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Configure Tracks on UCSC Genome Browser: Human Feb. 2009 (GRCh37/hg19)
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Control track and group visibility more selectively below.
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Assembly Assembly from Fragments
BAC End Pairs BAC End Pairs
BU ORChID ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius lab)
Chromosome Band Chromosome Bands Localized by FISH Mapping Clones
deCODE Recomb deCODE Recombination maps, 10Kb bin size, October 2010
ENCODE Pilot Regions Used for ENCODE Pilot Project (1%)
Exome Probesets Exome Capture Probesets and Targeted Region
FISH Clones Clones Placed on Cytogenetic Map Using FISH
Fosmid End Pairs Fosmid End Pairs
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
GRC Incident GRC Incident Database
GRC Map Contigs Genome Reference Consortium Map Contigs
p14 GRC Patches GRC Patches: Alt Haplotypes and Fix Sequences
Hg18 Diff Contigs New to GRCh37/(hg19), Not Carried Forward from NCBI Build 36(hg18)
Hg38 Diff Contigs Dropped or Changed from GRCh37(hg19) to GRCh38(hg38)
Hi Seq Depth Regions of Exceptionally High Depth of Aligned Short Reads
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
liftOver & ReMap UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg38
LRG Regions Locus Reference Genomic (LRG) / RefSeqGene Sequences Mapped to Feb. 2009 (GRCh37/hg19) Assembly
Map Contigs Physical Map Contigs
Mappability Mappability or Uniqueness of Reference Genome from ENCODE
Problematic Regions Problematic Regions for NGS or Sanger sequencing or very variable regions
Recomb Rate Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default)
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
STS Markers STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
-   Genes and Gene Predictions    
updated GENCODE V48lift37 GENCODE V48lift37
NCBI RefSeq RefSeq genes from NCBI
Genes Archive Previous versions of GENCODE/UCSC Genes (knownGene)
     GENCODE V45lift37     GENCODE V45lift37
     GENCODE V47lift37     GENCODE V47lift37
     UCSC Genes 2013     Legacy UCSC Genes track (knownGene) from 2013
CCDS Consensus CDS
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
Ensembl Genes Ensembl Genes
EvoFold EvoFold Predictions of RNA Secondary Structure
Exoniphy Exoniphy Human/Mouse/Rat/Dog
updated GENCODE Versions Container of all new and previous GENCODE releases
    new GENCODE V48lift37     GENCODE lifted annotations from V48lift37 (Ensembl 114)
     GENCODE V47lift37     GENCODE lifted annotations from V47lift37 (Ensembl 113)
     GENCODE V46lift37     GENCODE lifted annotations from V46lift37 (Ensembl 112)
     GENCODE V45lift37     GENCODE lifted annotations from V45lift37 (Ensembl 111)
     GENCODE V44lift37     GENCODE lifted annotations from V44lift37 (Ensembl 110)
     GENCODE V43lift37     GENCODE lifted annotations from V43lift37 (Ensembl 109)
     GENCODE V42lift37     GENCODE lifted annotations from V42lift37 (Ensembl 108)
     GENCODE V41lift37     GENCODE lifted annotations from V41lift37 (Ensembl 107)
     GENCODE V40lift37     GENCODE lifted annotations from V40lift37 (Ensembl 106)
     GENCODE V39lift37     GENCODE lifted annotations from V39lift37 (Ensembl 105)
     GENCODE V38lift37     GENCODE lifted annotations from V38lift37 (Ensembl 104)
     GENCODE V37lift37     GENCODE lifted annotations from V37lift37 (Ensembl 103)
     GENCODE V36lift37     GENCODE lifted annotations from V36lift37 (Ensembl 102)
     GENCODE V35lift37     GENCODE lifted annotations from V35lift37 (Ensembl 101)
     GENCODE V34lift37     GENCODE lifted annotations from V34lift37 (Ensembl 100)
     GENCODE V33lift37     GENCODE lifted annotations from V33lift37 (Ensembl 99)
     GENCODE V31lift37     GENCODE lifted annotations from V31lift37 (Ensembl 97)
     GENCODE V28lift37     GENCODE lifted annotations from V28lift37 (Ensembl 92)
     GENCODE Gene V27lift37     Gene Annotations from GENCODE Version 27lift37
     GENCODE Gene V24lift37     Gene Annotations from GENCODE Version 24lift37
     GENCODE Genes V19     Gene Annotations from GENCODE Version 19
     GENCODE Genes V17     Gene Annotations from ENCODE/GENCODE Version 17
     GENCODE Genes V14     Gene Annotations from ENCODE/GENCODE Version 14
     GENCODE Genes V7     Gene Annotations from ENCODE/GENCODE Version 7
H-Inv 7.0 H-Inv 7.0 Gene Predictions
updated HGNC HUGO Gene Nomenclature
IKMC Genes Mapped International Knockout Mouse Consortium Genes Mapped to Human Genome
lincRNAs Human Body Map lincRNAs and TUCP Transcripts
     lincRNA RNA-Seq Reads     lincRNA RNA-Seq reads expression abundances
     lincRNA Transcripts     lincRNA and TUCP transcripts
LRG Transcripts Locus Reference Genomic (LRG) / RefSeqGene Fixed Transcript Annotations
MGC/ORFeome Genes MGC/ORFeome Full ORF mRNA Clones
     MGC Genes     Mammalian Gene Collection Full ORF mRNAs
     ORFeome Clones     ORFeome Collaboration Gene Clones
Other RefSeq Non-Human RefSeq Genes
Pfam in GENCODE Pfam Domains in GENCODE Genes
Prediction Archive Gene Prediction Archive
     AceView Genes     AceView Gene Models With Alt-Splicing
     AUGUSTUS     AUGUSTUS ab initio gene predictions v3.1
     Geneid Genes     Geneid Gene Predictions
     Genscan Genes     Genscan Gene Predictions
     N-SCAN     N-SCAN Gene Predictions
     SGP Genes     SGP Gene Predictions Using Mouse/Human Homology
     SIB Genes     Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs
Retroposed Genes Retroposed Genes V5, Including Pseudogenes
sno/miRNA C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase
TransMap V5 TransMap Alignments Version 5
     TransMap Ensembl     TransMap Ensembl and GENCODE Mappings Version 5
     TransMap RefGene     TransMap RefSeq Gene Mappings Version 5
     TransMap RNA     TransMap GenBank RNA Mappings Version 5
     TransMap ESTs     TransMap EST Mappings Version 5
tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
UniProt UniProt SwissProt/TrEMBL Protein Annotations
Vega Genes Vega Annotations
Yale Pseudo60 Yale Pseudogenes based on Ensembl Release 60
-   Phenotypes, Variants, and Literature    
Publications Publications: Sequences in Scientific Articles
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     CADD 1.6 Score for all possible single-basepair mutations (zoom in for scores)
     CADD 1.6 Del     CADD 1.6 Score: Deletions - label is length of deletion
     CADD 1.6 Ins     CADD 1.6 Score: Insertions - label is length of insertion
CADD 1.7 CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions
     CADD 1.7     CADD 1.7 Score for all possible single-basepair mutations (zoom in for scores)
     CADD 1.7 Del     CADD 1.7 Score: Deletions - label is length of deletion
     CADD 1.7 Ins     CADD 1.7 Score: Insertions - label is length of insertion
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
     JARVIS     JARVIS: score to prioritize non-coding regions for disease relevance
     HMC     HMC - Homologous Missense Constraint Score on PFAM domains
     MetaDome     MetaDome - Tolerance Landscape score
     MetaDome All Data     MetaDome - Tolerance Landscape score all annotations
     MTR Scores     MTR - Missense Tolerance Ratio Scores by base
     MTR All Data     MTR - Missense Tolerance Ratio Scores all annotations
     LINSIGHT     LINSIGHT - Probability of deleterious fitness and negative selection on noncoding sites
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 GWAS v4     COVID risk variants from GWAS meta-analyses by the COVID-19 Host Genetics Initiative (Rel 4, Oct 2020)
     COVID GWAS v3     GWAS meta-analyses from the COVID-19 Host Genetics Initiative
     COVID Rare Harmful Var     Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort
DECIPHER DECIPHER
     DECIPHER CNVs     DECIPHER CNVs (not updated anymore - use the hg38 track)
     DECIPHER Population CNVs     DECIPHER: Population CNVs
new Deleteriousness Predictions Variant Deleteriousness / Variant Impact Prediction Scores
     BayesDel     BayesDel - deleteriousness meta-score
     M-CAP     M-CAP: High sensitivity pathogenicity classifier
     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
GAD View Genetic Association Studies of Complex Diseases and Disorders
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
Haploinsufficiency Haploinsufficiency predictions for genes from DECIPHER
HGMD public Human Gene Mutation Database - Public Version Dec 2024
Lens Patents Lens PatSeq Patent Document Sequences
LOVD Variants LOVD: Leiden Open Variation Database Public Variants
MGI Mouse QTL MGI Mouse Quantitative Trait Loci Coarsely Mapped to Human
new MITOMAP MITOMAP: A human mitochondrial genome database
Orphanet Orphadata: Aggregated Data From Orphanet
updated PanelApp Genomics England and Australia PanelApp Diagnostics
Polygenic Risk Scores Polygenic Risk Scores
     PRS eMERGE     Polygenic Risk Scores from NHGRI Electronic Medical Records and Genomics (eMERGE) project
REVEL Scores REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score)
RGD Human QTL Human Quantitative Trait Locus from RGD
RGD Rat QTL Rat Quantitative Trait Locus from RGD Coarsely Mapped to Human
SNPedia SNPedia
Splicing Impact Splicing Impact Prediction Scores and Databases
     AbSplice Scores     Aberrant Splicing Prediction Scores
     SpliceAI     SpliceAI: Splice Variant Prediction Score
UniProt Variants UniProt/SwissProt Amino Acid Substitutions
updated Variants in Papers Genetic Variants mentioned in scientific publications
     Avada Variants     Avada Variants extracted from full text publications
     enGenome VarChat     enGenome VarChat: Literature match and variant's summary
     Mastermind Variants     Genomenon Mastermind Variants extracted from full text publications
    new PubTator Variants     dbSNP variants and other genetic variants grounded to dbSNP by tmVar; collected by PubTator3
     Varaico Variants     Varaico Variants extracted from full text publications, titles, and abstracts
Web Sequences DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research
-   Variation    
dbSNP 155 Short Genetic Variants from dbSNP release 155
1000G Archive 1000 Genomes Archive
     1000G Ph1 Accsbl     1000 Genomes Project Phase 1 Paired-end Accessible Regions
     1000G Ph1 Vars     1000 Genomes Phase 1 Integrated Variant Calls: SNVs, Indels, SVs
     1000G Ph3 Accsbl     1000 Genomes Project Phase 3 Paired-end Accessible Regions
     1000G Ph3 Vars     1000 Genomes Phase 3 Integrated Variant Calls: SNVs, Indels, SVs
updated Array Probesets Microarray Probesets and OGM sites
dbSNP Archive dbSNP Track Archive
     dbSNP 153     Short Genetic Variants from dbSNP release 153
     Common SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples
     All SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151)
     Flagged SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(151)     Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci
     All SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150)
     Common SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples
     Flagged SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc
     Mult. SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) 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
     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(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(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(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
     All SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138)
     Common SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples
     Flagged SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138) Flagged as Clinically Assoc
     Mult. SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci
dbVar Common Struct Var NCBI Curated Common Structural Variants from dbVar
     dbVar Common SV     NCBI dbVar Curated Common Structural Variants
     dbVar Conflict SV     NCBI dbVar Curated Conflict Variants
denovo-db denovo-db v.1.6.1
DGV Struct Var Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)
EVS Variants NHLBI GO Exome Sequencing Project (ESP) - Variants from 6,503 Exomes
ExAC Exome Aggregation Consortium (ExAC) Variants and Calling Regions
Genome In a Bottle Genome In a Bottle Structural Variants and Trios
Genome Variants Personal Genome Variants
GIS DNA PET ENCODE Genome Institute of Singapore DNA Paired-End Ditags
gnomAD Genome Aggregation Database (gnomAD) - Variants, Coverage, and Constraint
     gnomAD Constraint Metrics     Genome Aggregation Database (gnomAD) - Predicted Constraint Metrics (pLI and Z-scores)
     gnomAD Coverage     Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage
     gnomAD Exomes Variants     Genome Aggregation Database (gnomAD) Exome Variants v2.1.1
     gnomAD Genomes Variants     Genome Aggregation Database (gnomAD) Genome Variants v2.1.1
     gnomAD pext     gnomAD Proportion Expression Across Transcript Scores (pext)
     gnomAD Structural Variants     Genome Aggregation Database (gnomAD) - Structural Variants
HAIB Genotype Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha
HapMap SNPs HapMap SNPs (rel27, merged Phase II + Phase III genotypes)
HGDP Allele Freq Human Genome Diversity Project SNP Population Allele Frequencies
Platinum Genomes Platinum genome variants
-   RNA and Transcriptome    
CGAP SAGE CGAP Long SAGE
Gene Bounds Gene Boundaries as Defined by RNA and Spliced EST Clusters
H-Inv H-Invitational Genes mRNA Alignments
Human ESTs Human ESTs Including Unspliced
Human mRNAs Human mRNAs from GenBank
Human RNA Editing Human RNA Editing from the DAtabase of RNa EDiting
Other ESTs Non-Human ESTs from GenBank
Other mRNAs Non-Human mRNAs from GenBank
Poly(A) Poly(A) Sites, Both Reported and Predicted
PolyA-Seq Poly(A)-sequencing from Merck Research Laboratories
SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics
Spliced ESTs Human ESTs That Have Been Spliced
UniGene UniGene Alignments
-   Expression    
GTEx Gene V8 Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019)
Allen Brain Allen Brain Atlas Probes
Burge RNA-seq Burge Lab RNA-seq Aligned by GEM Mapper
CSHL Small RNA-seq Small RNA-seq from ENCODE/Cold Spring Harbor Lab
ENC Exon Array ENCODE Exon Array
     Duke Affy Exon     Affymetrix Exon Array from ENCODE/Duke
     UW Affy Exon     Affymetrix Exon Array from ENCODE/University of Washington
ENC ProtGeno ENCODE Proteogenomics
     UNC/BSU ProtGenc     Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ.
     UNC/BSU ProtGeno     Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ.
ENC RNA-seq ENCODE RNA-seq
     Caltech RNA-seq     RNA-seq from ENCODE/Caltech
     CSHL Long RNA-seq     Long RNA-seq from ENCODE/Cold Spring Harbor Lab
     GIS RNA-seq     RNA-seq from ENCODE/Genome Institute of Singapore
     HAIB RNA-seq     RNA-seq from ENCODE/HAIB
     SYDH RNA-seq     RNA-seq from ENCODE/Stanford/Yale/USC/Harvard
EPDnew Promoters Promoters from EPDnew human version 006
Affy Archive Affymetrix Archive
     Affy Exon Array     Affymetrix Human Exon Array Probes and Probesets
     Affy GNF1H     Alignments of Affymetrix Consensus/Exemplars from GNF1H
     Affy RNA Loc     RNA Subcellular Localization by Tiling Microarray from ENCODE Affymetrix/CSHL
     Affy U95     Alignments of Affymetrix Consensus/Exemplars from HG-U95
     Affy U133     Alignments of Affymetrix Consensus/Exemplars from HG-U133
     Affy U133Plus2     Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0
GIS RNA PET RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS
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
Illumina WG-6 Alignments of Illumina WG-6 3.0 Probe Set
PeptideAtlas Peptide sequences identified from MS spectra of 971 samples by PeptideAtlas
qPCR Primers Human (hg19) Whole Transcriptome qPCR Primers
RIKEN CAGE Loc RNA Subcellular CAGE Localization from ENCODE/RIKEN
Sestan Brain Sestan Lab Human Brain Atlas Microarrays
-   Regulation    
ENCODE Regulation Integrated Regulation from ENCODE
     Transcription     Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE
     Layered H3K4Me1     H3K4Me1 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 H3K27Ac     H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from ENCODE
     DNase Clusters     DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE (V3)
     Txn Factr ChIP E3     Transcription Factor ChIP-seq Clusters (338 factors, 130 cell types) from ENCODE 3
     Txn Factor ChIP     Transcription Factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs
     Txn Fac ChIP V2     Transcription Factor ChIP-seq from ENCODE (V2)
CD34 DnaseI Eur. Inst. Oncology/J. C. Venter Inst. Nuclease Accessible Sites
CpG Islands CpG Islands (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
ENC Chromatin ENCODE Chromatin Interactions
     GIS ChIA-PET     Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan
     UMass 5C     Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass.
     UW 5C    DownloadsChromatin Interactions by 5C from ENCODE/University of Washington
ENC DNA Methyl ENCODE DNA Methylation
     HAIB Methyl RRBS     DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha
     HAIB Methyl450     CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB
ENC DNase/FAIRE ENCODE Open Chromatin by DNaseI HS and FAIRE
     Master DNaseI HS     DNaseI Hypersensitive Site Master List (125 cell types) from ENCODE/Analysis
     Uniform DNaseI HS     DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis
     Open Chrom Synth     DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA)
     Duke DNaseI HS     Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)
     UNC FAIRE     Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill)
     UW DNaseI DGF     DNaseI Digital Genomic Footprinting from ENCODE/University of Washington
     UW DNaseI HS     DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington
ENC Histone ENCODE Histone Modification
     Broad ChromHMM     Chromatin State Segmentation by HMM from ENCODE/Broad
     Broad Histone     Histone Modifications by ChIP-seq from ENCODE/Broad Institute
     SYDH Histone     Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard
     UW Histone     Histone Modifications by ChIP-seq from ENCODE/University of Washington
ENC RNA Binding ENCODE RNA Binding Proteins
     SUNY RIP GeneST     RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany
     SUNY RIP Tiling     RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany
     SUNY RIP-seq     RIP-seq from ENCODE/SUNY Albany
ENC TF Binding ENCODE Transcription Factor Binding
     ENCODE 3 TFBS     Transcription Factor ChIP-seq Peaks (338 factors in 130 cell types) from ENCODE 3
     Uniform TFBS     Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis
     HAIB TFBS     Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB
     SYDH TFBS     Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard
     UChicago TFBS     Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago
     UTA TFBS     Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin)
     UW CTCF Binding     CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington
FANTOM5 FANTOM5: Mapped transcription start sites (TSS) and their usage
     Enhancers     FANTOM5: Enhancers
     FANTOM-NET Enhancers     FANTOM5: FANTOM-NET Enhancers
     Enhancer - promoter correlations distances cell type     FANTOM5: Enhancer - promoter correlations distances cell type
     Enhancer - promoter correlations distances organ     FANTOM5: Enhancer - promoter correlations distances organ
     TSS peaks     FANTOM5: DPI peak, robust set
     Total counts of CAGE reads     FANTOM5: Total counts of CAGE reads
     Max counts of CAGE reads     FANTOM5: Max counts of CAGE reads
     FANTOM CAT     FANTOM5: atlas of human long non-coding RNAs with accurate 5' ends
     TSS activity - read counts     FANTOM5: TSS activity per sample read counts
     TSS activity (TPM)     FANTOM5: TSS activity per sample (TPM)
FSU Repli-chip Replication Timing by Repli-chip from ENCODE/FSU
GeneHancer GeneHancer Regulatory Elements and Gene Interactions
Genome Segments Genome Segmentations from ENCODE
GTEx Combined eQTL Combined Expression QTLs from 44 Tissues from GTEx (midpoint release, V6)
GTEx Tissue eQTL Expression QTLs in 44 tissues from GTEx (midpoint release, V6)
JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
NKI Nuc Lamina NKI Nuclear Lamina Associated Domains (LaminB1 DamID)
     LaminB1 (Tig3)     NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells)
     NKI LADs (Tig3)     NKI LADs (Lamina Associated Domains, Tig3 cells)
ORegAnno Regulatory elements from ORegAnno
Rao 2014 Hi-C Hi-C on 7 cell lines from Rao 2014
ReMap ChIP-seq ReMap Atlas of Regulatory Regions
Stanf Nucleosome Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU
SUNY SwitchGear RNA Binding Protein Associated RNA by SwitchGear from ENCODE/SUNY Albany
SwitchGear TSS SwitchGear Genomics Transcription Start Sites
TFBS Conserved HMR Conserved Transcription Factor Binding Sites
TS miRNA Targets TargetScan predicted microRNA target sites
     TS miRNA sites     TargetScan miRNA Regulatory Sites (Release 5.1, April 2009)
     TS miRNA v7.2     Predicted microRNA Target Sites from TargetScanHuman 7.2 (March 2018)
UCSF Brain Methyl UCSF Brain DNA Methylation
UMMS Brain Hist Brain Histone H3K4me3 ChIP-Seq from Univ. Mass. Medical School (Akbarian/Weng)
UW Repli-seq Replication Timing by Repli-seq from ENCODE/University of Washington
updated VISTA Enhancers VISTA Enhancers
-   Comparative Genomics    
Conservation Vertebrate Multiz Alignment & Conservation (100 Species)
Cons 46-Way Vertebrate Multiz Alignment & Conservation (46 Species)
Cons Indels MmCf Indel-based Conservation for Human hg19, Mouse mm8 and Dog canFam2
Evo Cpg Weizmann Evolutionary CpG Islands
GERP GERP Scores for Mammalian Alignments
phastBias gBGC phastBias gBGC predictions
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
+   Neandertal Assembly and Analysis    
+   Denisova Assembly and Analysis    
-   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 Human NumtS mitochondrial sequence
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
-   Autism Noncoding Project    
Agilent Capture information Agilent capture information
-   Morbidity Map    
AllControlCNVs 19584 cases AllControlCNVs 19584 cases
Signature 29085 Samples Rare UniqueCalls Signature 29085 Samples Rare UniqueCalls
-   Simons Genome Project    
SSC set1 WSSD Simons Set1 WSSD
SSC set1 SUNK Simons Set1 SUNK
-   other    
HGDP SNPs Human genome diversity panel SNPs