Track Data Hubs
 

Track data hubs are collections of external tracks that can be imported into the UCSC Genome Browser. Hub tracks show up under the hub's own blue label bar on the main browser page, as well as on the configure page. For more information, including where to host your track hub, see the User's Guide.To import a public hub click its "Connect" button below.

NOTE: Because Track Hubs are created and maintained by external sources, UCSC is not responsible for their content.

Enter search terms to find in public track hub description pages:

Filter hubs by assembly:

Clicking Connect redirects to the gateway page of the selected hub's default assembly.
Display Hub Name Description Assemblies
Bird assemblies Bird genome assemblies [+] GCF_000699105.1, GCF_000691975.1...
Blueprint Hub Blueprint Epigenomics Data Hub hg38
BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples hg19
Breast Cancer lncRNA Breast Cancer lncRNA PMID 26236012 hg19
Broad Improved Canine Annotation v1 Broad Institute CanFam3 Improved Annotation Data v1 canFam3
C_elegans_isolates C. elegans wild isolate assembly hub [+] CB4856Princeton_JR-contig...
CADD CADD Track for v1.3 to v1.6 hg19, hg38
Cancer Genomics Tracks TCGA and ICGC Cancer Mutations, TCGA Expression, Immune Epitopes Database (IEDB), Cancer Immunity Peptides Database, Dienstmann Variant/Cancer database, CIVIC, MyCancerGenome.org, OncoKB hg19
CEMT (CEEHRC) Epigenomic Data tracks from BCGSC, Vancouver, B.C. hg38, hg19
CESAR Gene Mappings Human Exons mapped by CESAR [+] bosTau7, ailMel1, allMis1, anoCar2, calJac3...
ChIP-seq data track HUBs from MSC cells from GSE79815 ChIP-seq data from the publication "Epigenetic plasticity drives adipogenic and osteogenic differentiation of marrow-derived mesenchymal stem cells" (10.1074/jbc.M116.736538) from GEO record GSE79815 mm9
Coloc segments Colocalized segments of human genome for Roadmap cell types hg19
Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at UConn Health hg19, mm9
Cotney Lab Human Embryonic Heart Hub Human Embryonic Heart Tissue Epigenomic and Transcriptomic Data from the Cotney Lab at UConn Health hg19, hg38
COVID-19 Gene Annotation GENCODE annotation of COVID-19 associated genes hg38
CPTAC Hub v1 Clinical Proteomic Tumor Analysis Consortium (CPTAC) Hub v1 hg19
Croc and Bird Hub Croc, Bird, and Archosaur Assembly Hub [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
DANIO-CODE Track Hub A Track Hub containing tracks produced with DANIO-CODE pipelines danRer10, danRer11
DASHR small ncRNA Hub DASHR Human small non-coding RNA data hg19
DASHR v2.0 Hub DASHR v2.0 Human small non-coding RNA data hub hg19, hg38
dbRIP_Hub "dbRIP: Database of Polymorphic and Species-specific Retrotransposons in Humans" hg19, hg38
dbVar Hub NCBI's database of human genomic Structural Variation -- large variants >50 bp hg19, hg38
DNA Methylation Hundreds of analyzed methylomes from bisulfite sequencing data [+] hg38, hg19, hg18, mm9, mm10, panTro2, panTro4, ponAbe2...
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
EPD Viewer Hub ERROR: Couldn't open https://epd.epfl.ch/ucsc/epdHub/epdHub.txt Debug Help [+] hg19, hg38, mm9, mm10, danRer7, rheMac8, galGal5, rn6...
FaceBase Hub Comprehensive craniofacial research data from FaceBase.org mm9, mm10, hg18, hg19
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8, galGal5
FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU hg19, hg18
Fish assemblies Fish genome assemblies [+] GCF_000485575.1, GCF_002910315.2...
GeneHancer GeneHancer: genome-wide integration of regulatory elements and target genes in GeneCards hg38, hg19
GRC Genome Issues under Review Genome Reference Consortium: Genome issues and other features hg38, hg19, mm10, mm9, danRer7, danRer10, danRer11
GTEx Analysis Hub Genotype Tissue Expression (GTEx) Project Analysis Hub hg19, hg38
GTEx RNA-seq Signal Hub RNA-seq read coverage in 53 tissues from GTEx V6 (7572 samples) hg19, hg38
Hippocampal DNA methylation and gene transcription Hippocampal DNA methylation and gene expression patterns in porcine biomedical models of cognitive development susScr3
Human cellular microRNAome microRNA RNA-seq based data from 46 primary cell types and 42 cancer or immortalized cell lines. hg38
Human cellular microRNAome barCharts Evaluation of >10 billion small RNA-seq reads from 78 primary cell types and 42 cancer or immortalized cell lines from 3 main studies. hg38
Human Global Reference Genomes Human Global Reference Genome assembly hub [+] GCA_003601015.1_HG03807_prelim_1.0...
Human Islet lncRNAs Pancreatic islet long non coding RNA transcripts (Akerman et al 2016) hg19
human p53 Binding And Expression Resource (BAER) hub human p53 ChIP-seq coverage depth (tracks) & SISSRs peak calls with associated differential gene expression from published data as of May 2015 hg19
IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm hg19
iPSCORE_RPE ERROR: Couldn't open http://flh1.ucsd.edu/RPE_public/iPSCORE_RPE/hub.txt Debug Help hg19
JASPAR TFBS TFBS predictions for profiles in the JASPAR CORE collections [+] hg19, hg38, ce10, dm6, sacCer3, danRer10, danRer11...
LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD hg19
LNCipedia 5.2 LNCipedia 5.2 - A comprehensive compendium of human long non-coding RNAs hg19, hg38
Mammal assemblies Mammal genome assemblies [+] GCF_000298275.1, GCF_000001905.1...
McGill EMC (CEEHRC) McGill Epigenomics Mapping Centre, Montreal, Quebec, Canada hg19
MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium mm10
miRcode microRNA sites Predicted microRNA target sites in GENCODE transcripts hg19
mm9.SMC1.ChIAPET Cohesin(Smc1)-associated chromatin interactions in murine embryonic stem cells mm9
Mouse strain assemblies Assembly and alignment data for 16 different mouse strains plus rat. [+] mm10, rn6, 129S1_SvImJ, WSB_EiJ, SPRET_EiJ, AKR_J...
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, hg19
Peterhof_yeasts Assemblies, SNV and CNV data for Saccharomyces cerevisiae strains of the Peterhof Genetic Collection [+] sacCer3, 1B_D1606_spades...
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF [+] hg19, hg38, mm10, galGal4, galGal6, dm6, ce11, wuhCor1...
Plants CSHL Biology of Genomes meeting 2013 demonstration assembly hub araTha1, braRap1, ricCom1
Polytract Repeats Very Short Tandem Repeats (MNR/DNR/TNR) hg38, mm10, rn6, dm6
Porcine DNA methylation DNA methylation levels from 9 week old Landrace x Yorkshire crossbred pigs and cell line 3D4/2. susScr3
Porcine DNA methylation and gene transcription DNA methylation and gene expression levels for eight tissues from the adult female Duroc chosen for production of the swine reference genome. susScr3
Primate x4 NeuroDiff and Human CRISPRa RNAseq coverage tracks from 4 Primate neuro-differentiation assays and a human CRISPRa assay hg19, panTro4, ponAbe2, rheMac8
Principal Splice Isoforms APPRIS Selects a single CDS variant for each gene as the 'PRINCIPAL' isoform based on the range of protein features. [+] hg38, hg19, mm10, danRer10, rn6, susScr3, panTro4, dm6...
Promoterome CAGE and nucleosome positioning Zebrafish promoterome based on Haberle et al. and Nepal et al. danRer7
Purple sea star Assembly Hub This is the Assembly Hub of the purple sea star (Pisaster ochraceus, assembly 12Jun2017_28pcJ) 12Jun2017_28pcJ
refTSS refTSS hg38, mm10
ReMap 2020 Regulatory Atlas ReMap 2020: An atlas of regulatory regions from an integrative analysis of Human and Arabidopsis thaliana DNA-binding sequencing experiments. Go to ReMap for more info. hg38, araTha1
ReMap2018 Regulatory Atlas ReMap2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. Go to ReMap for more info. Pubmed link. hg38
rfam12_ncRNA Rfam 12.0 non-coding RNA annotation hg38, mm10, ce10, galGal4, ci2, danRer7, dm6, sacCer3
Roadmap Epigenomics Data Complete Collection at Wash U VizHub Roadmap Epigenomics Human Epigenome Atlas Data Complete Collection, VizHub at Washington University in St. Louis hg19
Roadmap Epigenomics Integrative Analysis Hub Roadmap Epigenomics Integrative Analysis Hub at Washington University in St. Louis hg19
Seq-data on mm9 NS5 cells Set of sequencing data on mm9 NS5 cells mm9
Splice Site Usage Hub Splice Site Usage Values Calculated for 19 ENCODE Cell Lines from RNA-seq hg19
Synonymous Constraint Synonymous Constraint Elements and Synonymous Acceleration Elements in protein-coding regions hg19, hg38, wuhCor1
TOBIAS footprint prediction Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal hg38, mm10
Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track hg19
UCD Methylation UCD DNA methylation data [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...
UCSC Repeat Browser 2020 Update Human Repeat consensuses annotated with lifted tracks hg38reps, hg19, hg38
Ultraconserved Elements Ultra conserved Elements in the Human Genome. Science 304(5675) pp.1321-1325 (2004) hg19
Umap and Bismap mappability Uniquely mappable regions of genome and methylome hg38, hg19, mm9, mm10
UMassMed ZHub UMassMed H3K4me3 ChIP-seq data for Autistic brains hg19
UniBind UniBind: A map of direct TF-DNA interactions from ChIP-seq and TF binding profiles hg38
UniProt Features UniProtKB reviewed protein features mapped to the Ensembl genome assembly. hg38
Vertebrate assemblies Vertebrate genome assemblies [+] GCF_001663975.1, GCF_000281125.3...
VGP Vertebrate Genomes Project assemblies [+] GCA_003957555.2_bCalAnn1_v1.p...
Vista Enhancers Vista Browser Track Hub hg19, mm9, mm10
WormBase WormBase nematode genomes [+] brenneri, japonica, remanei, ovolvulus, briggsae...
Xmac Xiphophorus maculatus chromosome assembly version 5.0(SMRT) X.maculatus
ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources danRer11, danRer10, danRer7
Bird assemblies Bird genome assemblies [+] GCF_000699105.1, GCF_000691975.1...
Blueprint Hub Blueprint Epigenomics Data Hub hg38
BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples hg19
Breast Cancer lncRNA Breast Cancer lncRNA PMID 26236012 hg19
Broad Improved Canine Annotation v1 Broad Institute CanFam3 Improved Annotation Data v1 canFam3
C_elegans_isolates C. elegans wild isolate assembly hub [+] CB4856Princeton_JR-contig...
CADD CADD Track for v1.3 to v1.6 hg19, hg38
Cancer Genomics Tracks TCGA and ICGC Cancer Mutations, TCGA Expression, Immune Epitopes Database (IEDB), Cancer Immunity Peptides Database, Dienstmann Variant/Cancer database, CIVIC, MyCancerGenome.org, OncoKB hg19
CEMT (CEEHRC) Epigenomic Data tracks from BCGSC, Vancouver, B.C. hg38, hg19
CESAR Gene Mappings Human Exons mapped by CESAR [+] bosTau7, ailMel1, allMis1, anoCar2, calJac3...
ChIP-seq data track HUBs from MSC cells from GSE79815 ChIP-seq data from the publication "Epigenetic plasticity drives adipogenic and osteogenic differentiation of marrow-derived mesenchymal stem cells" (10.1074/jbc.M116.736538) from GEO record GSE79815 mm9
Coloc segments Colocalized segments of human genome for Roadmap cell types hg19
Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at UConn Health hg19, mm9
Cotney Lab Human Embryonic Heart Hub Human Embryonic Heart Tissue Epigenomic and Transcriptomic Data from the Cotney Lab at UConn Health hg19, hg38
COVID-19 Gene Annotation GENCODE annotation of COVID-19 associated genes hg38
CPTAC Hub v1 Clinical Proteomic Tumor Analysis Consortium (CPTAC) Hub v1 hg19
Croc and Bird Hub Croc, Bird, and Archosaur Assembly Hub [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
DANIO-CODE Track Hub A Track Hub containing tracks produced with DANIO-CODE pipelines danRer10, danRer11
DASHR small ncRNA Hub DASHR Human small non-coding RNA data hg19
DASHR v2.0 Hub DASHR v2.0 Human small non-coding RNA data hub hg19, hg38
dbRIP_Hub "dbRIP: Database of Polymorphic and Species-specific Retrotransposons in Humans" hg19, hg38
dbVar Hub NCBI's database of human genomic Structural Variation -- large variants >50 bp hg19, hg38
DNA Methylation Hundreds of analyzed methylomes from bisulfite sequencing data [+] hg38, hg19, hg18, mm9, mm10, panTro2, panTro4, ponAbe2...
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
EPD Viewer Hub ERROR: Couldn't open https://epd.epfl.ch/ucsc/epdHub/epdHub.txt Debug Help [+] hg19, hg38, mm9, mm10, danRer7, rheMac8, galGal5, rn6...
FaceBase Hub Comprehensive craniofacial research data from FaceBase.org mm9, mm10, hg18, hg19
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8, galGal5
FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU hg19, hg18
Fish assemblies Fish genome assemblies [+] GCF_000485575.1, GCF_002910315.2...
GeneHancer GeneHancer: genome-wide integration of regulatory elements and target genes in GeneCards hg38, hg19
GRC Genome Issues under Review Genome Reference Consortium: Genome issues and other features hg38, hg19, mm10, mm9, danRer7, danRer10, danRer11
GTEx Analysis Hub Genotype Tissue Expression (GTEx) Project Analysis Hub hg19, hg38
GTEx RNA-seq Signal Hub RNA-seq read coverage in 53 tissues from GTEx V6 (7572 samples) hg19, hg38
Hippocampal DNA methylation and gene transcription Hippocampal DNA methylation and gene expression patterns in porcine biomedical models of cognitive development susScr3
Human cellular microRNAome microRNA RNA-seq based data from 46 primary cell types and 42 cancer or immortalized cell lines. hg38
Human cellular microRNAome barCharts Evaluation of >10 billion small RNA-seq reads from 78 primary cell types and 42 cancer or immortalized cell lines from 3 main studies. hg38
Human Global Reference Genomes Human Global Reference Genome assembly hub [+] GCA_003601015.1_HG03807_prelim_1.0...
Human Islet lncRNAs Pancreatic islet long non coding RNA transcripts (Akerman et al 2016) hg19
human p53 Binding And Expression Resource (BAER) hub human p53 ChIP-seq coverage depth (tracks) & SISSRs peak calls with associated differential gene expression from published data as of May 2015 hg19
IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm hg19
iPSCORE_RPE ERROR: Couldn't open http://flh1.ucsd.edu/RPE_public/iPSCORE_RPE/hub.txt Debug Help hg19
JASPAR TFBS TFBS predictions for profiles in the JASPAR CORE collections [+] hg19, hg38, ce10, dm6, sacCer3, danRer10, danRer11...
LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD hg19
LNCipedia 5.2 LNCipedia 5.2 - A comprehensive compendium of human long non-coding RNAs hg19, hg38
Mammal assemblies Mammal genome assemblies [+] GCF_000298275.1, GCF_000001905.1...
McGill EMC (CEEHRC) McGill Epigenomics Mapping Centre, Montreal, Quebec, Canada hg19
MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium mm10
miRcode microRNA sites Predicted microRNA target sites in GENCODE transcripts hg19
mm9.SMC1.ChIAPET Cohesin(Smc1)-associated chromatin interactions in murine embryonic stem cells mm9
Mouse strain assemblies Assembly and alignment data for 16 different mouse strains plus rat. [+] mm10, rn6, 129S1_SvImJ, WSB_EiJ, SPRET_EiJ, AKR_J...
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, hg19
Peterhof_yeasts Assemblies, SNV and CNV data for Saccharomyces cerevisiae strains of the Peterhof Genetic Collection [+] sacCer3, 1B_D1606_spades...
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF [+] hg19, hg38, mm10, galGal4, galGal6, dm6, ce11, wuhCor1...
Plants CSHL Biology of Genomes meeting 2013 demonstration assembly hub araTha1, braRap1, ricCom1
Polytract Repeats Very Short Tandem Repeats (MNR/DNR/TNR) hg38, mm10, rn6, dm6
Porcine DNA methylation DNA methylation levels from 9 week old Landrace x Yorkshire crossbred pigs and cell line 3D4/2. susScr3
Porcine DNA methylation and gene transcription DNA methylation and gene expression levels for eight tissues from the adult female Duroc chosen for production of the swine reference genome. susScr3
Primate x4 NeuroDiff and Human CRISPRa RNAseq coverage tracks from 4 Primate neuro-differentiation assays and a human CRISPRa assay hg19, panTro4, ponAbe2, rheMac8
Principal Splice Isoforms APPRIS Selects a single CDS variant for each gene as the 'PRINCIPAL' isoform based on the range of protein features. [+] hg38, hg19, mm10, danRer10, rn6, susScr3, panTro4, dm6...
Promoterome CAGE and nucleosome positioning Zebrafish promoterome based on Haberle et al. and Nepal et al. danRer7
Purple sea star Assembly Hub This is the Assembly Hub of the purple sea star (Pisaster ochraceus, assembly 12Jun2017_28pcJ) 12Jun2017_28pcJ
refTSS refTSS hg38, mm10
ReMap 2020 Regulatory Atlas ReMap 2020: An atlas of regulatory regions from an integrative analysis of Human and Arabidopsis thaliana DNA-binding sequencing experiments. Go to ReMap for more info. hg38, araTha1
ReMap2018 Regulatory Atlas ReMap2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. Go to ReMap for more info. Pubmed link. hg38
rfam12_ncRNA Rfam 12.0 non-coding RNA annotation hg38, mm10, ce10, galGal4, ci2, danRer7, dm6, sacCer3
Roadmap Epigenomics Data Complete Collection at Wash U VizHub Roadmap Epigenomics Human Epigenome Atlas Data Complete Collection, VizHub at Washington University in St. Louis hg19
Roadmap Epigenomics Integrative Analysis Hub Roadmap Epigenomics Integrative Analysis Hub at Washington University in St. Louis hg19
Seq-data on mm9 NS5 cells Set of sequencing data on mm9 NS5 cells mm9
Splice Site Usage Hub Splice Site Usage Values Calculated for 19 ENCODE Cell Lines from RNA-seq hg19
Synonymous Constraint Synonymous Constraint Elements and Synonymous Acceleration Elements in protein-coding regions hg19, hg38, wuhCor1
TOBIAS footprint prediction Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal hg38, mm10
Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track hg19
UCD Methylation UCD DNA methylation data [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...
UCSC Repeat Browser 2020 Update Human Repeat consensuses annotated with lifted tracks hg38reps, hg19, hg38
Ultraconserved Elements Ultra conserved Elements in the Human Genome. Science 304(5675) pp.1321-1325 (2004) hg19
Umap and Bismap mappability Uniquely mappable regions of genome and methylome hg38, hg19, mm9, mm10
UMassMed ZHub UMassMed H3K4me3 ChIP-seq data for Autistic brains hg19
UniBind UniBind: A map of direct TF-DNA interactions from ChIP-seq and TF binding profiles hg38
UniProt Features UniProtKB reviewed protein features mapped to the Ensembl genome assembly. hg38
Vertebrate assemblies Vertebrate genome assemblies [+] GCF_001663975.1, GCF_000281125.3...
VGP Vertebrate Genomes Project assemblies [+] GCA_003957555.2_bCalAnn1_v1.p...
Vista Enhancers Vista Browser Track Hub hg19, mm9, mm10
WormBase WormBase nematode genomes [+] brenneri, japonica, remanei, ovolvulus, briggsae...
Xmac Xiphophorus maculatus chromosome assembly version 5.0(SMRT) X.maculatus
ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources danRer11, danRer10, danRer7
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