Track Data Hubs

Track data hubs are collections of external tracks that can be added to the UCSC Genome Browser. Click Connect to attach a hub and redirect to the assembly gateway page. Hub tracks will then show up in the hub's own blue bar track group under the browser graphic. For more information, including where to host your track hub, see our User's Guide.

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

The list below can be filtered on words in the hub description pages or by assemblies.
Search terms: Assembly:
Display Hub Name Description AssembliesClick to connect and browse directly
ABC of cellular microRNAome Advanced BarChart configuration of cellular microRNAome. Evaluation of >20 billion small RNA-seq reads from 196 primary cell types (+plasma, +platelets) across 175 main studies. hg38
ALFA Hub NCBI's Allele Frequency Aggregator (ALFA) allele frequency for variants in dbGaP studies. hg19, hg38
Bird Alignment (363 species) Bird Alignment (363 species) [+] Gallus_gallus, Acanthisitta_chloris...
Bird assemblies Bird genome assemblies [+] GCA_009769605.1, GCA_009769595.1...
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 Epigenomics Track Hub Breast Cancer Epigenomics Track Hub 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 v1.7 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,, OncoKB hg19
CCGP The California Conservation Genomics Project (CCGP) assemblies [+] GCA_026170555.1, GCA_026170545.1...
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, hg38
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
Croc and Bird Hub Croc, Bird, and Archosaur Assembly Hub [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
DANIO-CODE Track Hub DANIO-CODE: Central repository for zebrafish genomic datasets 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
dbVar Hub NCBI's database of human genomic Structural Variation -- large variants >50 bp hg19, hg38
Dfam database of TE families and annotations Dfam database of Transposable Element families and genome annotations hg38
Digital genomic footprinting (Vierstra et al., 2020) Digital genomic footprinting from 243 cell & tissue types hg38
DNA Methylation Hundreds of analyzed methylomes from bisulfite sequencing data [+] mm39, hg38, danRer11, canFam6, gorGor6, TAIR10, rn7...
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
ENCODE DNA Trackhub ENCODE Trackhub for DNA-based assays hg19, hg38, mm10
ENCODE integrative Trackhub ENCODE Trackhub for integrative results hg38, mm10
ENCODE RNA Trackhub ENCODE Trackhub for RNA-based assays hg19, hg38, mm10
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
EPD Viewer Hub Promoter specific experimental data and TSS annotation from the EPD database [+] hg19, hg38, mm9, mm10, danRer7, rheMac8, galGal5, rn6...
Exp/Meth VNTR hub Association of VNTRs with Expression and Methylation in GTEx, PCGC and PPMI hg19, hg38
EyeBrowse Eye tissue specific genes and markers, derived from NEIBank and other sources [+] hg19, bosTau6, canFam2, cavPor3, danRer6, danRer7...
FaceBase Hub Comprehensive craniofacial research data from mm9, mm10, hg18, hg19
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8, galGal5
Fish assemblies Fish genome assemblies [+] GCF_017589495.1, GCF_000485575.1...
Fungi assemblies Fungi genome assemblies [+] GCF_003184765.1, GCF_001890905.1...
GENCODE Annotation Updates Updates to GENCODE manual annotation since last release hg38, mm39, mm10
GeneCards ncRNAs An integrated compendium of ncRNA genes in GeneCards hg38
GeneHancer GeneHancer: genome-wide integration of regulatory elements and target genes in GeneCards hg38, hg19
Golden Hamster genome Genome assembly of Golden Hamster(Mesocricetus auratus) from Siomi lab MesAur2.0
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
HPRC The Human Pangenome Reference Consortium [+] GCA_018471515.1, GCA_018472595.1...
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 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
IMPACT regulatory element activity Cell-type-specific regulatory element activity profiles across 707 unique combinations of transcription factor-cell type pairs. IMPACT predicts the epigenetic regulatory activity related to a particular transcription factor in a given cell type. IMPACT sc hg19
Invertebrate assemblies Invertebrate genome assemblies [+] GCA_905333045.1, GCF_000005575.2...
JASPAR TFBS TFBS predictions for profiles in the JASPAR CORE collections [+] hg19, hg38, ce10, ce11, ci3, dm6, sacCer3, danRer10...
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 and Bird Alignment (605 species) Mammal and Bird Alignment (605 species) [+] Homo_sapiens, Gallus_gallus...
Mammal assemblies Mammal genome assemblies [+] GCF_000298275.1, GCA_011750645.1...
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...
MutScore Variant Pathogenicity MutScore Variant Pathogenicity hg38, hg19
ORF Predictions RNA-Seq, Ribo_Seq, and ORF Predictions wuhCor1
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, hg19
Peterhof_yeasts Peterhof_yeast [+] sacCer3, 1B_D1606_spades...
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF [+] hg19, hg38, mm10, mm39, galGal4, galGal6, dm6, ce11...
PhyloCSF++ Evolutionary protein-coding potential as measured by PhyloCSF++ rn6, fr3, gasAcu1, tarSyr2, sacCer3
Plant assemblies Plant genome assemblies [+] GCF_019202715.1, GCF_016808095.1...
Polytract Repeats Very Short Tandem Repeats (MNR/DNR/TNR) hg38, mm10, rn6, dm6
Predominant PAS and predominant hexamers Predominant polyA sites and predominant hexamers hg38, hg19
Primate assemblies Primate genome assemblies [+] GCF_000951035.1, GCA_023783095.1...
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
RefSeqFE Hub NCBI RefSeq Functional Elements interactions and features GCA_009914755.4, hg19, hg38, hs1, mm10, mm39
refTSS refTSS hg38, mm10
ReMap 2018 Regulatory Atlas ReMap 2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. Go to ReMap for more info. Pubmed link. hg38
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
ReMap 2022 Regulatory Atlas ReMap 2022: A database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments Go to ReMap2022 for more info. mm10, mm39, hg38, hg19, dm6, araTha1
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, hg38
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
SIHUMI simplified human intestinal microbiota HUB [+] bact, bifi, blautia, anaero, ery, clostri, lacto...
singing mouse genome hub This is the genome hub for Alston's singing mouse (Scotinomys teguina) steguina
Splice Site Usage Hub Splice Site Usage Values Calculated for 19 ENCODE Cell Lines from RNA-seq hg19
sunflower_sea_star Pycnopodia helianthoides (sunflower sea star) sunflower_sea_star
Synonymous Constraint Synonymous Constraint Elements and Synonymous Acceleration Elements in protein-coding regions hg19, hg38, wuhCor1
T_cell_ATAC_ChIP_Pipkin T cell ATACseq ChIPseq assembly by Pipkin lab mm10
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 ERROR: TCP non-blocking connect() to IP timed-out in select() after 10000 milliseconds. A connection timeout means that either the server is offline or its firewall, the UCSC firewall or any router between the two blocks the connection. Couldn't open Debug Help [+] 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 ERROR: Couldn't open Debug Help hg19
UniBind 2018 Hub UniBind: A map of direct TF-DNA interactions from ChIP-seq and TF binding profiles hg38
UniBind 2021 permissive Hub UniBind 2021 hub for permissive direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, spo2, sacCer3, rn6...
UniBind 2021 Robust Hub UniBind 2021 hub for robust direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, sacCer3, rn6, araTha1...
UniProt Features UniProtKB reviewed protein features mapped to the Ensembl genome assembly. hg38
Vertebrate assemblies Vertebrate genome assemblies [+] GCF_003597395.1, GCA_027172095.1...
VGP primary Vertebrate Genomes Project primary assemblies [+] GCA_009769605.1, GCF_027172205.1...