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.

Filter hubs by assembly:

Clicking Connect redirects to the gateway page of the selected hub's default assembly.
Display Hub Name Description Assemblies
Mouse strain assemblies Assembly and alignment data for 16 different mouse strains plus rat. [+] mm10, rn6, 129S1_SvImJ, WSB_EiJ, SPRET_EiJ, AKR_J...
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
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
Hippocampal DNA methylation and gene transcription Hippocampal DNA methylation and gene expression patterns in porcine biomedical models of cognitive development susScr3
DASHR small ncRNA Hub DASHR Human small non-coding RNA data hg19
dan_rer ZGA Hub UCSC Hub for transcripts detected via long-read seq in Zebrafish during ZGA danRer10
DNA Methylation Hundreds of analyzed methylomes from bisulfite sequencing data [+] hg38, hg19, hg18, mm9, mm10, panTro2, panTro4, ponAbe2...
ChIP-seq data track HUBs from MSC cells from GSE79815 ERROR: Couldn't open https://biochem.wisc.edu/sites/default/files/labs/pike/genome-ucsc/GSE79815_MSC_HUB/hub.txt Debug Help mm9
lncRNA in Breast Cancer ERROR: TCP non-blocking connect() to pecan.swmed.edu timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://pecan.swmed.edu/public/breast_cancer_lncrna_pmid_26236012/hub.txt Debug Help hg19
UCD Methylation ERROR: TCP non-blocking connect() to lasallelab.genomecenter.ucdavis.edu timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt Debug Help [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...
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...
GeneHancer enhancers GeneHancer: genome-wide integration of enhancers and target genes in GeneCards hg38, hg19
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
McGill EMC (CEEHRC) McGill Epigenomics Mapping Centre, Montreal, Quebec, Canada hg19
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, 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
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF hg19, hg38, mm10, galGal4, dm6, ce11
iPSCORE_RPE iPSCORE retinal pigment epithelium (RPE) epigenome hg19
miRcode microRNA sites Predicted microRNA target sites in GENCODE transcripts hg19
GTEx RNA-seq Signal Hub ERROR: Couldn't open http://hgdownload.soe.ucsc.edu/hubs/gtex/hg19/trackDb.txt Debug Help hg19, hg38
Broad Improved Canine Annotation v1 Broad Institute CanFam3 Improved Annotation Data v1 canFam3
UMassMed ZHub UMassMed H3K4me3 ChIP-seq data for Autistic brains hg19
CPTAC Hub v1 Clinical Proteomic Tumor Analysis Consortium (CPTAC) Hub v1 hg19
ReMap Regulatory Atlas ReMap: An atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments hg38
UniProt Features UniProtKB reviewed protein features mapped to the Ensembl genome assembly. hg38
Peterhof_yeasts Assemblies, SNV and CNV data for Saccharomyces cerevisiae strains of the Peterhof Genetic Collection [+] sacCer3, 1B_D1606_spades...
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
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...
C_elegans_isolates C. elegans wild isolate assembly hub [+] CB4856Princeton_JR-contig...
Umap and Bismap mappability Uniquely mappable regions of genome and methylome hg38, hg19, mm9, mm10
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8
ChromosomeAssembliesGR Comparative data and New chromosome assemblies for Falcon and Pigeon from Damas et al., 2016 Genome Research colLiv2, galGal4, falPer2
MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium mm10
Seq-data on mm9 NS5 cells Set of sequencing data on mm9 NS5 cells mm9
BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples hg19
EPD Viewer Hub Promoter specific experimental data and TSS annotation from the EPD database hg19, mm9, pfa2, amel5, araTha1, zm3, spo2
IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm hg19
Human Islet lncRNAs Pancreatic islet long non coding RNA transcripts (Akerman et al 2016) hg19
Porcine DNA methylation DNA methylation levels from 9 week old Landrace x Yorkshire crossbred pigs and cell line 3D4/2. susScr3
Promoterome CAGE and nucleosome positioning Zebrafish promoterome based on Haberle et al. and Nepal et al. danRer7
JASPAR 2018 TFBS TFBS predictions for all profiles in the JASPAR CORE collection (2018) hg19, hg38, ce10, dm6, sacCer3, danRer10, mm10
FaceBase Hub Comprehensive craniofacial research data from FaceBase.org mm9, mm10, hg18, hg19
WormBase WormBase nematode genomes [+] brenneri, japonica, remanei, ovolvulus, briggsae...
Roadmap Epigenomics Integrative Analysis Hub Roadmap Epigenomics Integrative Analysis Hub at Washington University in St. Louis hg19
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD hg19
Blueprint Hub Blueprint Epigenomics Data Hub hg38
GTEx Analysis Hub Allele-Specific Expression in 53 tissues from GTEx Analysis (NY Genome Center) hg19, hg38
FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU hg19, hg18
Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track hg19
LNCipedia 5.2 LNCipedia 5.2 - A comprehensive compendium of human long non-coding RNAs hg19, hg38
rfam12_ncRNA Rfam 12.0 non-coding RNA annotation hg38, mm10, ce10, galGal4, ci2, danRer7, dm6, sacCer3
Plants CSHL Biology of Genomes meeting 2013 demonstration assembly hub araTha1, braRap1, ricCom1
DASHR v2.0 Hub DASHR v2.0 Human small non-coding RNA data hub hg19, hg38
GRC Genome Issues under Review Genome Reference Consortium: Genome issues and other features hg38, hg19, mm10, mm9, danRer7, danRer10, danRer11
Ultraconserved Elements Ultra conserved Elements in the Human Genome Science 304(5675) pp.1321-1325 (2004) hg19
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
Croc and Bird Hub Croc, Bird, and Archosaur Assembly Hub [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
dbRIP_Hub "dbRIP: Database of Polymorphic and Species-specific Retrotransposons in Humans" hg19, hg38
mm9.SMC1.ChIAPET Cohesin(Smc1)-associated chromatin interactions in murine embryonic stem cells mm9
454 K562andHelaS3RNAseq Whole-Cell 454 Hela and K562 RNAseq hg19
ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources danRer10, danRer7
Vista Enhancers Vista Browser Track Hub hg19, mm9, mm10
Human cellular microRNAome microRNA RNA-seq based data from 46 primary cell types and 42 cancer or immortalized cell lines. hg38
Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at UConn Health hg19, 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...
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
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
Hippocampal DNA methylation and gene transcription Hippocampal DNA methylation and gene expression patterns in porcine biomedical models of cognitive development susScr3
DASHR small ncRNA Hub DASHR Human small non-coding RNA data hg19
dan_rer ZGA Hub UCSC Hub for transcripts detected via long-read seq in Zebrafish during ZGA danRer10
DNA Methylation Hundreds of analyzed methylomes from bisulfite sequencing data [+] hg38, hg19, hg18, mm9, mm10, panTro2, panTro4, ponAbe2...
ChIP-seq data track HUBs from MSC cells from GSE79815 ERROR: Couldn't open https://biochem.wisc.edu/sites/default/files/labs/pike/genome-ucsc/GSE79815_MSC_HUB/hub.txt Debug Help mm9
lncRNA in Breast Cancer ERROR: TCP non-blocking connect() to pecan.swmed.edu timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://pecan.swmed.edu/public/breast_cancer_lncrna_pmid_26236012/hub.txt Debug Help hg19
UCD Methylation ERROR: TCP non-blocking connect() to lasallelab.genomecenter.ucdavis.edu timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt Debug Help [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...
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...
GeneHancer enhancers GeneHancer: genome-wide integration of enhancers and target genes in GeneCards hg38, hg19
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
McGill EMC (CEEHRC) McGill Epigenomics Mapping Centre, Montreal, Quebec, Canada hg19
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, 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
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF hg19, hg38, mm10, galGal4, dm6, ce11
iPSCORE_RPE iPSCORE retinal pigment epithelium (RPE) epigenome hg19
miRcode microRNA sites Predicted microRNA target sites in GENCODE transcripts hg19
GTEx RNA-seq Signal Hub ERROR: Couldn't open http://hgdownload.soe.ucsc.edu/hubs/gtex/hg19/trackDb.txt Debug Help hg19, hg38
Broad Improved Canine Annotation v1 Broad Institute CanFam3 Improved Annotation Data v1 canFam3
UMassMed ZHub UMassMed H3K4me3 ChIP-seq data for Autistic brains hg19
CPTAC Hub v1 Clinical Proteomic Tumor Analysis Consortium (CPTAC) Hub v1 hg19
ReMap Regulatory Atlas ReMap: An atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments hg38
UniProt Features UniProtKB reviewed protein features mapped to the Ensembl genome assembly. hg38
Peterhof_yeasts Assemblies, SNV and CNV data for Saccharomyces cerevisiae strains of the Peterhof Genetic Collection [+] sacCer3, 1B_D1606_spades...
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
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...
C_elegans_isolates C. elegans wild isolate assembly hub [+] CB4856Princeton_JR-contig...
Umap and Bismap mappability Uniquely mappable regions of genome and methylome hg38, hg19, mm9, mm10
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8
ChromosomeAssembliesGR Comparative data and New chromosome assemblies for Falcon and Pigeon from Damas et al., 2016 Genome Research colLiv2, galGal4, falPer2
MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium mm10
Seq-data on mm9 NS5 cells Set of sequencing data on mm9 NS5 cells mm9
BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples hg19
EPD Viewer Hub Promoter specific experimental data and TSS annotation from the EPD database hg19, mm9, pfa2, amel5, araTha1, zm3, spo2
IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm hg19
Human Islet lncRNAs Pancreatic islet long non coding RNA transcripts (Akerman et al 2016) hg19
Porcine DNA methylation DNA methylation levels from 9 week old Landrace x Yorkshire crossbred pigs and cell line 3D4/2. susScr3
Promoterome CAGE and nucleosome positioning Zebrafish promoterome based on Haberle et al. and Nepal et al. danRer7
JASPAR 2018 TFBS TFBS predictions for all profiles in the JASPAR CORE collection (2018) hg19, hg38, ce10, dm6, sacCer3, danRer10, mm10
FaceBase Hub Comprehensive craniofacial research data from FaceBase.org mm9, mm10, hg18, hg19
WormBase WormBase nematode genomes [+] brenneri, japonica, remanei, ovolvulus, briggsae...
Roadmap Epigenomics Integrative Analysis Hub Roadmap Epigenomics Integrative Analysis Hub at Washington University in St. Louis hg19
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD hg19
Blueprint Hub Blueprint Epigenomics Data Hub hg38
GTEx Analysis Hub Allele-Specific Expression in 53 tissues from GTEx Analysis (NY Genome Center) hg19, hg38
FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU hg19, hg18
Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track hg19
LNCipedia 5.2 LNCipedia 5.2 - A comprehensive compendium of human long non-coding RNAs hg19, hg38
rfam12_ncRNA Rfam 12.0 non-coding RNA annotation hg38, mm10, ce10, galGal4, ci2, danRer7, dm6, sacCer3
Plants CSHL Biology of Genomes meeting 2013 demonstration assembly hub araTha1, braRap1, ricCom1
DASHR v2.0 Hub DASHR v2.0 Human small non-coding RNA data hub hg19, hg38
GRC Genome Issues under Review Genome Reference Consortium: Genome issues and other features hg38, hg19, mm10, mm9, danRer7, danRer10, danRer11
Ultraconserved Elements Ultra conserved Elements in the Human Genome Science 304(5675) pp.1321-1325 (2004) hg19
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
Croc and Bird Hub Croc, Bird, and Archosaur Assembly Hub [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
dbRIP_Hub "dbRIP: Database of Polymorphic and Species-specific Retrotransposons in Humans" hg19, hg38
mm9.SMC1.ChIAPET Cohesin(Smc1)-associated chromatin interactions in murine embryonic stem cells mm9
454 K562andHelaS3RNAseq Whole-Cell 454 Hela and K562 RNAseq hg19
ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources danRer10, danRer7
Vista Enhancers Vista Browser Track Hub hg19, mm9, mm10
Human cellular microRNAome microRNA RNA-seq based data from 46 primary cell types and 42 cancer or immortalized cell lines. hg38
Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at UConn Health hg19, mm9
No Unlisted Track Hubs
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