Configure Image
 
image width:pixels
label area width:characters
text size:
font:
style:
Display chromosome ideogram above main graphic
Show light blue vertical guidelines, or light red vertical window separators in multi-region view
Display labels to the left of items in tracks
Display description above each track
Show track controls under main graphic
Next/previous item navigation
Next/previous exon navigation
Show exon numbers
Enable highlight with drag-and-select (if unchecked, drag-and-select always zooms to selection)

Configure Tracks on UCSC Genome Browser: Human Dec. 2013 (GRCh38/hg38)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Autism studies    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
SPARK WES1 pro CNV SPARK WES1 pro CNV
     proband (inheritance unknown)     proband (inheritance unknown)
     proband (not passing RPKM filter)     proband (not passing RPKM filter)
     proband denovo     proband denovo
     proband inherited     proband inherited
SPARK WES1 sib CNV SPARK WES1 sib CNV
     sibling (inheritance unknown)     sibling (inheritance unknown)
     sibling (not passing RPKM filter)     sibling (not passing RPKM filter)
     sibling denovo     sibling denovo
     sibling inherited     sibling inherited
-   Ilumina Read Depth    
C-team Human Diversity Panel WSSD C-team Human Diversity Panel WSSD
C-team Human Diversity Panel SUNK C-team Human Diversity Panel SUNK
aDNA Genomes WSSD aDNA Genomes WSSD
Archaic Genomes WSSD Archaic Genomes WSSD
aDNA Genomes SUNK aDNA Genomes SUNK
Archaic Genomes SUNK Archaic Genomes SUNK
HGDP SUNK HGDP high coverage SUNK
     African_sunk     African_sunk
     American_sunk     American_sunk
     EastAsian_sunk     EastAsian_sunk
     European_sunk     European_sunk
     Melanesian_sunk     Melanesian_sunk
     MiddleEastern_sunk     MiddleEastern_sunk
     Siberian_sunk     Siberian_sunk
     SouthAsian_sunk     SouthAsian_sunk
HGDP WSSD HGDP high coverage WSSD
     African_wssd     African_wssd
     American_wssd     American_wssd
     EastAsian_wssd     EastAsian_wssd
     European_wssd     European_wssd
     Melanesian_wssd     Melanesian_wssd
     MiddleEastern_wssd     MiddleEastern_wssd
     Siberian_wssd     Siberian_wssd
     SouthAsian_wssd     SouthAsian_wssd
Non-Human Primate WSSD Non-Human Primate WSSD
Non-Human Primate SUNK Non-Human Primate SUNK
CHM1 hydatidiform mole WSSD CHM1 hydatidiform mole WSSD
CHM1 hydatidiform mole SUNK CHM1 hydatidiform mole SUNK
SAGE genomes wssd SAGE genomes wssd
SSC Genomes WSSD SSC Genomes WSSD
BAC library sunk BAC library sunk
BAC library wssd BAC library wssd
reference sunk reference sunk
reference wssd reference wssd
SSC Genomes SUNK SSC Genomes SUNK
-   Clone end mappings    
CH17 CH17 (mole)
CH251 (chimp) CH251 (chimp)
CH276 (orangutan) CH276 (orangutan)
CH277 (gorilla) CH277 (gorilla)
CH250 (macaque) CH250 (macaque)
CH259 (marmoset) CH259 (marmoset)
ABC9 ABC9
ABC10 ABC10
ABC11 ABC11
ABC12 ABC12
ABC13 ABC13
ABC14 ABC14
CH1277(gorilla_FES) CH1277(gorilla_FES)
CH276P95 (orangutan) CH276 95% identity (orangutan)
CH277P95 (gorilla) CH277 95% identity (gorilla)
-   Mapping and Sequencing    
p14 Fix Patches Reference Assembly Fix Patch Sequence Alignments
p14 Alt Haplotypes Reference Assembly Alternate Haplotype Sequence Alignments
Assembly Assembly from Fragments
Assembly Tracks Assembly identifiers, clones, and markers
     FISH Clones     Clones Placed on Cytogenetic Map Using FISH
     GRC Contigs     Genome Reference Consortium Contigs
     Scaffolds     GRCh38 Defined Scaffold Identifiers
     STS Markers     STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
Centromeres Centromere Locations
Chromosome Band Chromosome Bands Localized by FISH Mapping Clones
Clone Ends Mapping of clone libraries end placements
Exome Probesets Exome Capture Probesets and Targeted Region
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
GRC Incident GRC Incident Database
Hg19 Diff Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19)
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
LiftOver & ReMap UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg19
LRG Regions Locus Reference Genomic (LRG) / RefSeqGene Sequences Mapped to Dec. 2013 (GRCh38/hg38) Assembly
Mappability Hoffman Lab Umap and Bismap Mappability
     Bismap     Single-read and multi-read mappability after bisulfite conversion
     Umap     Single-read and multi-read mappability by Umap
updated Problematic Regions Problematic/special genomic regions for sequencing or very variable regions
     Problematic Regions     Problematic/special genomic regions for sequencing or very variable regions
     Highly Reproducible Regions     Highly Reproducible genomic regions for sequencing
    new GIAB Problematic Regions     Difficult regions from GIAB via NCBI
Recomb Rate Recombination rate: Genetic maps from deCODE and 1000 Genomes
     Recomb. deCODE Avg     Recombination rate: deCODE Genetics, average from paternal and maternal (mat for chrX)
     Recomb. deCODE Pat     Recombination rate: deCODE Genetics, paternal
     Recomb. deCODE Mat     Recombination rate: deCODE Genetics, maternal
     Recomb. deCODE Evts     Recombination events in deCODE Genetic Map (zoom to < 10kbp to see the events)
     Recomb. deCODE Dmn     Recombination rate: De-novo mutations found in deCODE samples
     Recomb. 1k Genomes     Recombination rate: 1000 Genomes, lifted from hg19 (PR Loh)
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Morbidity map    
Cases 29085 Samples Rare UniqueCalls Cases 29085 Samples Rare UniqueCalls
Cases_29085Samples_remap Cases_29085Samples_remap
Coe2014_controls Coe2014_controls
Controls 19584 Samples AllCalls Controls 19584 Samples AllCalls
Controls_19584Samples_remap Controls_19584Samples_remap
gnomad_SV_hg38 gnomad_SV_hg38
     CNV_MOPS     CNV_MOPS
     CNV_MOPS_MANTA     CNV_MOPS_MANTA
     DELLY     DELLY
     DELLY_CNV_MOPS     DELLY_CNV_MOPS
     DELLY_CNV_MOPS_MANTA     DELLY_CNV_MOPS_MANTA
     DELLY_MANTA     DELLY_MANTA
     MANTA     MANTA
Hakonarson_NatCom2020 Hakonarson_NatCom2020
SSC_cases_6way SSC_cases_6way
Coe_2014_regions Coe 2014 significant regions
-   Genes and Gene Predictions    
updated GENCODE V47 GENCODE V47
updated NCBI RefSeq RefSeq genes from NCBI
CCDS Consensus CDS
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
GENCODE Archive GENCODE Archive
     GENCODE V46     GENCODE V46
     GENCODE V45     GENCODE V45
     GENCODE V44     GENCODE V44
     GENCODE V43     GENCODE V43
     GENCODE V39     GENCODE V39
     GENCODE V38     GENCODE V38
     GENCODE V36     GENCODE V36
updated GENCODE Versions Container of all new and previous GENCODE releases
    new All GENCODE V47     All GENCODE annotations from V47 (Ensembl 113)
     All GENCODE V46     All GENCODE annotations from V46 (Ensembl 112)
     All GENCODE V45     All GENCODE annotations from V45 (Ensembl 111)
     All GENCODE V44     All GENCODE annotations from V44 (Ensembl 110)
     All GENCODE V43     All GENCODE annotations from V43 (Ensembl 109)
     All GENCODE V42     All GENCODE annotations from V42 (Ensembl 108)
     All GENCODE V41     All GENCODE annotations from V41 (Ensembl 107)
     All GENCODE V40     All GENCODE annotations from V40 (Ensembl 106)
     All GENCODE V39     All GENCODE annotations from V39 (Ensembl 105)
     All GENCODE V38     All GENCODE annotations from V38 (Ensembl 104)
     All GENCODE V37     All GENCODE annotations from V37 (Ensembl 103)
     All GENCODE V36     All GENCODE annotations from V36 (Ensembl 102)
     All GENCODE V35     All GENCODE annotations from V35 (Ensembl 101)
     All GENCODE V34     All GENCODE annotations from V34 (Ensembl 100)
     All GENCODE V33     All GENCODE annotations from V33 (Ensembl 99)
     All GENCODE V32     All GENCODE annotations from V32 (Ensembl 98)
     All GENCODE V31     All GENCODE annotations from V31 (Ensembl 97)
     All GENCODE V30     All GENCODE annotations from V30 (Ensembl 96)
     All GENCODE V29     All GENCODE annotations from V29 (Ensembl 94)
     All GENCODE V28     All GENCODE annotations from V28 (Ensembl 92)
     All GENCODE V27     All GENCODE annotations from V27 (Ensembl 90)
     All GENCODE V26     All GENCODE annotations from V26 (Ensembl 88)
     All GENCODE V25     All GENCODE transcripts including comprehensive set V25
     All GENCODE V24     All GENCODE transcripts including comprehensive set V24
     All GENCODE V23     All GENCODE transcripts including comprehensive set V23
     All GENCODE V22     All GENCODE transcripts including comprehensive set V22
     GENCODE V20 (Ensembl 76)     Gene Annotations from GENCODE Version 20 (Ensembl 76)
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
     MGC Genes     Mammalian Gene Collection Full ORF mRNAs
     ORFeome Clones     ORFeome Collaboration Gene Clones
Non-coding RNA RNA sequences that do not code for a protein
     lincRNA RNA-Seq     lincRNA RNA-Seq reads expression abundances
     lincRNA TUCP     lincRNA and TUCP transcripts
     sno/miRNA     C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase
     tRNA Genes     Transfer RNA Genes Identified with tRNAscan-SE
Old UCSC Genes Previous Version of UCSC Genes
Other RefSeq Non-Human RefSeq Genes
Pfam in GENCODE Pfam Domains in GENCODE Genes
Prediction Archive Gene Prediction Archive
     AUGUSTUS     AUGUSTUS ab initio gene predictions v3.1
     Geneid Genes     Geneid Gene Predictions
     Genscan Genes     Genscan Gene Predictions
     SGP Genes     SGP Gene Predictions Using Mouse/Human Homology
     SIB Genes     Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs
new Pseudogenes Pseudogenes and Parents
RetroGenes V9 Retroposed Genes V9, Including Pseudogenes
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
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     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
new CADD 1.7 CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions
    new CADD 1.7     CADD 1.7 Score for all possible single-basepair mutations (zoom in for scores)
    new CADD 1.7 Del     CADD 1.7 Score: Deletions - label is length of deletion
    new CADD 1.7 Ins     CADD 1.7 Score: Insertions - label is length of insertion
Cancer Gene Expr Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23)
     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)
new CIViC CIViC - Expert & crowd-sourced cancer variant interpretation
new 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
     UKB Depl. Rank Score     UK Biobank / deCODE Genetics Depletion Rank Score
Coriell CNVs Coriell Cell Line Copy Number Variants
updated 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
new DECIPHER DECIPHER
     DECIPHER CNVs     DECIPHER CNVs
    new DECIPHER Population CNVs     DECIPHER: Population CNVs
Development Delay Copy Number Variation Morbidity Map of Developmental Delay
Dosage Sensitivity pHaplo and pTriplo dosage sensitivity map from Collins et al 2022
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 Human Gene Mutation Database - Public Version Dec 2024
LOVD Variants LOVD: Leiden Open Variation Database Public Variants
new MITOMAP MITOMAP: A human mitochondrial genome database
Orphanet Orphadata: Aggregated Data From Orphanet
PanelApp Genomics England PanelApp Diagnostics
REVEL Scores REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score)
SNPedia SNPedia
new Splicing Impact Splicing Impact Prediction Scores and Databases
     AbSplice Scores     Aberrant Splicing Prediction Scores
     SpliceAI     SpliceAI: Splice Variant Prediction Score
    new SpliceVarDB     SpliceVarDB: Experimentally validated splicing variants
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
     Avada Variants     Avada Variants extracted from full text publications
    new enGenome VarChat     enGenome VarChat: Literature match and variant's summary
     Mastermind Variants     Genomenon Mastermind Variants extracted from full text publications
-   Variation    
dbSNP 155 Short Genetic Variants from dbSNP release 155
1000 Genomes 1000 Genomes Phase 3
     1000 Genomes Trios     Thousand Genomes Project Family VCF Trios
     1000G Ph3 Vars     1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels
Array Probesets Microarray Probesets
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
     Mult. SNPs(150)     Simple Nucleotide Polymorphisms (dbSNP 150) 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(147)     Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci
     Flagged SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc
     Common SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples
     All SNPs(147)     Simple Nucleotide Polymorphisms (dbSNP 147)
     Mult. SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci
     Flagged SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc
     Common SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples
     All SNPs(146)     Simple Nucleotide Polymorphisms (dbSNP 146)
     Mult. SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci
     Flagged SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc
     Common SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples
     All SNPs(144)     Simple Nucleotide Polymorphisms (dbSNP 144)
     Mult. SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci
     Flagged SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc
     Common SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples
     All SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142)
     Mult. SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) That Map to Multiple Genomic Loci
     Flagged SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc
     Common SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141) Found in >= 1% of Samples
     All SNPs(141)     Simple Nucleotide Polymorphisms (dbSNP 141)
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
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 Variants Genome Aggregation Database (gnomAD) Genome and Exome Variants
    new gnomAD v4.1     Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1
     gnomAD v3.1.1     Genome Aggregation Database (gnomAD) Genome Variants v3.1.1
     gnomAD v3.1     Genome Aggregation Database (gnomAD) Genome Variants v3.1
     gnomAD v3     Genome Aggregation Database (gnomAD) Genome Variants v3
     gnomAD v2     Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1
     gnomAD Mut Constraint     Gnocchi: Genome Aggregation Database (gnomAD) non-coding constraint of haploinsufficient variation, includes chrX
    new gnomAD Constraint Metrics     Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (LOEUF, pLI, and Z-scores)
    new gnomAD Rare CNV Variants     Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1
    new gnomAD Structural Variants     Genome Aggregation Database (gnomAD) - Structural Variants v4.1
Platinum Genomes Platinum genome variants
-   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 All Variants     HPRC variants decomposed from hprc-v1.0-mc.grch38.vcfbub.a100k.wave.vcf.gz (Liao et al 2023), no size filtering
     HPRC Variants <= 3bp     HPRC VCF variants filtered for items size <= 3bp
     HPRC Variants > 3bp     HPRC VCF variants filtered for items size > 3bp
-   mRNA and EST    
Human ESTs Human ESTs Including Unspliced
Human mRNAs Human mRNAs from GenBank
Other ESTs Non-Human ESTs from GenBank
Other mRNAs Non-Human mRNAs from GenBank
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 GNF1H     Alignments of Affymetrix Consensus/Exemplars from GNF1H
     Affy U133     Alignments of Affymetrix Consensus/Exemplars from HG-U133
     Affy U95     Alignments of Affymetrix Consensus/Exemplars from HG-U95
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
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    
ENCODE cCREs ENCODE Candidate Cis-Regulatory Elements (cCREs) combined from all cell types
ENCODE Regulation Integrated Regulation from ENCODE
     TF rPeak Clusters     Transcription Factor Representative Peak (rPeak) Clusters (912 factors in 1152 biosamples) from ENCODE 4
     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 Regulatory Elements) on 7 cell lines from ENCODE
     DNase Clusters     DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)
     DNase Signal     DNase I Hypersensitivity Signal Colored by Similarity from ENCODE
     DNase HS     DNase I Hypersensitivity in 95 cell types from ENCODE
     TF Clusters     Transcription Factor ChIP-seq Clusters (340 factors, 129 cell types) from ENCODE 3
     TF ChIP     Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3
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)
FANTOM5 FANTOM5: Mapped transcription start sites (TSS) and their usage
     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
     TSS activity - read counts     FANTOM5: TSS activity per sample read counts
     TSS activity (TPM)     FANTOM5: TSS activity per sample (TPM)
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
JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
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,
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
+   Experimental    
-   CCDG genomes    
canvas_case_ssc_cnv_trueset canvas_case_ssc_cnv_trueset
canvas_ctrl_ssc_cnv_trueset canvas_ctrl_ssc_cnv_trueset
CNVnator100_case_ssc_cnv_trueset CNVnator100_case_ssc_cnv_trueset
CNVnator100_ctrl_ssc_cnv_trueset CNVnator100_ctrl_ssc_cnv_trueset
lumpy_case_ssc_cnv_trueset lumpy_case_ssc_cnv_trueset
lumpy_ctrl_ssc_cnv_trueset lumpy_ctrl_ssc_cnv_trueset
manta_case_ssc_cnv_trueset manta_case_ssc_cnv_trueset
manta_ctrl_ssc_cnv_trueset manta_ctrl_ssc_cnv_trueset
pav_case_ssc_cnv_trueset pav_case_ssc_cnv_trueset
pav_ctrl_ssc_cnv_trueset pav_ctrl_ssc_cnv_trueset
pbsv_case_ssc_cnv_trueset pbsv_case_ssc_cnv_trueset
pbsv_ctrl_ssc_cnv_trueset pbsv_ctrl_ssc_cnv_trueset
4 way merge [CNVnator, Lumpy, CANVAS, MANTA] 4 way merge [CNVnator, Lumpy, CANVAS, MANTA]
individual CNV callers individual CNV callers
     CANVAS     CANVAS
     CNVnator     CNVnator
     Delly     Delly
     GenomeStrip     GenomeStrip
     Lumpy     Lumpy
     MANTA     MANTA
     WHAMG     WHAMG
per sample calls per sample calls
     11003_fa     11003_fa
     11003_mo     11003_mo
     11003_p1     11003_p1
     11003_s1     11003_s1
     11004_fa     11004_fa
     11004_mo     11004_mo
     11004_p1     11004_p1
     11004_s1     11004_s1
     11006_fa     11006_fa
     11006_mo     11006_mo
     11006_p1     11006_p1
     11006_s1     11006_s1
     11008_fa     11008_fa
     11008_mo     11008_mo
     11008_p1     11008_p1
     11008_s1     11008_s1
     11009_fa     11009_fa
     11009_mo     11009_mo
     11009_p1     11009_p1
     11009_s1     11009_s1
     11010_fa     11010_fa
     11010_mo     11010_mo
     11010_p1     11010_p1
     11010_s1     11010_s1
     11012_fa     11012_fa
     11012_mo     11012_mo
     11012_p1     11012_p1
     11012_s1     11012_s1
     11013_fa     11013_fa
     11013_mo     11013_mo
     11013_p1     11013_p1
     11013_s1     11013_s1
     11014_fa     11014_fa
     11014_mo     11014_mo
     11014_p1     11014_p1
     11014_s1     11014_s1
     11017_fa     11017_fa
     11017_mo     11017_mo
     11017_p1     11017_p1
     11017_s1     11017_s1
     11018_fa     11018_fa
     11018_mo     11018_mo
     11018_p1     11018_p1
     11018_s1     11018_s1
     11022_fa     11022_fa
     11022_mo     11022_mo
     11022_p1     11022_p1
     11022_s1     11022_s1
     11023_fa     11023_fa
     11023_mo     11023_mo
     11023_p1     11023_p1
     11023_s1     11023_s1
     11024_fa     11024_fa
     11024_mo     11024_mo
     11024_p1     11024_p1
     11024_s1     11024_s1
     11027_fa     11027_fa
     11027_mo     11027_mo
     11027_p1     11027_p1
     11027_s1     11027_s1
     11028_fa     11028_fa
     11028_mo     11028_mo
     11028_p1     11028_p1
     11028_s1     11028_s1
     11029_fa     11029_fa
     11029_mo     11029_mo
     11029_p1     11029_p1
     11029_s1     11029_s1
     11030_fa     11030_fa
     11030_mo     11030_mo
     11030_p1     11030_p1
     11030_s1     11030_s1
     11031_fa     11031_fa
     11031_mo     11031_mo
     11031_p1     11031_p1
     11031_s1     11031_s1
     11033_fa     11033_fa
     11033_mo     11033_mo
     11033_p1     11033_p1
     11033_s1     11033_s1
     11037_fa     11037_fa
     11037_mo     11037_mo
     11037_p1     11037_p1
     11037_s1     11037_s1
     11038_fa     11038_fa
     11038_mo     11038_mo
     11038_p1     11038_p1
     11038_s1     11038_s1
     11041_fa     11041_fa
     11041_mo     11041_mo
     11041_p1     11041_p1
     11041_s1     11041_s1
     11042_fa     11042_fa
     11042_mo     11042_mo
     11042_p1     11042_p1
     11042_s1     11042_s1
     11043_fa     11043_fa
     11043_mo     11043_mo
     11043_p1     11043_p1
     11043_s1     11043_s1
     11045_fa     11045_fa
     11045_mo     11045_mo
     11045_p1     11045_p1
     11045_s1     11045_s1
     11046_fa     11046_fa
     11046_mo     11046_mo
     11046_p1     11046_p1
     11046_s1     11046_s1
     11047_fa     11047_fa
     11047_mo     11047_mo
     11047_p1     11047_p1
     11047_s1     11047_s1
     11048_fa     11048_fa
     11048_mo     11048_mo
     11048_p1     11048_p1
     11048_s1     11048_s1
     11051_fa     11051_fa
     11051_mo     11051_mo
     11051_p1     11051_p1
     11051_s1     11051_s1
     11054_fa     11054_fa
     11054_mo     11054_mo
     11054_p1     11054_p1
     11054_s1     11054_s1
     11055_fa     11055_fa
     11055_mo     11055_mo
     11055_p1     11055_p1
     11055_s1     11055_s1
     11056_fa     11056_fa
     11056_mo     11056_mo
     11056_p1     11056_p1
     11056_s1     11056_s1
     11057_fa     11057_fa
     11057_mo     11057_mo
     11057_p1     11057_p1
     11057_s1     11057_s1
     11060_fa     11060_fa
     11060_mo     11060_mo
     11060_p1     11060_p1
     11060_s1     11060_s1
     11062_fa     11062_fa
     11062_mo     11062_mo
     11062_p1     11062_p1
     11062_s1     11062_s1
     11063_fa     11063_fa
     11063_mo     11063_mo
     11063_p1     11063_p1
     11063_s1     11063_s1
     11064_fa     11064_fa
     11064_mo     11064_mo
     11064_p1     11064_p1
     11064_s1     11064_s1
     11066_fa     11066_fa
     11066_mo     11066_mo
     11066_p1     11066_p1
     11066_s1     11066_s1
     11067_fa     11067_fa
     11067_mo     11067_mo
     11067_p1     11067_p1
     11067_s1     11067_s1
     11069_fa     11069_fa
     11069_mo     11069_mo
     11069_p1     11069_p1
     11069_s1     11069_s1
     11071_fa     11071_fa
     11071_mo     11071_mo
     11071_p1     11071_p1
     11071_s1     11071_s1
     11073_fa     11073_fa
     11073_mo     11073_mo
     11073_p1     11073_p1
     11073_s1     11073_s1
     14455_fa     14455_fa
     14455_mo     14455_mo
     14455_p1     14455_p1
     14455_s1     14455_s1