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Configure Tracks on UCSC Genome Browser: Human Dec. 2013 (GRCh38/hg38)
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Control track and group visibility more selectively below.
+   Mapping and Sequencing    
-   Genes and Gene Predictions    
GENCODE V49 GENCODE V49
NCBI RefSeq RefSeq genes from NCBI
CCDS Consensus CDS
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
GENCODE Archive GENCODE Archive
     GENCODE V36     GENCODE V36
     GENCODE V38     GENCODE V38
     GENCODE V39     GENCODE V39
     GENCODE V43     GENCODE V43
     GENCODE V44     GENCODE V44
     GENCODE V45     GENCODE V45
     GENCODE V46     GENCODE V46
     GENCODE V47     GENCODE V47
     GENCODE V48     GENCODE V48
GENCODE Versions Container of all new and previous GENCODE releases
     GENCODE V20 (Ensembl 76)     Gene Annotations from GENCODE Version 20 (Ensembl 76)
     All GENCODE V22     All GENCODE transcripts including comprehensive set V22
     All GENCODE V23     All GENCODE transcripts including comprehensive set V23
     All GENCODE V24     All GENCODE transcripts including comprehensive set V24
     All GENCODE V25     All GENCODE transcripts including comprehensive set V25
     All GENCODE V26     All GENCODE annotations from V26 (Ensembl 88)
     All GENCODE V27     All GENCODE annotations from V27 (Ensembl 90)
     All GENCODE V28     All GENCODE annotations from V28 (Ensembl 92)
     All GENCODE V29     All GENCODE annotations from V29 (Ensembl 94)
     All GENCODE V30     All GENCODE annotations from V30 (Ensembl 96)
     All GENCODE V31     All GENCODE annotations from V31 (Ensembl 97)
     All GENCODE V32     All GENCODE annotations from V32 (Ensembl 98)
     All GENCODE V33     All GENCODE annotations from V33 (Ensembl 99)
     All GENCODE V34     All GENCODE annotations from V34 (Ensembl 100)
     All GENCODE V35     All GENCODE annotations from V35 (Ensembl 101)
     All GENCODE V36     All GENCODE annotations from V36 (Ensembl 102)
     All GENCODE V37     All GENCODE annotations from V37 (Ensembl 103)
     All GENCODE V38     All GENCODE annotations from V38 (Ensembl 104)
     All GENCODE V39     All GENCODE annotations from V39 (Ensembl 105)
     All GENCODE V40     All GENCODE annotations from V40 (Ensembl 106)
     All GENCODE V41     All GENCODE annotations from V41 (Ensembl 107)
     All GENCODE V42     All GENCODE annotations from V42 (Ensembl 108)
     All GENCODE V43     All GENCODE annotations from V43 (Ensembl 109)
     All GENCODE V44     All GENCODE annotations from V44 (Ensembl 110)
     All GENCODE V45     All GENCODE annotations from V45 (Ensembl 111)
     All GENCODE V46     All GENCODE annotations from V46 (Ensembl 112)
     All GENCODE V47     All GENCODE annotations from V47 (Ensembl 113)
     All GENCODE V48     All GENCODE annotations from V48 (Ensembl 114)
     All GENCODE V49     All GENCODE annotations from V49 (Ensembl 115)
HGNC HUGO Gene Nomenclature
IKMC Genes Mapped International Knockout Mouse Consortium Genes Mapped to Human Genome
LRG Transcripts Locus Reference Genomic (LRG) / RefSeqGene Fixed Transcript Annotations
MANE MANE Select Plus Clinical: Representative transcript from RefSeq & GENCODE
MGC/ORFeome Genes MGC/ORFeome Full ORF mRNA Clones
     ORFeome Clones     ORFeome Collaboration Gene Clones
     MGC Genes     Mammalian Gene Collection Full ORF mRNAs
new NMD Escape NMD Escape: Predicted regions where premature termination codons escape NMD
     NMDetective-B PTC     NMDetective-B: Decision tree NMD efficiency for first out-of-frame PTC
     NMDetective-A PTC     NMDetective-A: Random forest NMD efficiency for first out-of-frame PTC
     NMDetective-B     NMDetective-B: Decision tree prediction of NMD efficiency (Lindeboom 2016)
     NMDetective-A     NMDetective-A: Random forest prediction of NMD efficiency (Lindeboom 2016)
     NMDetective-AI variants     NMDetective-AI: Per-stop-gain predictions for every codon (MANE Select only)
     NMDetective-AI     NMDetective-AI: Deep-learning NMD efficiency prediction per position (MANE Select only)
     NMD Escape RefSeq     NMD escape predictions: NCBI RefSeq Curated transcripts
     NMD Escape Gencode     NMD escape predictions: Gencode transcripts
     NMD Escape MANE     NMD escape predictions: MANE Select Plus Clinical transcripts
Non-canonical ORFs Non-canonical Open Reading Frames
     UTRannotator uORFs     ncORFs: Upstream Open Reading Frames (uORFs) from UTRannotator
     OpenProt (MS>=2)     ncORFs: OpenProt - proteins with at least 2 MS peptides v2.2
     OpenProt     ncORFs: OpenProt - alternative and reference proteins v2.2
     nuORFdb     ncORFs: nuORFdb - non-canonical ORFs from nuORFdb v1.2
     MetamORF     ncORFs: MetamORF - meta-database of non-canonical ORFs
     GENCODE Phase II ncORFs Prim     ncORFs: GENCODE Phase II non-canonical ORFs - primary
     GENCODE Phase II ncORFs Compr     ncORFs: GENCODE Phase II non-canonical ORFs - comprehensive
Non-coding RNA RNA sequences that do not code for a protein
     tRNA Genes     Transfer RNA Genes Identified with tRNAscan-SE
     sno/miRNA     C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase
     lincRNA TUCP     lincRNA and TUCP transcripts
     lincRNA RNA-Seq     lincRNA RNA-Seq reads expression abundances
Other RefSeq Non-Human RefSeq Genes
Pfam in GENCODE Pfam Domains in GENCODE Genes
Prediction Archive Gene Prediction Archive
     SIB Genes     Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs
     SGP Genes     SGP Gene Predictions Using Mouse/Human Homology
     Genscan Genes     Genscan Gene Predictions
     Geneid Genes     Geneid Gene Predictions
     AUGUSTUS     AUGUSTUS ab initio gene predictions v3.1
Pseudogenes Pseudogenes and Parents
RetroGenes V9 Retroposed Genes V9, Including Pseudogenes
TransMap V5 TransMap Alignments Version 5
     TransMap ESTs     TransMap EST Mappings Version 5
     TransMap RNA     TransMap GenBank RNA Mappings Version 5
     TransMap RefGene     TransMap RefSeq Gene Mappings Version 5
     TransMap Ensembl     TransMap Ensembl and GENCODE Mappings Version 5
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
UniProt UniProt SwissProt/TrEMBL Protein Annotations
-   Phenotypes, Variants, and Literature    
AlphaMissense AlphaMissense Score for all possible single-basepair mutations (zoom in for scores)
CADD 1.6 CADD 1.6 Score for all single-basepair mutations and selected insertions/deletions
     CADD 1.6 Ins     CADD 1.6 Score: Insertions - label is length of insertion
     CADD 1.6 Del     CADD 1.6 Score: Deletions - label is length of deletion
     CADD 1.6     CADD 1.6 Score for all possible single-basepair mutations (zoom in for scores)
CADD 1.7 CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions
     CADD 1.7 Ins     CADD 1.7 Score: Insertions - label is length of insertion
     CADD 1.7 Del     CADD 1.7 Score: Deletions - label is length of deletion
     CADD 1.7     CADD 1.7 Score for all possible single-basepair mutations (zoom in for scores)
Cancer Gene Expr Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23)
     Cancer Transc Expr     Transcript-level Expression in 33 TCGA Cancer Tissues (GENCODE v23)
     Cancer Gene Expr     Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23)
CIViC CIViC - Expert & crowd-sourced cancer variant interpretation
ClinGen ClinGen curation activities (Dosage Sensitivity and Gene-Disease Validity)
ClinGen CNVs Clinical Genome Resource (ClinGen) CNVs
ClinVar Variants ClinVar Variants
Constraint scores Human constraint scores
     UKB Depl. Rank Score     UK Biobank / deCODE Genetics Depletion Rank Score
     HMC     HMC - Homologous Missense Constraint Score on PFAM domains
     JARVIS     JARVIS: score to prioritize non-coding regions for disease relevance
Coriell CNVs Coriell Cell Line Copy Number Variants
COSMIC Catalogue of Somatic Mutations in Cancer V101
COSMIC Regions Catalogue of Somatic Mutations in Cancer V82
COVID Data Container of SARS-CoV-2 data
     COVID Rare Harmful Var     Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort
     COVID GWAS v3     GWAS meta-analyses from the COVID-19 Host Genetics Initiative
     COVID GWAS v4     COVID risk variants from GWAS meta-analyses by the COVID-19 Host Genetics Initiative (Rel 4, Oct 2020)
DECIPHER DECIPHER
     DECIPHER Population CNVs     DECIPHER: Population CNVs
     DECIPHER CNVs     DECIPHER CNVs
updated Deleteriousness Predictions Variant Deleteriousness / Variant Impact Prediction Scores
    new PromoterAI     PromoterAI Promoter Variant Impact Scores (zoom for exact score)
    new PrimateAI-3D     PrimateAI-3D Pathogenicity Predictions for Missense Variants
     MutScore     MutScore: Variant clustering in 3D protein structures
Development Delay Copy Number Variation Morbidity Map of Developmental Delay
Dosage Sensitivity pHaplo and pTriplo dosage sensitivity map from Collins et al 2022
G2P Project Gene2Phenotype Project
GenCC GenCC: The Gene Curation Coalition Annotations
Gene Interactions Protein Interactions from Curated Databases and Text-Mining
GeneReviews GeneReviews
GWAS Catalog NHGRI-EBI Catalog of Published Genome-Wide Association Studies
HGMD Public 2025 Human Gene Mutation Database - Public Version 2025
LOVD Variants LOVD: Leiden Open Variation Database Public Variants
MITOMAP MITOMAP: A human mitochondrial genome database
Orphanet Orphadata: Aggregated Data From Orphanet
PanelApp Genomics England and Australia PanelApp Diagnostics
REVEL Scores REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score)
SNPedia SNPedia
Splicing Impact Splicing Impact Prediction Scores and Databases
     SpliceVarDB     SpliceVarDB: Experimentally validated splicing variants
     AbSplice Scores     Aberrant Splicing Prediction Scores
     SpliceAI Wildtype     SpliceAI Wildtype: Splicing of the reference genome sequence
     SpliceAI Variants     SpliceAI: Splice Variant Prediction Score
TCGA Pan-Cancer TCGA Pan-Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)
UniProt Variants UniProt/SwissProt Amino Acid Substitutions
updated Variants in Papers Genetic Variants mentioned in scientific publications
    updated Varaico Variants (suppl)     Varaico Variants extracted from Supplementary Data
    updated Varaico Variants     Varaico Variants extracted from full text publications, titles, and abstracts
     PubTator Variants     dbSNP variants and other genetic variants grounded to dbSNP by tmVar; collected by PubTator3
     enGenome VarChat     enGenome VarChat: Literature match and variant's summary
     Avada Variants     Avada Variants extracted from full text publications
-   Variation    
dbSNP 155 Short Genetic Variants from dbSNP release 155
1000 Genomes 1000 Genomes Phase 3
     1000G Ph3 Vars     1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels
     1000 Genomes Trios     Thousand Genomes Project Family VCF Trios
Ancient Hominids Ancient Hominid DNA Variants
     Arcseqhub Neanderthal     Ancient Hominids: Arcseqhub Neanderthal VCF Variants
     Arcseqhub Denisovan     Ancient Hominids: Arcseqhub Denisovan VCF Variants
Array Probesets Microarray Probesets and OGM sites
dbSNP Archive dbSNP Track Archive
     All SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141)
     Common SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) Found in >= 1% of Samples
     Flagged SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) That Map to Multiple Genomic Loci
     All SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142)
     Common SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples
     Flagged SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci
     All SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144)
     Common SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples
     Flagged SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci
     All SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146)
     Common SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples
     Flagged SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci
     All SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147)
     Common SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples
     Flagged SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci
     Flagged SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc
     Common SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples
     All SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150)
     Mult. SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci
     Mult. SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci
     Flagged SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc
     All SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151)
     Common SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples
     dbSNP 153     Short Genetic Variants from dbSNP release 153
dbVar Struct Var NCBI dbVar Structural Variants
     dbVar Somatic SV     NCBI dbVar Somatic Structural Variants
     dbVar Other SV     NCBI dbVar Other Structural Variants
     dbVar Conflict SV     NCBI dbVar Curated Conflict Variants
     dbVar Common SV     NCBI dbVar Curated Common Structural Variants
DGV Struct Var Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)
Genome In a Bottle Genome In a Bottle Structural Variants and Trios
new gnomAD Genome Aggregation Database (gnomAD)
     gnomAD Structural Variants     Genome Aggregation Database (gnomAD) - Structural Variants v4.1
    new gnomAD STR     Genome Aggregation Database (gnomAD) - Short Tandem Repeat Genotypes at Disease-Associated Loci
     gnomAD Rare CNV Variants     Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1
     gnomAD pext     Genome Aggregation Database (gnomAD) Proportion Expression Across Transcript Scores (pext)
     gnomAD Constraint Metrics     Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (LOEUF, pLI, and Z-scores)
     gnomAD Mut Constraint     Gnocchi: Genome Aggregation Database (gnomAD) non-coding constraint of haploinsufficient variation, includes chrX
     gnomAD v3 Genome Coverage     Genome Aggregation Database (gnomAD) Genome Sample Coverage v3.0.1
     gnomAD v4 Exome Coverage     Genome Aggregation Database (gnomAD) Exome Sample Coverage v4.0
     gnomAD v2     Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1
     gnomAD v3     Genome Aggregation Database (gnomAD) Genome Variants v3
     Deprecated: gnomAD v3.1     Deprecated: Genome Aggregation Database (gnomAD) Genome Variants v3.1
     gnomAD v3.1.1     Genome Aggregation Database (gnomAD) Genome Variants v3.1.1
     gnomAD v4.1     Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1
Long-read Variants Long-read Variants
     CoLoRSdb structural variants     CoLoRSdb long-read structural variants
     CoLoRSdb small variants     CoLoRSdb long-read small variants
new Phased Variants Phased Variants from various sequencing projects
     gnomAD HGDP+1000G 4k WGS     Phased Variants: gnomAD HGDP + 1000 genomes callset - 4094 whole genomes, 80 populations
     Simons Genome Diversity Project 0.3k WGS     Phased Variants: Simons Genome Diversity Project - 279 samples, unmixed populations
     Human Genome Diversity Project, 1k WGS     Phased Variants: Human Genome Diversity Project (HGDP) - 1043 samples, isolated populations
     Mexico Biobank, 6k Array     Phased Variants: Mexico Biobank 6k Array
Platinum Genomes Platinum genome variants
new SNV Frequencies SNV Frequencies from various cohorts or national projects
     UK Biobank 361k imputed     SNV Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed
     Taiwan TPMI Axiom array     SNV Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese
     Sweden SweGen 1k WGS     SNV Frequencies: Sweden SweGen - 1k WGS
     SVatalog 101 WGS     SNV Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs
     Singapore NPM 9.7k WGS     SNV Frequencies: NPM Singapore - 9,770 WGS samples
     SGDP 279 WGS     SNV Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations
     SFARI SPARK 140k WES     SNV Frequencies: SFARI SPARK - 140k WES
     SFARI SPARK 12k WGS     SNV Frequencies: SFARI SPARK - 12,519 WGS
     SCHEMA 121k WES Sz     SNV Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls
     Saudi Genome 302 WGS     SNV Frequencies: Saudi Genome Project - 302 WGS samples
     NHLBI TOPMed 10 151k WGS     SNV Frequencies: NHLBI TOPMed - 151k WGS
     Netherlands GoNL 498 WGS     SNV Frequencies: Genome of the Netherlands - 250 Dutch trios
     NCBI ALFA 408k mixed     SNV Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants
     Mexico Biobank 6k Array     SNV Frequencies: Mexico Biobank - 6,011 individuals, genotyping array
     Korea KOVA 5.3k mixed     SNV Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES
     Japan ToMMo 61k WGS     SNV Frequencies: Japan 61k - ToMMo SNV+Indels
     India IndiGenomes 1k WGS     SNV Frequencies: IndiGenomes India - 1,029 samples
     India GenomeIndia 9.7k WGS     SNV Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025)
     HRC 30k WGS     SNV Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes)
     GREGoR R4 3.6k WGS     SNV Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families
     gnomAD HGDP+1kG 4k WGS     SNV Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations
     GenomeAsia 1.7k SNVs     SNV Frequencies: GenomeAsia Pilot - Substitutions
     GenomeAsia 1.7k Indels     SNV Frequencies: GenomeAsia Pilot - Indels
     GA4K 552 PacBio LR     SNV Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD
     FinnGen R12 500k imputed     SNV Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS
     CoLoRSdb 1k LR SNV/Ind     SNV Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset
     China WBBC 4.5k WGS     SNV Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups
     China ChinaMAP 10.5k WGS     SNV Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population
     Brazil ABraOM 1k WGS     SNV Frequencies: ABraOM Brazil - 1,171 unrelated individuals
     Australia MGRB 4k WGS     SNV Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS
     AllOfUs v7 245k WGS     SNV Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20
     12 Afr Pops 180 WGS     SNV Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023)
     Genotyping Array Databases Combined     SNV Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed)
     Disease cohorts     SNV Frequencies: variants in ~130,000 affected or case individuals (autism, schizophrenia, rare disease cohorts)
     Population reference     SNV Frequencies: variants in ~1.5 million individuals from population cohorts and unaffected or control arms
new Tandem Repeat Variation Tandem Repeat Variation
     WebSTR     WebSTR Short Tandem Repeat Loci (EnsembleTR Panel, 1000 Genomes)
     TRExplorer     TRExplorer V2 Tandem Repeat Catalog
     ToMMo 61k STR     ToMMo 61KJPN Short Tandem Repeat Allele Counts (Expansion Hunter)
     STRchive     STRchive Disease-Associated Short Tandem Repeat Loci
     1KG Vienna ONT VNTR     1000 Genomes Vienna ONT VNTR Allele Statistics (VAMOS, 1,019 samples, long-read)
-   Human Pangenome - HPRC    
Multiple Alignment Multiple Alignment on 90 human genome assemblies
Pairwise Alignments Human Genomes, Chain/Net pairwise alignments, as mapped by the HPRC project
Rearrangements Rearrangements including indels, inversions, and duplications
Short Variants Short Variants
     HPRC Variants > 3bp     HPRC VCF variants filtered for items size > 3bp
     HPRC Variants <= 3bp     HPRC VCF variants filtered for items size <= 3bp
     HPRC All Variants     HPRC variants decomposed from hprc-v1.0-mc.grch38.vcfbub.a100k.wave.vcf.gz (Liao et al 2023), no size filtering
-   RNA and Transcriptome    
Human ESTs Human ESTs Including Unspliced
Human mRNAs Human mRNAs from GenBank
Long-read Transcripts Transcripts and other data generated using long-read sequencing technology (PacBio and Oxford Nanopore)
     ENCODE4 Transcripts     ENCODE4 Long Read Transcripts
     CLS long-read RNAs     Capture long-seq long-read lncRNAs
Other ESTs Non-Human ESTs from GenBank
Other mRNAs Non-Human mRNAs from GenBank
new recount3 recount3 introns
SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics
Spliced ESTs Human ESTs That Have Been Spliced
-   Expression    
GTEx Gene V8 Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019)
GTEx RNA-Seq Coverage GTEx V8 RNA-Seq Read Coverage by Tissue
Affy Archive Affymetrix Archive
     Affy U95     Alignments of Affymetrix Consensus/Exemplars from HG-U95
     Affy U133     Alignments of Affymetrix Consensus/Exemplars from HG-U133
     Affy GNF1H     Alignments of Affymetrix Consensus/Exemplars from GNF1H
EPDnew Promoters Promoters from EPDnew
GNF Atlas 2 GNF Expression Atlas 2
GTEx Gene Gene Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors)
GTEx Transcript Transcript Expression in 53 tissues from GTEx RNA-seq of 8555 samples/570 donors
GWIPS-viz Riboseq Ribosome Profiling from GWIPS-viz
MaveDB Experiments Heatmaps and Alignment for MaveDB
     MaveDB Heatmaps     Variant Effect Maps from MaveDB
     MaveDB Alignments     MaveDB Experiment Sequence Alignments
miRNA Tissue Atlas Tissue-Specific microRNA Expression from Two Individuals
Single Cell Expression Single cell RNA expression levels cell types from many organs
+   Single Cell RNA-seq    
-   Regulation    
new ENCODE cCREs ENCODE Registry of cCREs (candidate Cis-Regulatory Elements)
     ENCODE3 cCREs     ENCODE3 Registry of candidate Cis-Regulatory Elements (cCREs)
     ENCODE4 Core Collection     ENCODE4 Core Collection of 170 biosamples with sample-specific cCRE annotations & epigenomic signals
     ENCODE4 cCREs     ENCODE4 Registry of candidate Cis-Regulatory Elements (cCREs)
new ENCODE4 Regulation Integrated Regulation from ENCODE 4
     TF ChIP-seq (Indiv.)     Peaks and signal from individual transcription factor ChIP experiments from ENCODE 4
     RNA-seq (Indiv.)     Signal from individual total RNA-seq experiments from ENCODE 4
     DNase/ATAC/Histone/CTCF (Indiv.)     Peaks and signal from individual DNase, ATAC, histone, and CTCF experiments from ENCODE 4
     TF rPeaks     Transcription factor representative peak (rPeak) clusters from ENCODE 4
     Transcription (Layered)     Strand-specific transcription signal measured by total RNA-seq, averaged by organ/tissue
     CTCF (Layered)     CTCF binding signal from ChIP-seq, averaged by organ/tissue
     H3K27ac (Layered)     H3K27ac signal marking active enhancers and promoters, averaged by organ/tissue
     H3K4me3 (Layered)     H3K4me3 signal marking active and poised promoters, averaged by organ/tissue
     ATAC (Layered)     Chromatin accessibility from ATAC-seq signal, averaged by organ/tissue
     DNase (Layered)     Chromatin accessibility from DNase-seq signal, averaged by organ/tissue
ENCODE Regulation Integrated Regulation from ENCODE
     TF ChIP     Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3
     TF Clusters     Transcription Factor ChIP-seq Clusters (340 factors, 129 cell types) from ENCODE 3
     DNase HS     DNase I Hypersensitivity in 95 cell types from ENCODE
     DNase Signal     DNase I Hypersensitivity Signal Colored by Similarity from ENCODE
     DNase Clusters     DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)
     Layered H3K27Ac     H3K27Ac Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
     Layered H3K4Me3     H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE
     Layered H3K4Me1     H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
     Transcription     Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE
     TF rPeak Clusters     Transcription Factor Representative Peak (rPeak) Clusters (912 factors in 1152 biosamples) from ENCODE 4
new DNA Methylation DNA Methylation
     Human Methylation Atlas Signals     Human Methylation Atlas WGBS cell type signals
     Human Methylation Atlas Summary     Human Methylation Atlas summary regions and enhancers
CpG Islands CpG Islands (Islands < 300 Bases are Light Green)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
FANTOM5 FANTOM5: Mapped transcription start sites (TSS) and their usage
     TSS activity (TPM)     FANTOM5: TSS activity per sample (TPM)
     TSS activity - read counts     FANTOM5: TSS activity per sample read counts
     Max counts of CAGE reads     FANTOM5: Max counts of CAGE reads
     Total counts of CAGE reads     FANTOM5: Total counts of CAGE reads
     TSS peaks     FANTOM5: DPI peak, robust set
GeneHancer GeneHancer Regulatory Elements and Gene Interactions
GTEx cis-eQTLs GTEx fine-mapped cis-eQTLs
Hi-C and Micro-C Comparison of Micro-C and In situ Hi-C protocols in H1-hESC and HFFc6
updated JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
new MPRAs Massively Parallel Reporter Assays
     MPRAVarDB     MPRAs: MPRAVarDB - MPRA-tested Regulatory Variant Effects
     MPRA Base     MPRAs: MPRA Base Enhancer Elements
ORegAnno Regulatory elements from ORegAnno
RefSeq Func Elems NCBI RefSeq Functional Elements
ReMap ChIP-seq ReMap Atlas of Regulatory Regions
VISTA Enhancers VISTA Enhancers
-   Comparative Genomics    
UCSC 100 Vertebrates UCSC 100 Vertebrates - 100 vertebrate genomes aligned with MultiZ by the UCSC Browser Group
Zoonomia 241 Placent Zoonomia Alignment - 241 Placental Mammal Genomes aligned by the Zoonomia Project with Cactus
UCSC 30 Primates UCSC 30 Primates - 30 primate genomes aligned with MultiZ by the UCSC Browser Group
Primate Chain/Net Primate Genomes, Chain and Net Alignments
Placental Chain/Net Non-primate Placental Mammal Genomes, Chain and Net Alignments
Vertebrate Chain/Net Non-placental Vertebrate Genomes, Chain and Net Alignments
CHM13 alignments CHM13 (GCA_009914755.4) v1_nfLO liftOver alignments
Hiller Lab 470 Mammals Hiller Lab 470 Mammals - 470 mammalian genomes aligned with Multiz by Michael Hiller's Group,
Unusually Conserved Unusually Conserved Regions - Ultracons, HARs, etc.
Zoonomia+Primates 447 Zoonomia+Primates 447 - 447 mammals, including 233 primates, aligned with Cactus, for Kuderna et al. 2023
-   Repeats    
RepeatMasker Repeating Elements by RepeatMasker
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
NuMTs Sequence Nuclear mitochondrial DNA segments
RepeatMasker Viz. Detailed Visualization of RepeatMasker Annotations
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
Self Alignment Human Chained Self Alignments
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust