.), and Integrated DNA Technologies (IDT),\ Inc. (U.S.) for making these data available and to Tiana Pereira, Pranav Muthuraman, Began Nguy\ and Anna Benet-Pages for enginering these tracks.\

\ \ \ \ map 1 allButtonPair on\ compositeTrack on\ group map\ longLabel Exome Capture Probesets and Targeted Region\ shortLabel Exome Probesets\ track exomeProbesets\ type bigBed\ visibility hide\ fantom5 FANTOM5 FANTOM5: Mapped transcription start sites (TSS) and their usage 0 100 0 0 0 127 127 127 0 0 0

Description

\ \

Display Conventions and Configuration

\ \

Items in this track are colored according to their strand orientation. Blue\ indicates alignment to the negative strand, and red indicates\ alignment to the positive strand.\

\ \

Methods

Protocol

hCAGE
LQhCAGE

Samples

Primary cell
Tissue
Cell Line
Time course
Fractionation

TSS peaks

TSS (CAGE) peaks\
- the robust peaks
\
TSS summary profiles\
- Total counts and TPM (tags per million) in all the samples
- Maximum counts and TPM among the samples
\

\ \

TSS activity

\ \

Categories of individual samples: - Cell Line hCAGE; - Cell Line LQhCAGE; - fractionation hCAGE; - Primary cell hCAGE; - Primary cell LQhCAGE; - Time course hCAGE; - Tissue hCAGE

\ \

Data Access

\ \

\ \ \ \ \ singleCell 1 barChartBars F M\ barChartColors #dbb410 #e6ba08\ barChartLimit 2\ barChartMetric mean\ barChartStatsUrl /gbdb/hg38/bbi/fetalGeneAtlas/sex.stats\ barChartUnit UMI/cell\ bigDataUrl /gbdb/hg38/bbi/fetalGeneAtlas/sex.bb\ defaultLabelFields name2\ html fetalGeneAtlas\ labelFields name,name2\ longLabel Fetal Gene Atlas binned by sex from Cao et al 2020\ parent fetalGeneAtlas\ shortLabel Fetal Sex\ track fetalGeneAtlasSex\ transformFunc NONE\ url https://cells.ucsc.edu/?ds=fetal-gene-atlas+all&gene=$$\ urlLabel View on the UCSC Cell Browser:\ visibility hide\ fishClones FISH Clones bed 5 + Clones Placed on Cytogenetic Map Using FISH 0 100 0 150 0 127 202 127 0 0 0

Description

\ This track shows the location of fluorescent in situ hybridization \ (FISH)-mapped clones along the assembly sequence. The locations of\ these clones were obtained from the NCBI Human BAC Resource\ here. Earlier versions of this track obtained this\ information directly from the paper Cheung, et al. (2001).\

\ \

\ More information about the BAC clones, including how they may be obtained, \ can be found at the \ Human BAC Resource and the \ Clone Registry web sites hosted by \ NCBI.\ To view Clone Registry information for a clone, click on the clone name at \ the top of the details page for that item.

\ \

Using the Filter

\ This track has a filter that can be used to change the color or \ include/exclude the display of a dataset from an individual lab. This is \ helpful when many items are shown in the track display, especially when only \ some are relevant to the current task. The filter is located at the top of \ the track description page, which is accessed via the small button to the \ left of the track's graphical display or through the link on the track's \ control menu. To use the filter:\

In the pulldown menu, select the lab whose data you would like to \ highlight or exclude in the display. \
Choose the color or display characteristic that will be used to highlight \ or include/exclude the filtered items. If "exclude" is chosen, the \ browser will not display clones from the lab selected in the pulldown list. \ If "include" is selected, the browser will display clones only \ from the selected lab.\

\ When you have finished configuring the filter, click the Submit \ button.

\ \

Credits

\ We would like to thank all of the labs that have contributed to this resource:\

\ \

References

\ map 1 color 0,150,0,\ group map\ longLabel Clones Placed on Cytogenetic Map Using FISH\ origAssembly hg18\ pennantIcon 18.jpg ../goldenPath/help/liftOver.html "lifted from hg18"\ shortLabel FISH Clones\ superTrack assemblyContainer pack\ track fishClones\ type bed 5 +\ visibility hide\ gap Gap bed 3 + Gap Locations 0 100 0 0 0 127 127 127 0 0 0

Description

\ This track shows the gaps in the GRCh38 (hg38) genome assembly defined in the\ AGP file delivered with the sequence. These gaps are being closed during the \ finishing process on the human genome. For information on the AGP file format, see the NCBI \ AGP Specification. The NCBI website also provides an \ overview of genome assembly procedures, as well as \ specific information about the hg38 assembly.\

\ Gaps are represented as black boxes in this track.\ If the relative order and orientation of the contigs on either side\ of the gap is supported by read pair data, \ it is a bridged gap and a white line is drawn \ through the black box representing the gap. \

This assembly contains the following principal types of gaps:\

short_arm - short arm gaps (count: 5; size range: 5,000,000 - 16,990,000 bases)
heterochromatin - heterochromatin gaps (count: 11; size range: 20,000 - 30,000,000 bases)
telomere - telomere gaps (count: 48; all of size 10,000 bases)
contig - gaps between contigs in scaffolds (count: 285; size range: 100 - 400,000 bases)
scaffold - gaps between scaffolds in chromosome assemblies (count: 470; size range: 10 - 624,000 bases)

\ map 1 group map\ html gap\ longLabel Gap Locations\ shortLabel Gap\ track gap\ type bed 3 +\ visibility hide\ gc5BaseBw GC Percent bigWig 0 100 GC Percent in 5-Base Windows 0 100 0 0 0 128 128 128 0 0 0

Description

\ The GC percent track shows the percentage of G (guanine) and C (cytosine) bases\ in 5-base windows. High GC content is typically associated with\ gene-rich areas.\

\ This track may be configured in a variety of ways to highlight different\ apsects of the displayed information. Click the\ "Graph configuration help"\ link for an explanation of the configuration options.\ \

Credits

The data and presentation of this graph were prepared by\ Hiram Clawson.\

\ \ map 0 altColor 128,128,128\ autoScale Off\ color 0,0,0\ graphTypeDefault Bar\ gridDefault OFF\ group map\ html gc5Base\ longLabel GC Percent in 5-Base Windows\ maxHeightPixels 128:36:16\ shortLabel GC Percent\ track gc5BaseBw\ type bigWig 0 100\ viewLimits 30:70\ visibility hide\ windowingFunction Mean\ genCC GenCC bigBed 9 + 33 GenCC: The Gene Curation Coalition Annotations 0 100 0 0 0 127 127 127 0 0 0 https://search.thegencc.org/genes/$

Description

\ \

\ This track shows annotations from The Gene Curation Coalition (GenCC).\ The GenCC provides information pertaining to the validity of gene-disease relationships, \ with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted \ by GenCC member organizations that currently provide online resources (e.g. ClinGen, DECIPHER, \ Orphanet, etc.), as well as diagnostic laboratories that have committed to sharing their internal \ curated gene-level knowledge (e.g. Ambry Genetics, Illumina, Invitae, etc.).

\ The GenCC aims to clarify overlap between gene curation efforts and develop\ consistent terminology for validity, allelic requirement and mechanism\ of disease. Each item on this track corresponds with a gene, and contains\ a large number of information such as associated disease, evidence classification,\ specific submission notes and identifiers from different databases. In cases where\ multiple annotations exist for the same gene, multiple items are displayed.

\ \

Display Conventions and Configuration

\ Each item displayed represents a submission to the GenCC database. The displayed \ name is a combination of the gene symbol and the disease's original submission ID. \ This submission ID is either the OMIM#, MONDO# or Orphanet#. Clicking\ on any item will display the complete meta data for that item, including\ linkouts to the GenCC, NCBI, Ensembl, HGNC, GeneCards, Pombase (MONDO),\ and Human Phenotype Ontology (HPO). Mousing over any item will display the\ associated disease title, the classification title, and the mode of inheritance\ title.

\ \

\ Items are colored based on the GenCC classification, or validation, of the\ evidence in the color scheme seen in the table below. \ For more information on this process, see the GenCC\ validity terms FAQ. A filter for the track is also available\ to display a subset of the items based on their classification.

\ \

\ \ \ \ \ \ \ \ \ \ \ \ \ \
Color Evidence classification
Definitive
Strong
Moderate
Supportive
Limited
Disputed Evidence
Refuted Evidence
No Known Disease Relationship
\

\ \

\ Limitations: Most entries include both NM_ accessions as well as ENST and ENSG identifiers.\ From the original file, which contains no coordinates, two genes were not mapped\ to the hg38 genome, SLCO1B7 and ATXN8. This means that the hg38 track has 2 fewer items\ than what can be found in the GenCC download file. For hg19, one additional\ gene was not mapped, KCNJ18. In addition to this, the GenCC data in the Genome\ Browser does not include OMIM data due to licensing restrictions. For more\ information, see the Methods section below.

\ \

Data Access

\ The source data can be explored in \ GenCC database. The source files can also be found on the GenCC downloads page.

\ \

\ The GenCC data on the UCSC Genome Browser can be explored interactively with the\ Table Browser or the\ Data Integrator.\ For automated download and analysis, the genome annotation is stored at UCSC in bigBed\ files that can be downloaded from\ our download server.\ The data may also be explored interactively using our\ REST API.

\ \

\ The file for this track may also be locally explored using our tools bigBedToBed \ which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here.\ The tools can also be used to obtain features confined to a given range, e.g.,\

\ bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/genCC.bb stdout

\ \

Methods

\ The data were downloaded from the GenCC downloads page in tsv format. Manual\ curation was performed on the file to remove newline characters and tab characters present in \ the submission notes, in total fewer than 20 manual edits were made.

\ The track was first built on hg38 by associating the gene symbols with the NCBI MANE 1.0 \ release transcripts. These coordinates were added to the items as well as the NM_ accession,\ ENST ID and ENSG ID. For items where there was no gene symbol match in MANE (~130), the gene\ symbols were queried against GENCODEv40 comprehensive set release. In places where multiple\ transcript matches were found, the earliest transcription start and latest end site was used\ from among the transcripts to encompass the entire gene coordinates. Two genes were not able\ to be mapped for hg38, SLCO1B7 and ATXN8, resulting in two missing submissions in the Genome\ Browser when compared to the raw file. Lastly, the items were colored according to their\ evidence classification as seen on the GenCC database.

\ For hg19, the hg38 NM_ accessions were used to convert the item coordinates according to the\ latest hg19 refseq release. For items that failed to convert, the gene symbols were queried\ using the GENCODEv40 hg19 lift comprehensive set. One additional gene symbol failed to map in\ hg19, KCNJ18, leading to 3 fewer items on this track when compared to the raw file.

\ GENCODE version 47\ corresponds to Ensembl 113.\

\ GENCODE version 46\ corresponds to Ensembl 112.\

\ GENCODE version 45\ corresponds to Ensembl 111.\

\ GENCODE version 44\ corresponds to Ensembl 110.\

\ GENCODE version 43\ corresponds to Ensembl 109.\

\ GENCODE version 42\ corresponds to Ensembl 108.\

\ GENCODE version 41\ corresponds to Ensembl 107.\

\ GENCODE version 40\ corresponds to Ensembl 106.\

\ GENCODE version 39\ corresponds to Ensembl 105.\

\ GENCODE version 38\ corresponds to Ensembl 104.\

\ GENCODE version 37\ corresponds to Ensembl 103.\

\ GENCODE version 36\ corresponds to Ensembl 102.\

\ GENCODE version 35\ corresponds to Ensembl 101.\

\ GENCODE version 34\ corresponds to Ensembl 100.\

\ GENCODE version 33\ corresponds to Ensembl 99.\

\ GENCODE version 30\ corresponds to Ensembl 96.\

\ GENCODE version 29\ corresponds to Ensembl 94.\

\ GENCODE version 28\ corresponds to Ensembl 92.\

\ GENCODE version 27\ corresponds to Ensembl 90.\

\ GENCODE version 26\ corresponds to Ensembl 88.\

\ GENCODE version 24\ corresponds to Ensembl 84.\

\ GENCODE version 23\ corresponds to Ensembl 81.\

\ GENCODE version 22\ corresponds to Ensembl 79.\

\ GENCODE version 20\ corresponds to Ensembl 76.\

\ \

Credits

\ \

References

\ \ \

A full list of GENCODE publications are available\ at The GENCODE\ Project web site.\

\ \

Data Release Policy

GENCODE data are available for use without restrictions.

\ \ genes 0 group genes\ longLabel Container of all new and previous GENCODE releases\ pennantIcon Updated red ../goldenPath/newsarch.html#110824 "Updated Nov. 8, 2024"\ shortLabel GENCODE Versions\ superTrack on\ track wgEncodeGencodeSuper\ trackHandler wgEncodeGencode\ interactions Gene Interactions bigBed 9 Protein Interactions from Curated Databases and Text-Mining 0 100 0 0 0 127 127 127 0 0 0

Description

\ The Pathways and Gene Interactions track shows a summary of gene interaction and pathway data\ collected from two sources: curated pathway/protein-interaction databases and interactions found\ through text mining of PubMed abstracts.

\ \

Display Conventions and Configuration

Track Display

\ The track features a single item for each gene loci in the genome. On the item itself, the gene\ symbol for the loci is displayed followed by the top gene interactions noted by their gene symbol.\ Clicking an item will take you a\ gene interaction graph\ that includes detailed information on the support for the various interactions.

\ \

\ The full set of elements and interactions is included, along with a highly filtered \ "double elite" subset.\ \

Display Conventions

\ Each GeneHancer regulatory element is identified by a GeneHancer id. \ For example: GH0XJ101383 is located on chromosome X, with starting position of 101,383 kb\ (GRCh38/hg38 reference).\ Based on the id, one can obtain full GeneHancer information, as displayed in the Genomics \ section within the gene-centric web pages of GeneCards. Links to the GeneCards information pages\ are provided on the track details pages.

\ \

\ For the interaction tracks (Clusters and Interactions) a slight offset can be noticed between \ the line endpoints. This helps to identify the start and end of the feature. In this case,\ the higher point is the source (enhancers) and the lower point is the target.

\ \

Regulatory elements

\ Colors are used to distinguish promoters and enhancers and to indicate the GeneHancer element confidence score:

\ Promoters: \ High\ Medium\ Low\

\ Enhancers: \ High\ Medium\ Low\

\ \

Gene TSS

\ Colors are used to improve gene and interactions visibility. \ Successive genes are colored in different colors, and interactions of a gene have the same color.

\ \

Interactions

\ The Interactions view in Full mode shows GeneHancers and target genes connected by curves or \ half-rectangles (when one of the connected regions is off-screen). \ Configuration options are available to change the drawing style, and to limit the view to\ interactions with one or both connected items in the region.\ Interactions are identified on mouseover or clicked on for details at the end regions, or at \ the curve peak, which is marked with a gray ring shape. Interactions in the reverse direction\ (Gene TSS precedes GeneHancer on the genome) are drawn with a dashed line.\ \

Clusters

\ The Clusters view groups interactions by target gene; the target gene and all GeneHancers \ associated with it are displayed in a single browser item. The gene TSS and associated GeneHancers \ are shown as blocks linked together, with the TSS drawn as a "tall" item, and the \ GeneHancers drawn "short". \ A user configuration option is provided to change the view to group by GeneHancer \ (with tall GeneHancer and short TSS's). \ Clusters composed of interactions with a single gene are colored to correspond to the gene, \ and those composed of interactions with multiple genes are colored dark gray.

\ \

Methods

\ GeneHancer identifications were created from >1 million regulatory elements \ obtained from seven genome-wide databases:\

ENCODE project\ Z-Lab Enhancer-like regions (version v3)
Ensembl regulatory build (version 92)
FANTOM5 atlas of active enhancers
VISTA Enhancer Browser
dbSUPER super-enhancers
EPDnew promoters
UCNEbase ultra-conserved noncoding elements

\ Employing an integration algorithm that removes redundancy, the GeneHancer pipeline\ identified ˜250k integrated candidate regulatory elements (GeneHancers).\ Each GeneHancer is assigned an annotation-derived confidence score. \ The GeneHancers that are derived from more than one information source are defined \ as "elite" GeneHancers.

\ Gene-GeneHancer associations, and their likelihood-based scores, were generated \ using information that helps link regulatory elements to genes:\

eQTLs (expression quantitative trait loci) from GTEx (version v6p)
Capture Hi-C promoter-enhancer long range interactions
FANTOM5 eRNA-gene expression correlations
Cross-tissue expression correlations between a transcription factor interacting \ with a GeneHancer and a candidate target gene
Distance-based associations, including several approaches: \
1. Nearest neighbors, where each GeneHancer is associated with its two proximal genes
2. Overlaps with the gene territory (intragenic)
3. Proximity to the gene TSS (<2kb)
\

\ Associations that are derived from more than one information source are defined \ as "elite" associations, which leads to the definition of the "double elite"\ dataset - elite gene associations of elite GeneHancers.

\ More details are provided at the GeneCards\ \ information page.\ For a full description of the methods used, refer to the GeneHancer manuscript¹.

\ Source data for the GeneHancer version 4.8 was downloaded during May 2018.

\ \

Data Access

\ Due to our agreement with the Weizmann Institute, we cannot allow full genome \ queries from the Table Browser or share download files. You can still access \ data for individual chromosomes or positional data from the \ Table Browser.

\ \

\ GeneHancer is the property of the Weizmann Institute of Science and \ is not available for download or mirroring by any third party \ without permission. Please contact the Weizmann Institute directly for \ data inquiries.

\ \

Credits

\ Thanks to Simon Fishilevich, Marilyn Safran, Naomi Rosen, and Tsippi Iny Stein of the GeneCards \ group and Shifra Ben-Dor of the Bioinformatics Core group at the Weizmann Institute, \ for providing this data and documentation, creating track hub versions of these tracks \ as prototypes, and overall responsiveness during development of these tracks.

Description

\ \

\ GeneReviews is an online collection of expert-authored, peer-reviewed\ articles that describe specific gene-related diseases. GeneReviews articles are\ searchable by disease name, gene symbol, protein name, author, or title. GeneReviews\ is supported by the National Institutes of Health, hosted at NCBI as part of the\ \ Genetic Testing Registry (GTR). The GeneReviews data underlying this track will be updated frequently. \

\ \

The GeneReviews track allows the user to locate the NCBI GeneReviews resource\ quickly from the Genome Browser. Hovering the mouse on track items shows the gene symbol and \ associated diseases. A condensed version of the GeneReviews article\ name and its related diseases are displayed on the item details page as links. Similar\ information, when available, is provided in the details page of items from the UCSC Genes,\ RefSeq Genes, and OMIM Genes tracks.\

\ \

Data Access

\ The raw data for the GeneReviews track can be explored interactively with the\ Table Browser. Cross-referencing can be done with\ Data Integrator. The complete source file,\ in bigBed format, \ can be downloaded from our\ downloads directory.\ For automated analysis,\ the data may be queried from our\ REST API.\

\ \

\ Previous versions of this track can be found on our archive download server.\

\ \

References

\ \

\ Pagon RA, Adam MP, Bird TD, et al., editors. GeneReviews^® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2014. Available from: \ \ https://www.ncbi.nlm.nih.gov/books/NBK1116.\

\ \ phenDis 1 bigDataUrl /gbdb/hg38/geneReviews/geneReviews.bb\ color 0, 80, 0\ group phenDis\ html geneReviews\ longLabel GeneReviews\ mouseOver $name disease(s): $diseases\ noScoreFilter on\ shortLabel GeneReviews\ track geneReviews\ type bigBed 9 +\ url https://www.ncbi.nlm.nih.gov/books/NBK1116/?term=$$\ visibility hide\ giab Genome In a Bottle bed 3 Genome In a Bottle Structural Variants and Trios 0 100 0 0 0 127 127 127 0 0 0

Description

\ The tracks listed here contain data from\ The Genome in a\ Bottle Consortium (GIAB), an open, public consortium hosted by \ NIST. The priority of GIAB is to develop \ reference standards, reference methods, and reference data by authoritative characterization of \ human genomes for use in benchmarking, including analytical validation and technology \ development that will support translation of whole human genome sequencing to clinical practice. The\ sole purpose of this work is to provide validated variants and regions to enable technology and \ bioinformatics developers to benchmark and optimize their detection methods.\

\ The Ashkenazim and the Chinese Trio tracks show benchmark SNV calls from two \ son/father/mother trios of Ashkenazi Jewish and Han Chinese ancestry from the \ Personal Genome Project, \ consented for commercial redistribution.\

\ The Genome In a Bottle Structural Variants track shows benchmark SV calls (nssv) \ and variant regions (nsv) (5,262 insertions and 4,095 deletions, > 50 bp, in 2.51 Gb of \ the genome) from the son (HG002/NA24385) from the Ashkenazi Jewish trio.\

\ Samples are disseminated as National Institute of Standards and Technology (NIST)\ Reference Materials.\

Display Conventions and Configuration

\ These tracks are multi-view composite tracks that contain multiple data types (views). Each view \ within a track has separate display controls, as described \ here.\

\ Unlike a regular genome browser track, the Ashkenazim and the Chinese Trio tracks display \ the genome variants of each individual as two haplotypes; SNPs, small insertions and deletions\ are mapped to each haplotype based on the phasing information of the VCF file. The\ haplotype 1 and the haplotype 2 are displayed as two separate black lanes for the\ browser window region. Each variant is drawn as a vertical dash. Homozygous variants will\ show two identical dashes on both haplotype lanes. Phased heterozygous variants are placed on\ one of the haplotype lanes and unphased heterozygous variants are displayed in the area\ between the two haplotype lanes.\

\ Predicted de novo variants and variants that are inconsistent with phasing in the trio son can be \ colored in red using the track Configuration options.\

\ \

\ This track follows the display conventions for\ gene prediction\ tracks.\

\ \

\ The track description page offers the following filter and configuration\ options:\

Color track by codons: Select the genomic codons option\ to color and label each codon in a zoomed-in display to facilitate validation\ and comparison of gene predictions. Go to the\ \ Coloring Gene Predictions and Annotations by Codon page for more\ information about this feature.

\ \

Methods

\ \

\ For a description of the Genscan program and the model that underlies it,\ refer to Burge and Karlin (1997) in the References section below.\ The splice site models used are described in more detail in Burge (1998)\ below.\

\ \

Credits

\ \ Thanks to Chris Burge for providing the Genscan program.\ \

References

\ \

\ Burge C.\ Modeling Dependencies in Pre-mRNA Splicing Signals.\ In: Salzberg S, Searls D, Kasif S, editors.\ Computational Methods in Molecular Biology.\ Amsterdam: Elsevier Science; 1998. p. 127-163.\

\ \

\ Burge C, Karlin S.\ \ Prediction of complete gene structures in human genomic DNA.\ J. Mol. Biol. 1997 Apr 25;268(1):78-94.\ PMID: 9149143\

\ genes 1 color 170,100,0\ group genes\ html ../../genscan\ longLabel Genscan Gene Predictions\ parent genePredArchive\ shortLabel Genscan Genes\ track genscan\ type genePred genscanPep\ visibility hide\ encTfChipPkENCFF567NFS GM12878 CUX1 narrowPeak Transcription Factor ChIP-seq Peaks of CUX1 in GM12878 from ENCODE 3 (ENCFF567NFS) 0 100 85 152 255 170 203 255 0 0 0 regulation 1 color 85,152,255\ longLabel Transcription Factor ChIP-seq Peaks of CUX1 in GM12878 from ENCODE 3 (ENCFF567NFS)\ parent encTfChipPk off\ shortLabel GM12878 CUX1\ subGroups cellType=GM12878 factor=CUX1\ track encTfChipPkENCFF567NFS\ gnfAtlas2 GNF Atlas 2 expRatio GNF Expression Atlas 2 0 100 0 0 0 127 127 127 0 0 0

Description

This track shows expression data from the GNF Gene Expression\ Atlas 2. This contains two replicates each of 79 human\ tissues run over Affymetrix microarrays. \ By default, averages of related tissues are shown. Display all tissues\ by selecting "All Arrays" from the "Combine arrays" menu\ on the track settings page.\ As is standard with microarray data red indicates overexpression in the \ tissue, and green indicates underexpression. You may want to view gene\ expression with the Gene Sorter as well as the Genome Browser.

\ There are two "groups" of tracks in this set, and three gnomAD versions (v2.1.1, v4.0, and v4.1):\

Gene/Transcript LoF Constraint tracks: Predicted constraint metrics at the whole gene\ level or whole transcript level for three different types of variation: missense, synonymous,\ and predicted loss of function. The Gene Constraint track displays metrics for a canonical \ transcript per gene defined as the longest isoform. The Transcript Constraint track displays \ metrics for all transcript isoforms. Items on both tracks are shaded according to the pLI score,\ with outlier items shaded in grey.\

\ Please note there is no gene-level track available for v4.0 and v4.1.\
Gene/Transcript Missense Constraint tracks: The missense constraint tracks are built\ similarly to the LoF constraint tracks, however the items displayed are based on \ missense Z scores.\ All items are colored black, and individual Z scores can be seen on mouseover. \

\ All tracks follow the general configuration settings for bigBed tracks. Mouseover on the \ Gene/Transcript Constraint tracks shows the pLI score and the loss of function \ observed/expected upper bound fraction (LOEUF), while mouseover on the Regional\ Constraint track shows only the missense O/E ratio. Clicking on items in any track brings\ up a table of constraint metrics.\

\ \

\ Clicking the grey box to the left of the track, or right-clicking and choosing the Configure option,\ brings up the interface for filtering items based on their pLI score, or labeling the items\ based on their Ensembl identifier and/or Gene Name.\

\ \

Methods

\ Please see the gnomAD browser help page and FAQ for further explanation of the topics below.

\ \

Observed and Expected Variant Counts

\ Observed count: The number of unique single-nucleotide variants in each transcript/gene\ with 123 or fewer alternative alleles (MAF < 0.1%).\

\ Expected count: A depth-corrected probability prediction model that takes into account\ sequence context, coverage, and methylation was used to predict expected\ variant counts. For more information please see Lek et al., 2016.\

\ Variants found in exons with a median depth < 1 were removed from both counts.\

\ The O/E constraint score is the ratio of the observed/expected variants in that gene. Each item in\ this track shows the O/E ratio for three different types of variation: missense, synonymous, and\ loss-of-function. The O/E ratio is a continuous measurement of how tolerant a gene or\ transcript is to a certain class of variation. When a gene has a low O/E value, it is under stronger\ selection for that class of variation than a gene with a higher O/E value. Because Counts depend on\ gene size and sample size, the precision of the values varies a lot from one gene to the next. \ Therefore, the 90% confidence interval (CI) is also displayed along with the O/E ratio to better\ assist interpretation of the scores.\

\ When evaluating how constrained a gene is, it is essential to consider the CI when using O/E. In \ research and clinical interpretation of Mendelian cases, pLI > 0.9 has been widely used for \ filtering. Accordingly, the Gnomad team suggests using the upper bound of the O/E confidence interval\ LOEUF < 0.35 as a threshold if needed.\

\ Please see the Methods section below for more information about how the scores were calculated.\

\ \

pLI and Z-scores

\ The pLI and Z-scores of the deviation of observed variant counts relative to the expected number \ are intended to measure how constrained or intolerant a gene or transcript is to a specific type of\ variation. Genes or transcripts that are particularly depleted of a specific class of variation\ (as observed in the gnomAD data set) are considered intolerant of that specific type of variation.\ Z-scores are available for the missense and synonynmous categories and pLI scores are available for\ the loss-of-function variation.\

\ Missense and Synonymous: Positive Z-scores indicate more constraint (fewer observed \ variants than expected), and negative scores indicate less constraint (more observed variants than\ expected). A greater Z-score indicates more intolerance to the class of variation. Z-scores\ were generated by a sequence-context-based mutational model that predicted the number of expected\ rare (< 1% MAF) variants per transcript. The square root of the chi-squared value of the \ deviation of observed counts from expected counts was multiplied by -1 if the observed count was\ greater than the expected and vice versa. For the synonymous score, each Z-score was corrected by\ dividing by the standard deviation of all synonymous Z-scores between -5 and 5. For the missense\ scores, a mirrored distribution of all Z-scores between -5 and 0 was created, and then all missense\ Z-scores were corrected by dividing by the standard deviation of the Z-score of the mirror\ distribution.\

\ Loss-of-function: pLI closer to 1 indicates that the gene or transcript cannot tolerate\ protein truncating variation (nonsense, splice acceptor and splice donor variation). The gnomAD\ team recommends transcripts with a pLI >= 0.9 for the set of transcripts extremely intolerant\ to truncating variants. pLI is based on the idea that transcripts can be classified into three\ categories:\

null: heterozygous or homozygous protein truncating variation is completely tolerated\
recessive: heterozygous variants are tolerated but homozygous variants are not\
haploinsufficient: heterozygous variants are not tolerated\

\ An expectation-maximization algorithm was then used to assign a probability of belonging in each\ class to each gene or transcript. pLI is the probability of belonging in the haploinsufficient class.\

\ \

\ Please see Samocha et al., 2014 and Lek et al., 2016 for further discussion of these metrics.\

\ \

Transcripts Included

\ For version 2.1.1 only, the GENCODE transcripts were filtered according to the following criteria:\

Must have methionine at start of coding sequence\
Must have stop codon at end of coding sequence\
Must be divisible by 3\
Must have at least one observed variant when removing exons with median depth < 1\
Must have reasonable number of missense and synonymous variants as determined by a Z-score cutoff\

\ For version v2.1.1, the gnomAD gene/transcript data is based on hg19. In order to map transcripts and genes to the hg38 genome the following steps were taken:\

Transcript track: The gnomAD ENST identifiers were attempted to be matched to all GENCODE versions\ between V20 and V44, giving coordinate priorities to the most recent models. In total 74550/80950 \ transcripts were mapped.
Genes track: The gnomAD file ENSG identifiers were attempted to be matched to all GENCODE versions\ between V20 and V44, giving coordinate priorities to the most recent models. This mapped 19221/19704\ genes. The remainder of the genes were attempted to be mapped using the same strategy, but matching\ on gene symbols instead of ENSG identifiers. In total 19567/19704 genes were mapped.

\ \

\ For version v4.0 and v4.1, the gnomAD transcript data is based on hg38. In order to map the\ transcripts to hg38, the transcript version numbers in the gnomAD download file were joined with\ GENCODE V39 and NCBI RefSeq coordinates available at UCSC.\

\ \

UCSC Track Methods

Version based on gnomAD v2.1.1

Gene and Transcript Constraint tracks

\ Per gene and per transcript data were downloaded from the gnomAD Google Storage bucket:\

\
gs://gnomad-public/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz\
gs://gnomad-public/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_transcript.txt.bgz\

\ These data were then joined to the Gencode set of genes/transcripts available at the UCSC\ Genome Browser (see previous section) and then transformed into a bigBed 12+5. For the full list of commands used to\ make this track please see the\ makedoc.\

\ \

Version based on gnomAD v4.0

Gene and Transcript Constraint tracks

\ Per gene and per transcript data were downloaded from the gnomAD Google Storage bucket:\

\
https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/constraint/gnomad.v4.0.constraint_metrics.tsv\

\ These data were then joined to the Gencode/NCBI set of genes/transcripts available at the UCSC\ Genome Browser and then transformed into a bigBed 12+5. For the full list of commands used to\ make this track please see the\ makedoc.\

\ \

Version based on gnomAD v4.1

Gene and Transcript Constraint tracks

\ Per gene and per transcript data were downloaded from the gnomAD Google Storage bucket:\

\
https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/constraint/gnomad.v4.1.constraint_metrics.tsv\

\ \

Data Access

\ The raw data can be explored interactively with the Table Browser, or\ the Data Integrator. For automated access, this track, like all \ others, is available via our API. However, for bulk \ processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed \ file that can be downloaded from the\ download server. The exact\ filenames can be found in the track configuration file. Annotations can be converted to ASCII text\ by our tool bigBedToBed which can be compiled from the source code or downloaded as\ a precompiled binary for your system. Instructions for downloading source code and binaries can be\ found here. The tool\ can also be used to obtain only features within a given range, for example:

\
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/pLI/pliByTranscript.bb -chrom=chr6 -start=0 -end=1000000 stdout\

\ Please refer to our\ mailing list archives\ for questions and example queries, or our\ Data Access FAQ\ for more information.\

\ \

\ More information about using and understanding the gnomAD data can be found in the\ gnomAD FAQ site.\

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the ODC Open Database License\ (ODbL) as described here.\

\ \

References

\ \

\ Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill\ AJ, Cummings BB et al.\ \ Analysis of protein-coding genetic variation in 60,706 humans.\ Nature. 2016 Aug 18;536(7616):285-91.\ PMID: 27535533; PMC: PMC5018207\

\ \

\ Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM,\ Ganna A, Birnbaum DP et al.\ \ The mutational constraint spectrum quantified from variation in 141,456 humans.\ Nature. 2020 May;581(7809):434-443.\ PMID: 32461654; PMC: PMC7334197\

\ \

\ Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C,\ Gauthier LD, Wang H et al.\ \ A structural variation reference for medical and population genetics.\ Nature. 2020 May;581(7809):444-451.\ PMID: 32461652; PMC: PMC7334194\

\ \

\ Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J,\ Satterstrom FK, O'Donnell-Luria AH et al.\ \ Transcript expression-aware annotation improves rare variant interpretation.\ Nature. 2020 May;581(7809):452-458.\ PMID: 32461655; PMC: PMC7334198\

\ \ varRep 1 compositeTrack On\ dataVersion Release v4.1 (April 19, 2024), Release v4 (November 2023), Release 2.1.1 (March 6, 2019)\ group varRep\ html gnomadPLI.html\ labelFields name,geneName\ longLabel Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (LOEUF, pLI, and Z-scores)\ parent gnomadVariants\ pennantIcon New red ../goldenPath/newsarch.html#093024 "September 30, 2024"\ shortLabel gnomAD Constraint Metrics\ subGroup1 view Views v2=constraintV2 v4=constraintV4 v4_1=constraintV4.1\ track gnomadPLI\ type bigBed 12\ visibility hide\ gnomadCopyNumberVariants gnomAD Rare CNV Variants bigBed 9 + Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1 0 100 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_cnv_r4

Description

\ The Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1 track set shows rare autosomal coding copy number variants (CNVs) with an overall\ site frequency of less than 1%. These variants were identified from exome sequencing (ES) data of\ 464,297 individuals. The data can also be explored via the\ gnomAD browser.\ \

Display Conventions and Configuration

\ \

\ Items are colored by the type of variant:\ \ \ \ \ \ \ \ \ \ \ \
Variant Type
Deletion (DEL) 20989
Duplication (DUP) 25026
.

\ \

Mouseover on an item will display the position, size of variant, genes impacted by\ variant (>=10% CDS overlap by deletion or >=75% CDS overlap by duplication), and site\ frequency of non-neuro control samples. Item description pages include a linkout to\ the gnomAD browser showing additional genetic ancestry group information.

\ \ \

Methods

\ \

Exome CNV Discovery Method: GATK-gCNV

\ To identify rare coding CNVs from the ES data of 464,297 individuals in gnomAD v4, the GATK-gCNV\ method was employed, as described in Babadi et al., Nat Genet, 2023.

\ \

The CNV discovery process started with collecting the number of reads mapped to 363,301 autosomal\ target intervals derived from protein-coding exons (Fig. 1a, b; Babadi et al.). These read counts\ were used to capture sample-level technical variability, such as differences in exome capture kits\ or sequencing centers, and generated 1,045 different batches of samples for parallel processing\ (Fig. 1c). For each of these batches, 200 random samples were selected for training GATK-gCNV in\ cohort mode,which can be thought of as the creation of a "panel of normals" (PoN). The resulting\ PoN models were then used to efficiently delineate CNV events on all of the samples of their\ respective cohorts using the GATK-gCNV case mode (Fig. 1d,e).\

\ \

\ The raw, individual-level CNV calls produced by GATK-gCNV for all samples were then collated,\ and variants observed in multiple individuals were clustered using single-linkage clustering.\ Quality filtering followed the procedures outlined in Babadi et al., filtering CNVs based on\ sample-level (number of events per individual) and call-level (frequency, size, quality score) metrics\ Due to the significant increase in cohort size and heterogeneity compared to the datasets reported\ in Babadi et al., additional filters were applied. Samples with more than five chromosomes harboring\ rare CNVs, as well as those containing more than three rare terminal CNVs, were excluded. 1,049\ sites producing noisy normalized read-depth signals were masked. The final retained CNVs and sites\ were subsequently annotated for impacted genes and frequencies.

\ \

Limitations of ES-based rare coding CNVs in gnomAD v4

This dataset includes only rare coding CNVs, filtered to <1% site frequency in the overall\ dataset.
This dataset only includes variants that span three or more exons that received sufficient\ coverage.
This dataset is limited to autosomal CNVs for now.

\ \

\ More information can be found at the\ \ gnomAD site.

\ \

\ The bed files was obtained from the gnomAD Google Storage bucket:

\ \

\
https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/exome_cnv/gnomad.v4.1.cnv.non_neuro_controls.bed\

\ \ The data was then transformed into a bigBed track. For the full list of commands used to make this\ track please see the "gnomAD CNVs v4.1" section of the\ makedoc.

\ \ \

Data Access

\ The raw data can be explored interactively with the Table Browser, or\ the Data Integrator. For automated access, this track, like all \ others, is available via our API. However, for bulk \ processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed \ file that can be downloaded from the\ download server.\ The exact filenames can be found in the track configuration file. Annotations can be converted to\ ASCII text by our tool bigBedToBed which can be compiled from the source code or\ downloaded as a precompiled binary for your system. Instructions for downloading source code and\ binaries can be found\ here. The tool can\ also be used to obtain only features within a given range, for example:

\ \

\
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v4/cnv/gnomad.v4.1.cnv.non_neuro_controls.bb -chrom=chr6 -start=0 -end=1000000 stdout\

\ \

\ Please refer to our\ mailing list archives\ for questions and example queries, or our\ Data Access FAQ\ for more information.

\ \

\ More information about using and understanding the gnomAD data can be found in the\ gnomAD FAQ site.\

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the ODC Open Database License\ (ODbL) as described here.\

\ \ \

References

\ \

\ Babadi M, Fu JM, Lee SK, Smirnov AN, Gauthier LD, Walker M, Benjamin DI, Zhao X, Karczewski KJ, Wong\ I et al.\ \ GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data.\ Nat Genet. 2023 Sep;55(9):1589-1597.\ PMID: 37604963; PMC: PMC10904014\

\ \

\ varRep 1 bigDataUrl /gbdb/hg38/gnomAD/v4/cnv/gnomad.v4.1.cnv.non_neuro_controls.bb\ dataVersion Release 4.1 (November 01, 2023)\ filterLabel.svtype Type of Variation\ filterValues.svtype DEL|Deletion,DUP|Duplication\ html gnomadCNV\ itemRgb on\ longLabel Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1\ mouseOver Position: $chrom:${chromStart}-${chromEnd}
Size of variant: ${svlen}
Genes impacted by variant: ${genes}
Site frequency (non-neuro control samples): ${sf}\ parent gnomadVariants on\ pennantIcon New red ../goldenPath/newsarch.html#093024 "September 30, 2024"\ searchIndex name\ shortLabel gnomAD Rare CNV Variants\ track gnomadCopyNumberVariants\ type bigBed 9 +\ url https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_cnv_r4\ urlLabel gnomAD Copy number variants Browser\ visibility hide\ gnomadStructuralVariants gnomAD Structural Variants bigBed 9 + Genome Aggregation Database (gnomAD) - Structural Variants v4.1 0 100 0 0 0 127 127 127 0 0 0 https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_sv_r4

Description

\ The Genome Aggregation Database (gnomAD) - Structural Variants v4.1 track set shows structural variants calls (>=50 nucleotides) from the gnomAD v4.1\ release on 63,046 unrelated genomes. It mostly (but not entirely) overlaps with the genome set used\ for the gnomAD short variant release. For more information see the following blog post, \ \ Structural variants in gnomAD.

\ \

Display Conventions and Configuration

\ \

\ Items are shaded according to variant type, mouseover on items indicates affected\ protein-coding genes, size of the variant (which may differ from the chromosomal coordinates in\ cases like insertions), variant type (insertion, duplication, etc), allele count, allele number,\ and allele frequency. When more than 2 genes are affected by a variant, the full list can be\ obtained by clicking on the item and reading the details page. A short summary is available in the\ below table:

\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \

Variant Type	All SV's
Breakend (BND)	356035
Complex (CPX)	15189
Translocation (CTX)	99
Deletion (DEL)	1206278
Duplication (DUP)	269326
Insertion (INS)	304645
Inversion (INV)	2193
Copy number variants (CNV)	721

\ \

\ Detailed information on the CNV color code is described \ here. All tracks can be \ filtered according to the size of the variant and variant type, using the track Configure\ options.\

\ \

Filtering Options

\ Three filters are available for this track:\

Variant Size: Used to exclude/include variants according to the size.\
Non-neurological allele frequency: Used to exclude/include allele frequency of variants in\ individuals who do not have a neurological condition, as identified in a case-control study.\
Common disease control allele frequency: Used to exclude/include allele frequency of\ variants in individuals not identified as cases in a case-control study of common disease.\ \

\ \

Methods

\ The bed files was obtained from the gnomAD Google Storage bucket:\ \

\
https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/genome_sv/gnomad.v4.1.sv.non_neuro_controls.sites.bed.gz\

\ \ The data was then transformed into a bigBed track. For the full list of commands used to make this\ track please see the "gnomAD Structural Variants v4" section of the\ makedoc.

\ \ \

Data Access

\ The raw data can be explored interactively with the Table Browser, or\ the Data Integrator. For automated access, this track, like all \ others, is available via our API. However, for bulk \ processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed \ file that can be downloaded from the\ download server.\ The exact filenames can be found in the track configuration file. Annotations can be converted to\ ASCII text by our tool bigBedToBed which can be compiled from the source code or\ downloaded as a precompiled binary for your system. Instructions for downloading source code and\ binaries can be found\ here. The tool can\ also be used to obtain only features within a given range, for example:

\ \

\
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v4/structuralVariants/gnomad.v4.1.sv.non_neuro_controls.sites.bb -chrom=chr6 -start=0 -end=1000000 stdout\

\ \

\ Please refer to our\ mailing list archives\ for questions and example queries, or our\ Data Access FAQ\ for more information.

\ \

\ More information about using and understanding the gnomAD data can be found in the\ gnomAD FAQ site.\

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the ODC Open Database License\ (ODbL) as described here.\

\ \ \

References

\ \

\ \ varRep 1 bigDataUrl /gbdb/hg38/gnomAD/v4/structuralVariants/gnomad.v4.1.sv.non_neuro_controls.sites.bb\ dataVersion Release 4.1 (November 01, 2023)\ filter.af_controls 0:1\ filter.af_non_neuro 0:1\ filter.svlen 50:199840172\ filterByRange.af_controls on\ filterByRange.af_non_neuro on\ filterByRange.svlen on\ filterLabel.af_controls Filter by common disease control allele frequency\ filterLabel.af_non_neuro Filter by non-neurological allele frequency\ filterLabel.svlen Filter by Variant Size\ filterLabel.svtype Type of Variation\ filterLimits.af_controls 0:1\ filterLimits.af_non_neuro 0:1\ filterValues.svtype BND|Breakend,CPX|Complex,CTX|Translocation,DEL|Deletion,DUP|Duplication,INS|Insertion,INV|Inversion,MCNV|Multi-allele CNV\ html gnomadSv.html\ itemRgb on\ longLabel Genome Aggregation Database (gnomAD) - Structural Variants v4.1\ mouseOverField _mouseOver\ parent gnomadVariants on\ pennantIcon New red ../goldenPath/newsarch.html#093024 "September 30, 2024"\ shortLabel gnomAD Structural Variants\ track gnomadStructuralVariants\ type bigBed 9 +\ url https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_sv_r4\ urlLabel gnomAD Structural Variant Browser\ visibility hide\ gnomadVariants gnomAD Variants Genome Aggregation Database (gnomAD) Genome and Exome Variants 0 100 0 0 0 127 127 127 0 0 0

Description

\ \

\ gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the\ GRCh38/hg38 lift-over provided by gnomAD on their downloads site.\

\ \

\ For questions on the gnomAD data, also see the gnomAD FAQ.

\ More details on the Variant type(s) can be found on the Sequence Ontology page.

\ \

Display Conventions and Configuration

gnomAD v4.1

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

\ \

gnomAD v3.1.1

\ The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,\ except as noted below.

\ \

There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).\
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one\ variant, with additional information available on the details page, which has roughly halved the\ number of items in the bigBed.\
The bigBed has been split into two files, one with the information necessary for the track\ display, and one with the information necessary for the details page. For more information on\ this data format, please see the Data Access section below.\
The VEP annotation is shown as a table instead of spread across multiple fields.\
Intergenic variants have not been pre-filtered.\

\ \

gnomAD v3.1

\ By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters\ described below), before the track switches to dense display mode.\

\ \

\ Mouse hover on an item will display many details about each variant, including the affected gene(s),\ the variant type, and annotation (missense, synonymous, etc).\

\ \

\ Clicking on an item will display additional details on the variant, including a population frequency\ table showing allele count in each sub-population.\

\ \

\ Following the conventions on the gnomAD browser, items are shaded according to their Annotation\ type:\ \ \ \ \ \
pLoF
Missense
Synonymous
Other
\

\ Four filters are available for these tracks, the same as the underlying VCF:\

AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))\
InbreedingCoeff: Inbreeding Coefficient < -0.3\
RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)\
Pass: Variant passes all 3 filters\

\ \

\ There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.\

\ \ \

UCSC Methods

\ The gnomAD v3.1.1 and v4.1 data is unfiltered.

\ For the v3.1 update only, in order to cut \ down on the amount of displayed data, the following variant\ types have been filtered out, but are still viewable in the gnomAD browser:\

Regulatory Region Variants\
Downstream/Upstream Gene Variants\
Transcription Factor Binding Site Variants\

\ \

\ For the full steps used to create the gnomAD tracks at UCSC, please see the\ hg38 gnomad makedoc.\

\ \ \

Data Access

\ \

\
# find item of interest:\
bigBedToBed genomes.bb stdout | head -4 | tail -1\
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted for brevity..]    chr1-12417-G-A    67293    902\
\
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:\
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz\
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant",  [..omitted for brevity..]\

\ \

\ The data can also be found directly from the gnomAD downloads page. Please refer to\ our mailing list archives for questions, or our Data Access FAQ for more information.

\ \

Credits

\ Thanks to the Genome Aggregation\ Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.\

\ \

\ Please note that some annotations within the provided files may have restrictions on usage. See here for more information. \

\ \

References

\ \

\ varRep 0 cartVersion 6\ group varRep\ html gnomadV4.1\ longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants\ pennantIcon New red ../goldenPath/newsarch.html#093024 "September 30, 2024"\ shortLabel gnomAD Variants\ superTrack on\ track gnomadVariants\ ctgPos2 GRC Contigs ctgPos Genome Reference Consortium Contigs 3 100 0 0 0 127 127 127 0 0 24 chr1,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chrX,chrY, https://www.ncbi.nlm.nih.gov/nuccore/$$

Description

\ This track shows the names of the assembled supercontigs for the GRCh38 (hg38) assembly \ determined by the Genome Reference Consortium (GRC).\

\ Data for this track were obtained from \ localId2acc files downloaded from GenBank.\

\ map 0 chromosomes chr1,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chrX,chrY\ longLabel Genome Reference Consortium Contigs\ shortLabel GRC Contigs\ superTrack assemblyContainer pack\ track ctgPos2\ type ctgPos\ url https://www.ncbi.nlm.nih.gov/nuccore/$$\ grcIncidentDb GRC Incident bigBed 4 + GRC Incident Database 0 100 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=$$

Description

\ This track shows locations in the human assembly where assembly\ problems have been noted or resolved, as reported by the\ Genome Reference Consortium (GRC). \

\ Details on GTEx v8 analysis, including code, can be found in the\ GTEx GWAS Analysis Github.\

\ \

\ Raw data for these analyses are available from the\ GTEx Portal.\

\ \

CAVIAR

\ The CAVIAR\ track at UCSC was created using the CAVIAR high-confidence set, which\ represents the high causal variants that have a causal posterior probability\ (CPP) of > 0.1.\

\ \

DAP-G

\ The DAP-G track at\ UCSC was created using the DAP-G 95% credible set, which represents varaints\ with strong eQTLs signals, which are signal clusters with signal-level\ posterior inclusion probability (SPIP) > 0.95.\

\ \

Data Access

\ The raw data for this track can be accessed in multiple ways. It can be explored interactively \ using the Table Browser or \ Data Integrator. You can also access the data\ entries in JSON format through our \ JSON API.

\ \

\ The data in this track are organized in bigBed file format. The underlying files\ can be obtained from our downloads server:\

GTEx CAVIAR - gtexCaviar.bb\
GTEx DAP-G - gtexDapg.bb\

\ \ Individual regions or the whole set of genome-wide annotations can be obtained using our tool\ bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system from the utilities directory linked below. For example, to extract only\ annotations in a given region, you could use the following command:

\ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gtex/eQtl/gtexCaviar.bb\ -chrom=chr16 -start=34990190 -end=36727467 stdout

\ \

Credits

\ Thanks to GTEx investigators, analysts, and portal team for providing this data.\ \

References

\ GTEx Consortium.\ \ The GTEx Consortium atlas of genetic regulatory effects across human tissues.\ Science. 2020 Sep 11;369(6509):1318-1330.\ PMID: 32913098; PMC: PMC7737656\

\ Lee Y, Luca F, Pique-Regi R, Wen X.\ \ Bayesian Multi-SNP Genetic Association Analysis: Control of FDR and Use of\ Summary Statistics.\ bioRxiv. 2018 May 8.\

\ Wen X, Lee Y, Luca F, Pique-Regi R.\ \ Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of\ Posteriors.\ Am J Hum Genet. 2016 Jun 2;98(6):1114-1129.\ PMID: 27236919; PMC: PMC4908152\

\ Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O.\ \ Fast and efficient QTL mapper for thousands of molecular phenotypes.\ Bioinformatics. 2016 May 15;32(10):1479-85.\ PMID: 26708335; PMC: PMC4866519\

\ Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E.\ \ Identifying causal variants at loci with multiple signals of association.\ Genetics. 2014 Oct;198(2):497-508.\ PMID: 25104515; PMC: PMC4196608\

\ GTEx Consortium.\ \ The Genotype-Tissue Expression (GTEx) project.\ Nat Genet. 2013 Jun;45(6):580-5.\ PMID: 23715323; PMC: PMC4010069\

\ \ GTEx Portal Documentation\

\ regulation 1 compositeTrack off\ group regulation\ itemRgb on\ longLabel GTEx fine-mapped cis-eQTLs\ shortLabel GTEx cis-eQTLs\ track gtexEqtlHighConf\ type bigBed\ visibility hide\ gtexGene GTEx Gene bed 6 + Gene Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors) 0 100 0 0 0 127 127 127 1 0 0

\ The scientific goal of the GTEx project required that the donors and their biospecimen \ present with no evidence of disease. \ The tissue types collected were chosen based on their clinical significance, logistical \ feasibility and their relevance to the scientific goal of the project and the \ research community. \ Postmortem samples were collected from non-diseased donors with ages ranging from 20 to 79. 34.4% of donors were female and 65.6% male. \

\ Additional summary plots of GTEx sample characteristics are available at the \ \ GTEx Portal Tissue Summary page.

\ \ \

Data Access

\ The raw data for the GTEx Gene expression track can be accessed interactively through the \ \ Table Browser or Data Integrator. Metadata can be \ found in the connected tables below.\

\ gtexGeneModel describes the gene names and coordinates in genePred format.
\ hgFixed.gtexTissue lists each of the 53 tissues in alphabetical order,\ corresponding to the comma separated expression values in gtexGene.
\ hgFixed.gtexSampleData has RPKM expression scores for each individual gene-sample \ data point, connected to gtexSample.
\ hgFixed.gtexSample contains metadata about sample time, collection site,\ and tissue, connected to the donor field in the gtexDonor table.
\ hgFixed.gtexDonor has anonymized information on the tissue donor.

\ For automated analysis and downloads, the track data files can be downloaded from \ our downloads server\ or the JSON API.\ Individual regions or the whole genome annotation can be accessed as text using our utility\ bigBedToBed. Instructions for downloading the utility can be found \ here. \ That utility can also be used to obtain features within a given range, e.g. \ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/gtex/gtexTranscExpr.bb -chrom=chr21\ -start=0 -end=100000000 stdout

\ Data can also be obtained directly from GTEx at the following link:\ \ https://gtexportal.org/home/datasets

\ \

Credits

\ Statistical analysis and data interpretation was performed by The GTEx Consortium Analysis \ Working Group. \ Data was provided by the GTEx LDACC at The Broad Institute of MIT and Harvard.

\ \

References

\ GTEx Consortium.\ \ The Genotype-Tissue Expression (GTEx) project.\ Nat Genet. 2013 Jun;45(6):580-5.\ PMID: 23715323; \ PMC: PMC4010069\

\ \

\ Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET et al.\ \ A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project.\ Biopreserv Biobank. 2015 Oct;13(5):311-9.\ PMID: 26484571; \ PMC: PMC4675181

\ \

\ \ expression 1 group expression\ html gtexGeneExpr\ longLabel Gene Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors)\ maxItems 200\ pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"\ shortLabel GTEx Gene\ spectrum on\ track gtexGene\ type bed 6 +\ visibility hide\ gtexTranscExpr GTEx Transcript bigBarChart Transcript Expression in 53 tissues from GTEx RNA-seq of 8555 samples/570 donors 0 100 0 0 0 127 127 127 0 0 0

Description

\ The\ NIH Genotype-Tissue Expression (GTEx)\ project was created to establish a sample and data resource for studies on the relationship\ between genetic variation and gene expression in multiple human tissues. \ This track displays median transcript expression levels in 53 tissues, based on\ RNA-seq data from the GTEx midpoint milestone data release (V6, October 2015).\ To view the GTEx tissues in anatomical context, see the \ GTEx Body Map.\

\ Data for this track were computed at UCSC from GTEx RNA-seq sequence data using the\ Toil\ pipeline running the kallisto transcript-level quantification tool.

\ \

Display Conventions

\ In Full and Pack display modes, expression for each transcript is represented by a colored \ bar chart, where the height of each bar represents the median expression level across all \ samples for a tissue, and the bar color indicates the tissue.\

\ The bar chart display has the same width and tissue order for all transcripts.\ Mouse hover over a bar will show the tissue and median expression level.\ The Squish display mode draws a rectangle for each gene, colored to indicate the tissue\ with highest expression level if it contributes more than 10% to the overall expression\ (and colored black if no tissue predominates).\ In Dense mode, the darkness of the grayscale rectangle displayed for the transcript reflects \ the total median expression level across all tissues.

\ Click-through on a graph displays a boxplot of expression level quartiles with outliers, \ per tissue.

\ \

Methods

\ Sequence reads for this track were quantified to the hg38/GRCh38 human genome using kallisto\ assisted by the GENCODE v23 transcriptome definition. Read quantification was performed at UCSC\ by the Computational Genomics lab, using the Toil pipeline. The resulting kallisto files were\ combined to generate a transcript per million (TPM) expression matrix using the UCSC tool,\ kallistoToMatrix. Average TPM expression values for each tissue were calculated and \ used to generate a bed6+5 file that is the base of the track. This was done using the UCSC\ tool, expMatrixToBarchartBed. The bed track was then converted to a bigBed file using the \ UCSC tool, bedToBigBed.

\ \

Methods

\ \

\ From http://www.ebi.ac.uk/gwas/docs/methods:\

\ The GWAS Catalog data is extracted from the literature. Extracted information\ includes publication information, study cohort information such as cohort size,\ country of recruitment and subject ethnicity, and SNP-disease association\ information including SNP identifier (i.e. RSID), p-value, gene and risk\ allele. Each study is also assigned a trait that best represents the phenotype\ under investigation. When multiple traits are analysed in the same study either\ multiple entries are created, or individual SNPs are annotated with their\ specific traits. Traits are used both to query and visualise the data in the\ Catalog's web form and diagram-based query interfaces.\

\ Data extraction and curation for the GWAS Catalog is an expert activity; each\ step is performed by scientists supported by a web-based tracking and data\ entry system which allows multiple curators to search, annotate, verify and\ publish the Catalog data. Papers that qualify for inclusion in the Catalog are\ identified through weekly PubMed searches. They then undergo two levels of\ curation. First all data, including association information for SNPs, traits\ and general information about the study, are extracted by one curator. A second\ curator then performs an additional round of curation to double-check the\ accuracy and consistency of all the information. Finally, an automated pipeline\ performs validation of the extracted data, see the\ Quality control and SNP mapping section below for more\ details. This information is then used for queries and in the production of the\ diagram.\

\ \

Credits

\ \

\ Thanks to Audrey Michel, Stephen Kiniry and GWIPS-viz for providing the data for\ this track. If you wish to cite this track, please reference:\

\ \

\ Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM, Mullan JP, Donohue CA, Higgins DG,\ Baranov PV.\ GWIPS-viz: development of a ribo-seq genome browser.\ Nucleic Acids Res. 2014 Jan;42(Database issue):D859-64.\ PMID: 24185699; PMC: PMC3965066\

\ \

References

\ \

Data

\ \

\ Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y.\ \ Impact of regulatory variation from RNA to protein.\ Science. 2015 Feb 6;347(6222):664-7.\ PMID: 25657249;\ PMC: PMC4507520\

\ \

\ Cenik C, Cenik ES, Byeon GW, Grubert F, Candille SI, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H et al.\ \ Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans.\ Genome Res. 2015 Nov;25(11):1610-21.\ PMID: 26297486;\ PMC: PMC4617958\

\ \ \

\ Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AM, Wolf E, Lorenzin F, Eilers M et al.\ \ Myc coordinates transcription and translation to enhance transformation and suppress invasiveness.\ EMBO Rep. 2015 Dec;16(12):1723-36.\ PMID: 26538417;\ PMC: PMC4687422\

\ \

\ Jang C, Lahens NF, Hogenesch JB, Sehgal A.\ \ Ribosome profiling reveals an important role for translational control in circadian gene expression.\ Genome Res 2015 Dec;25(12):1836-47.\ PMID: 26338483;\ PMC: PMC4665005\

\ \

\ Ji Z, Song R, Regev A, Struhl K.\ \ Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins.\ Elife. 2015 Dec 19;4.\ PMID: 26687005;\ PMC: PMC4739776\

\ \

\ Sidrauski C, McGeachy AM, Ingolia NT, Walter P.\ \ The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly.\ Elife. 2015 Feb 26;4.\ PMID: 25719440;\ PMC: PMC4341466\

\ \

\ Tanenbaum ME, Stern-Ginossar N, Weissman JS, Vale RD.\ \ Regulation of mRNA translation during mitosis.\ Elife. 2015 Aug 25;4.\ PMID: 26305499;\ PMC: PMC4548207\

\ \

\ Tirosh O, Cohen Y, Shitrit A, Shani O, Le-Trilling VT, Trilling M, Friedlander G, Tanenbaum M, Stern-Ginossar N.\ \ The transcription and translation landscapes during human cytomegalovirus infection reveal novel host-pathogen interactions.\ PLoS Pathog. 2015 Nov 24;11(11):e1005288.\ PMID: 26599541;\ PMC: PMC4658056\

\ \

\ Werner A, Iwasaki S, McGourty CA, Medina-Ruiz S, Teerikorpi N, Fedrigo I, Ingolia NT, Rape M.\ \ Cell fate determination by ubiquitin-dependent regulation of translation.\ Nature. 2015 Sep 24;525(7570):523-7.\ PMID: 26399832;\ PMC: PMC4602398\

\ \

Protocol/Technique

\ \

\ Ingolia NT.\ \ Ribosome profiling: new views of translation, from single codons to genome scale.\ Nat Rev Genet. 2014 Mar;15(3):205-13.\ PMID: 24468696\

\ \

\ Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS.\ \ The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-\ protected mRNA fragments.\ Nat Protoc. 2012 Jul 26;7(8):1534-50.\ PMID: 22836135; PMC: PMC3535016\

\ \

\ Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS.\ \ Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.\ Science. 2009 Apr 10;324(5924):218-23.\ PMID: 19213877; PMC: PMC2746483\

\ \

\ Michel AM, Baranov PV.\ \ Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale.\ Wiley Interdiscip Rev RNA. 2013 Sep-Oct;4(5):473-90.\ PMID: 23696005; PMC: PMC3823065\

\ expression 0 autoScale off\ group expression\ html gwipsvizRiboseq\ longLabel Ribosome Profiling from GWIPS-viz\ maxHeightPixels 100:32:8\ shortLabel GWIPS-viz Riboseq\ track gwipsvizRiboseq\ type bigWig 0 3589344\ viewLimits 0:2000\ visibility hide\ heartCellAtlas Heart Cell Atlas Heart single cell RNA data from https://heartcellatlas.com 0 100 0 0 0 127 127 127 0 0 0

Description

\ This track displays data from \ Cells of the adult human heart. Single-cell and single-nucleus RNA\ sequencing (RNA-seq) was used to profile transcriptomes from six regions of the heart:\ the interventricular septum (SP), apex (AX), left ventricle (LV), right\ ventricle (RV), left atrium (LA), and right atrium (RA). A total of 11 cardiac\ cell types were identified along with their marker genes after uniform manifold\ approximation and projection (UMAP) embedding of 487,106 cells. Note that the RNA-seq\ data is generated using Tag-sequencing (Tag-seq) and does not cover all exons.

\ \

\ This track collection contains nine bar chart tracks of RNA expression in the\ human heart where cells are grouped by cell type \ (Heart HCA Cells), age \ (Heart HCA Age), donor \ (Heart HCA Donor), region of the heart \ (Heart HCA Region),\ sample (Heart HCA Sample), sex \ (Heart HCA Sex), source \ (Heart HCA Source), cell\ state (Heart HCA State), \ and 10x chemistry version \ (Heart HCA Version). \ The default track displayed is \ Heart HCA Cells.

\ \

Display Conventions

\ The cell types are colored by which class they belong to according to the following table.

\ \

\ \ \ \ \ \ \ \ \ \ \ \ \ \
Color Cell classification
neural
adipose
fibroblast
immune
muscle
lymphoid
epithelial
endothelial
\

\ \

\ Cells that fall into multiple classes will be colored by blending the colors associated\ with those classes. The colors will be purest in the \ Heart HCA Cells subtrack, where the \ bars represent relatively pure cell types. They can give an overview of the cell composition \ within other categories in other subtracks as well.

\ \

Method

\ Healthy heart tissues were obtained from 14 UK and North American transplant\ organ donors ages 40-75. Tissues were taken from deceased donors after\ circulatory death (DCD) and after brain death (DBD). To minimize\ transcriptional degradation, heart tissues were stored and transported on ice\ until freezing or tissue dissociation. Single nuclei were isolated from\ flash-frozen tissue using mechanical homogenization with a glass Dounce tissue\ grinder. Fresh heart tissues were enzymatically dissociated and automatically\ digested using gentleMACS Octo Dissociator. Next, Hoechst-positive single\ nuclei were FACS sorted prior to library preparation. In parallel, Cell\ suspensions from fresh heart tissue were enriched for CD45+ cells using MACS LS\ columns. Libraries of single cell and single nuclei were prepared using 10x\ Genomics 3' v2 or v3. 3' gene expression libraries were sequenced on an\ Illumina HiSeq4000 and NextSeq500. In total 45,870 cells, 78,023 CD45+ enriched\ cells, and 363,213 nuclei were profiled for 11 major cell types of the heart.