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UCSC Genome Browser @GenomeBrowser

The UCSC Genome Browser is a public, freely available, open-source web-based graphical viewer for the display of genome sequences and their annotations.

Joined May 2011
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245 Photos and videos
New on the UCSC Genome Browser (hg38): MPRA tracks. MPRA Base catalogs 40,938 experimentally tested enhancer elements across 6 cell lines; MPRAVarDB scores 239,028 allelic variant effects from 18 studies. Great for GWAS fine-mapping. Learn more: bit.ly/4a8KDPD
MPRA Base elements and MPRAVarDB variants at the TERT promoter (chr5, GRCh38/hg38). MPRA Base (top) shows reporter activity for melanoma risk variants tested in HEK293FT and UACC903 cells (Choi et al., 2020). MPRAVarDB (bottom) highlights high-confidence allelic effects from saturation mutagenesis of the TERT promoter (Kircher et al., 2019).

ALT MPRA Base elements and MPRAVarDB variants at the TERT promoter (chr5, GRCh38/hg38). MPRA Base (top) shows reporter activity for melanoma risk variants tested in HEK293FT and UACC903 cells (Choi et al., 2020). MPRAVarDB (bottom) highlights high-confidence allelic effects from saturation mutagenesis of the TERT promoter (Kircher et al., 2019).

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Two new variant-impact tracks from Illumina on the UCSC Genome Browser: PrimateAI-3D scores every coding missense variant (hg38/hg19); PromoterAI scores every non-coding substitution near transcription start sites (hg38). See our news for more: bit.ly/illuminaTracks
PrimateAI-3D and PromoterAI at the start of HBB on hg38 (chr11:5,226,883-5,227,212). PrimateAI-3D scores every coding missense variant as red (pathogenic) or blue (benign), while the four PromoterAI per-allele bigWig subtracks score every possible non-coding substitution in the 5′ UTR and proximal promoter just upstream of the HBB start codon.

ALT PrimateAI-3D and PromoterAI at the start of HBB on hg38 (chr11:5,226,883-5,227,212). PrimateAI-3D scores every coding missense variant as red (pathogenic) or blue (benign), while the four PromoterAI per-allele bigWig subtracks score every possible non-coding substitution in the 5′ UTR and proximal promoter just upstream of the HBB start codon.

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Check out our new NMD Escape tracks on hg38! They predict where premature stop codons escape nonsense-mediated decay. Useful for interpreting truncating variants under ACMG PVS1. Includes GENCODE RefSeq rulesets predictive scores. See our news for more: bit.ly/browserNMD
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New "Tandem Repeat Variation" tracks on hg38. Browse STR/VNTR data from WebSTR, STRchive, TRExplorer, ToMMo, and 1000 Genomes ONT, plus gnomAD STR genotypes at 87 disease loci. Explore allele frequencies across diverse populations. Read more at: genome.ucsc.edu/goldenPath/n…
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New heatmap display mode for bigBed tracks in the UCSC Genome Browser! Visualize multi-sample quantitative data as color-coded grids directly in genomic context, great for variant effects, expression & methylation. See our docs & try it out: bit.ly/ucscGBheatmap
Heatmap display in the UCSC Genome Browser

ALT Heatmap display in the UCSC Genome Browser
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The supertrack configuration page has new controls for track visibility. "Apply visibility" buttons set visibility across visible or all tracks, Hide/Dense/Squish/Pack/Full buttons replace dropdowns, folder icons indicate container tracks. More info: genome.ucsc.edu/goldenPath/n…
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We are excited to announce the release of the Human Methylation Atlas Summary and Signals tracks for hg38 and hg19. The tracks display genome-wide DNA methylation profiles across 39 primary human cell types from 205 healthy tissue samples. Learn more at bit.ly/humanMethylationAtlas…
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We've added two gnomAD coverage tracks on human hg38: gnomAD v4 Exome Coverage — mean/median depth & sample % at 1X–100X thresholds across exome samples. gnomAD v3 Genome Coverage — same metrics for 71,702 whole-genome samples. Learn more at: genome.ucsc.edu/goldenPath/n…
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New Recent Genomes & Connected Hub Assemblies lists on the Gateway page, plus genome search across more tools. Recent Genomes also appears in the blue bar under Genomes. Species Tree now hidden by default (click “Show species tree” to view). More info at genome.ucsc.edu/goldenPath/n…
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We are happy to announce our new public hub, VRMOD CRM for hg38/mm10. It shows experimentally defined, predicted, and epigenomically supported cis-regulatory elements across tissues & cell types: bit.ly/VRMOD_CRMs Thanks to Zhao Lab at WashU Medicine for creating this hub.

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@gzhao11 @tascya @bijeshgeorge3 @WashUGenetics @WashUNeurology @IGVFConsortium @AvrahamOshri @twang5 @YangEricLi @lidaof @LabPiao @Gabel_Lab @ccrugom @chengran2020
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We are happy to announce the JASPAR 2026 tracks for hg38, mm39, danRer11, galGal6, dm6, ce11, ci3, and sacCer3, which represent genome-wide predicted binding sites for transcription factors with binding profiles in the JASPAR CORE collection. More info: bit.ly/JASPAR2026
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A new Phased Variants container track for hg38 and hg19, and brings phased individual-level genotype data from: Human Diversity Genome Project, Simons Genome Diversity Project, gnomad's HGDP 1000 Genomes callset, and the Mexico Biobank. Learn more at: bit.ly/4rxS60Q
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We are happy to announce the recount3 tracks for hg38 and mm10: uniformly processed RNA-seq data from multiple studies, featuring intron data, split read counts, and splice junction motifs for cross-study comparisons and meta-analyses. Learn more at: bit.ly/recount3_track
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We are excited to introduce Hub Space, a new hosting service that enables users to upload and visualize track hub files directly on the UCSC Genome Browser without relying on third-party hosting services such as Dropbox, Google Drive, or AWS. Learn more: bit.ly/3NTZBkq

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We are excited to announce that the Genome Browser now includes a dynamic track group that automatically displays all currently visible tracks in one convenient location. The group has more than 32 tracks available for a genome assembly. Read more here: bit.ly/4qj1jt7
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We are proud to announce a new ENCODE Registry of cCREs (candidate Cis-Regulatory Elements) track for hg38 as described in Moore et al., Nature 2026. See our news for more: bit.ly/ucscENCODE4cCREs
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These data display regions identified by biochemical signatures predicted to regulate gene expression as promoters, enhancers, or other regulatory elements. We would like to thank @ENCODE_NIH, @ZhipingWeng, and @MooreJillE for their work in producing and displaying these data.
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We recently added Neanderthal and Denisova variant tracks for GRCh38/hg38. Thanks to the Archaic Sequence Hub (arcseqhub.com/plot/-1/) for compiling the data and making it available. View the data on the Genome Browser: bit.ly/ancientHominids.
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We are pleased to announce the release of the EVA SNP Release 8 tracks, now available for 41 assemblies and covering 945 million variants. Learn more at genome.ucsc.edu/goldenPath/n…
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