We are excited to announce the ENCODE4 data collection on the UCSC Genome Browser for hg38 and mm10. This release consists of two major components: the ENCODE Registry of cCREs and the new ENCODE4 Regulation container. Learn more at: bit.ly/Encode4Release

🧬 New: Long-read Structural Variants tracks for human (hg38 & T2T-CHM13/hs1). SV callsets from 14 long-read studies merged into ~2.3M sites, so you can compare structural variation across populations. See our news to learn more: bit.ly/UCSClong-readSVs

26 years ago today, the first public assembly of the human genome went online at UC Santa Cruz. Today, we release version 500 of the UCSC Genome Browser. From Jim Kent's first assembly to thousands of genomes, the data is still free and open. genome.ucsc.edu/gold...

Which variants are common in your ancestry but rare globally? New on hg38: SNV Frequencies. Over 1.2 billion variants pooled from ~1.5M people across 30+ cohorts, including population references, biobanks, and disease case/control studies. Learn more: bit.ly/GBsnvFrequencies

We are happy to announce Release 3 of the Varaico Variants and Varaico Variants (suppl) tracks for hg38/hg19. This release contains a precision improvement and an update of the underlying literature. Learn more at: genome.ucsc.edu/gold...

We are pleased to announce our new public hub, EVA score for synthetic gRNA efficiency for hg38, hg19 & mm39. Named after MPI-EVA, it predicts on-target SpCas9 cutting activity using chemically synthesized gRNAs: https://bit.ly/MPI-EVA. Thanks to Tomislav Maricic at MPI-EVA.

New on the UCSC Genome Browser: a Non-canonical ORFs track collection for hg38! Explore 1M+ ORFs outside annotated coding genes — uORFs, sORFs & more — from UTRannotator, GENCODE, 5ULTRA, nuORFdb, MetamORF & OpenProt, all colored by Kozak strength. genome.ucsc.edu/gold...

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: https://bit.ly/4a8KDPD

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

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

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/gold...

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

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/gold...

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/humanMethylat...

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/gold...

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/gold...

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.

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: http://bit.ly/JASPAR...

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: https://bit.ly/4rxS60Q

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

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: https://bit.ly/3NTZBkq

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: https://bit.ly/4qj1jt7

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

We recently added Neanderthal and Denisova variant tracks for GRCh38/hg38. Thanks to the Archaic Sequence Hub (http://www.arcseqhub...) for compiling the data and making it available. View the data on the Genome Browser: bit.ly/ancientHominids.

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 http://genome.ucsc.e...

The new public hub from @GHFC_lab displays genes connected with autism and neurodevelopmental disorders. It additionally displays variants from diagnosed autistic individuals and their undiagnosed families. View it on the Genome Browser here: https://bit.ly/4pUpC1e.

We recently added a public track hub of "cancer effect size" across 20 TCGA cancer cohorts. Thank you to @jeffreytownsend.bsky.social and his lab at Yale University for providing the data. View it on the Genome Browser here: https://bit.ly/496Cx92.

QuickLift is now available for beta testing. It maps genome annotations to another assembly (LiftOver) on demand, in real time, lifting only the annotations in the currently visible region. As a beta feature, it may contain bugs. More details at

QuickLift_guide

BETA: QuickLift is in beta testing, which means it is not polished and will contain bugs. See the Bugs section at the end of this page for known issues. If you would like to report a bug or have any questions, please contact us at genome-www@soe.ucsc.edu. Overview An alignment between two DNA se...

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📢 We're hiring a Genomics Senior Systems Architect! The incumbent will be responsible for the Genomics Institute's complex computing infrastructure, including central and departmental systems, high-throughput storage, web systems, & cloud environments. Apply at jobs.ucsc.edu using job code 82880.

New gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track for hg19. It shows a score that identifies missense-depleted regions using rare missense variation in 125,748 gnomAD v2.1.1 exomes. OE values: yellow=low, blue-purple=high. More at genome.ucsc.edu/gold...