We would like to thank the ReCount team for making this data available. We would also like to thank Jeltje van Baren, Mark Diekhans, and Gerardo Perez for their efforts on this release.

Feb. 03, 2026 New "Visible Tracks" group feature

We are excited to announce a new improvement to the UCSC Genome Browser: the Visible Tracks group. The Genome Browser now includes a dynamic track group that automatically displays all currently visible tracks in one convenient location. This means you no longer need to hunt through multiple track categories to adjust tracks you've already turned on.

Previously, managing visible tracks required navigating back to their original categories — whether that was Genes and Gene Predictions, Conservation, Variation, or any other group. Now, all your active tracks appear together in the Visible Tracks group, making it faster and easier to adjust display modes for visible tracks.

The "Visible Tracks" group will appear only when more than 32 tracks are available for a genome assembly.

We would like to thank Chris Lee and Jairo Navarro Gonzalez for releasing this feature.

Feb. 03, 2026 Hub Space: Host Your Track Hubs Directly on the Genome Browser

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.

Hub Space Features:
Each account is allocated 10 GB of storage space. While we strive to maintain uninterrupted access, please maintain your own backups. Data persistence over the long term is not guaranteed. To request additional storage space, please contact us.

Jan. 15, 2026 New ENCODE cCREs track available for human (hg38)

We are proud to announce a new ENCODE Registry of cCREs (candidate Cis-Regulatory Elements) container track for the hg38/GRCh38 genome as described in Moore et al., Nature 2026. This container contains candidate Cis-Regulatory Elements (cCREs) generated by the ENCODE Consortium during Phase 4 (ENCODE4) and Phase 3 (ENCODE3). The previous "ENCODE3 cCREs" track is retained for archival purposes. The tracks include both integrated (biosample-agnostic) and biosample-specific annotations derived from core epigenomic assays.

The cCREs are colored by their putative functional assignment based on biochemical signatures and genomic context:

Dec. 15, 2025 Ancient Hominids track for hg38

We are happy to announce the release of the Ancient Hominids track featuring data from Archaic Sequence Hub (ArcSeqHub). This track shows variants identified by ArcSeqHub's remapping of high-quality Altai Neanderthal and Denisovan genomes onto the hg38/GRCh38 genome. Variants are divided into two subtracks, one for Denisovan variants and another for Neanderthal variants. UCSC has removed those positions from the VCF without an alternate allele to show only variants that are present in the ancient genomes.

We would like to thank the ArcSeqHub authors for making the data available. We would also like to thank Maximilian Haeussler and Matthew Speir for the creation and release of this track.

Dec. 03, 2025 New gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track for hg19

We are happy to announce the release of the gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track for hg19, now available in the gnomAD superTrack. This track shows a score that tries to identify missense-depleted regions using the patterns of rare missense variation in 125,748 gnomAD v2.1.1 exomes, compared to a null mutational model. Missense-depleted regions are enriched for ClinVar pathogenic variants, de novo missense variants in individuals with neurodevelopmental disorders (NDDs), and complex trait heritability. This track can be used to aid in interpreting missense variants.

Transcript regions with constraint predictions are colored using the viridis palette, where yellow indicates the lowest OE values and dark blue-purple indicates the highest.

A corresponding MPC version for hg38 is planned for release by the gnomAD team in 2026.

We would like to thank Kaitlin Samocha for suggesting this track and the Genome Aggregation Database Consortium (gnomAD) for making the data available. We would also like to thank Maximilian Haeussler, Luis Nassar, and Gerardo Perez for the creation and release of this track.

Nov. 14, 2025 Updated Varaico Variants track and new Varaico Variants (suppl) track for hg38 and hg19

We are pleased to announce the release 2 of the Varaico Variants track and the addition of a new Varaico Variants (suppl) track for the human assemblies hg38/GRCh38 and hg19/GRCh37. The Varaico tracks are generated using literature mining methods similar to those used for the AVADA resource. With this update, the Varaico Variants track now contains more than 5.5 million variants.

The Varaico Variants (suppl) track shows variants extracted from supplementary data files using similar methods to those used for the primary Varaico track.

We would like to thank Johannes Birgmeier for generating and making the Varaico data available. We would also like to thank Maximilian Haeussler, Jairo Navarro Gonzalez, and Gerardo Perez for creating and releasing these tracks.

Oct. 31, 2025 New GENCODE "knownGene" V49 for human (hg38/hg19) and VM38 for mouse (mm39)

We are happy to announce the new GENCODE gene annotation tracks, corresponding to @@ -860,58 +860,56 @@ We are pleased to announce the release of the SpliceAI Wildtype tracks for hg38, available in the Splicing Impact superTrack. These tracks show the scores for the genome sequence itself, without variants, from predicted splice donor (5' intron boundaries) and splice acceptor (3' intron boundaries) sites. Predictions are strand-specific, with separate subtracks for the plus and minus strands.

These tracks are useful in combination with the variants track for evaluating new transcript models. They can be used to assess potential exon boundaries or possible splice acceptor sites.

We would like to thank Illumina for making SpliceAI available, both the model and the precomputed data files. Thanks to Francois Lecoquierre from the University of Oxford, Jean-Madeleine de Sainte Agathe from Institut Pasteur Paris, and Michael Hiller from the Senckenberg Museum Frankfurt for suggesting and then creating the SpliceAI Wildtype annotations. We would also like to thank Max Haeussler and Gerardo Perez for their efforts on this release.

Sep. 25, 2025 Panmask Easy 151b Regions track for hg38

We are happy to announce the release of the Panmask Easy 151b Regions track for hg38. This new track is available in the Problematic Regions superTrack. The track contains a set of sample-agnostic easy regions where short-read variant calling reaches high accuracy. Easy regions are derived for variant filtration agnostic to individual samples. They are genomic intervals where general variant callers achieve high accuracy without sophisticated filtering.

The pm151 regions are used to filter spurious variant calls in centromeres, long repeats, and other genomic regions where short-read mapping is often problematic. They cover 88.2% of hg38, 92.2% of coding regions, and 96.3% of ClinVar pathogenic variants. The track can be used to filter variant calls for clinical or research human samples. It shows regions that are easy to sequence, rather than those that are problematic. The data was derived from the HPRC assemblies, and this track presents the 151b-easy panmask set.

We would like to thank Heng Li's group at Harvard Medical School for making this data available. We would also like to thank Max Haeussler and Gerardo Perez for their efforts on this release.

Sep. 24, 2025 CoLoRSdb small and structural variants for hg38 and hs1

Each track includes allele frequency and sample count annotations, with additional filtering options for variant size and type. Users can click on individual variants to view detailed metadata, such as allele counts, homozygous/heterozygous call distributions, and Hardy-Weinberg equilibrium values.

We would like to thank Mike Schatz, Evan Eichler, and all CoLoRSdb investigators for generating and making the data publicly available. We would also like to thank Karen Wang and Jairo Navarro Gonzalez for the creation and release of these tracks.

Sep. 19, 2025 Developmental Disorders Gene2Phenotype (DDG2P) for hg38 and hg19

We would like to thank the G2P project for making this data publicly available. We would also like to thank Jaidan Jenkins-Kiefer and Jairo Navarro Gonzalez for the creation and release of the Genome Browser tracks.

Aug. 21, 2025 MaveDB Experiment Heatmaps and Alignment track for hg38

We are excited to announce the release of the MaveDB Experiment Heatmaps and Alignment track for hg38. This release provides heatmaps of multiplexed assays of variant effects (MAVE) from MaveDB. Each heatmap presents the results of an experiment where many small substitutions were tested within a gene to examine their functional consequences. Accompanying tracks display alignments of each experiment sequence to the genome.

Please note that only a subset of MaveDB experiments could be displayed as heatmaps; the sequence alignments in this track only cover those experiments.

Hover over each item in the heatmap to see the consequence of substituting individual amino acids within the genome with alternatives. Score ranges vary among experiments, but each is presented with the highest scores in red, the lowest scores in blue, and scores at the midpoint between the two in silver. Higher scores correspond to a higher enrichment level for that variant compared to others in the experiment set.

We would like to thank Jeremy Arbesfeld and the MaveDB team for making this data publicly available. We would also like to thank Melissa Cline, Jonathan Casper, and Jairo Navarro for the @@ -1076,31 +1071,31 @@ available in the PanelApp composite track. The PanelApp track shows expert, crowdsourced diagnostic disease panels among genes, copy-number variants (CNV), and short tandem repeats (STR). PanelApp Australia was originally launched by Australian Genomics in 2019 in collaboration with Genomics England and is currently supported by Genomics Australia. The PanelApp Australia track contains data that differs from the Genomics England PanelApp; more details are available on the track description page.

We have also updated the mouse hover for the Genomics England PanelApp track, which now shows the gene name, associated panel, mode of inheritance (if known), related phenotypes, and confidence level.

We want to thank Jean-Madeleine for this data request and feedback, as well as Zornitza Stark from Australia PanelApp for providing guidance. We would also like to thank Beagan Nguy, Lou Nassar, and Gerardo Perez of the Genome Browser team for the development and release of this track.

Aug. 01, 2025 PubTator Variants track for human, hg38 and hg19

We are excited to announce the release of the PubTator Variants track for human assemblies, hg38 and hg19. These tracks were created using PubTator3 data and are freely accessible to the research community. PubTator3 is a web-based system that offers a comprehensive set of features and tools that allow researchers to explore biomedical literature for knowledge discovery. It uses @@ -1120,31 +1115,31 @@ methylation data: bedMethyl. This format, and its binary-indexed counterpart, bigMethyl, is designed to represent methylation calls from bisulfite sequencing or similar methods at single-base resolution across the genome.

The bedMethyl format extends the standard BED 9 format to include additional fields such as coverage, percent methylation, and the number of modified and canonical bases. When viewed in the Genome Browser, hovering over or clicking an item reveals these additional details. Items are color-coded from 0% methylated (blue) to 100% (red). Methylation calls are shown separately for CpG sites (m) and non-CpG (CHG/CHH) sites (h).

The bigMethyl format allows fast access to large methylation datasets and is ideal for displaying these tracks at scale in the Genome Browser.

We would like to thank Brian Joseph Raney, Max Haeussler, and Gerardo Perez for their work developing and testing this track format.

July 15, 2025 ENCODE4 Long-read RNA-seq Transcripts

We are pleased to announce the release of the ENCODE4 long-read RNA-seq transcripts track for hg38 and mm10. This track annotates transcripts using numerical triplets representing the identity of the start site, exon junction chain, and transcript end site of each transcript. This is presented alongside sample enrichment information to show how promoter selection, splice pattern, and 3’ processing are deployed across human tissues.

Transcripts are labeled with triplets, e.g. [1,1,1] or [1,1,3] or [2,1,3]. If transcripts share a number in any of the positions that means they share that feature, e.g. sharing a 8 in the second position but different numbers in the others means those two transcripts share the same set of exons, but different start and end sites.

This track is part of a "Long-read Transcripts" supertrack that will consist of other datasets derived from third-generation sequencing technology, such as PacBio and Oxford Nanopore.

Varaico variants are generated by an automated process that extracts purely factual information about genes from scientific papers (by matching strings against gene names) and HGVS variant descriptions (using regular expressions). Varaico aims to reduce false-positive gene and variant mentions and link them together appropriately, but nonetheless, many variants displayed are not mapped to the genomic position intended by the authors. Visit the Varaico website for more details.

Mouse over the variants to show the gene, variant, latest author/year/title, number of publications mentioning the variant, and variant effect. Varaico variants may or may not be disease-causing.

We would like to thank Johannes Birgmeier for generating and making the Varaico data available. We would also like to thank Maximilian Haeussler and Jairo Navarro Gonzalez for creating and releasing these tracks.

May 19, 2025 New GENCODE "knownGene" V48 for human (hg38/hg19) and VM37 for mouse (mm39)

We are pleased to announce the release of the GENCODE Genes V48 for human @@ -1683,32 +1677,31 @@ expression levels across 50 tissues from the Genotype Tissue Expression (GTEx) v10 dataset, showing a comprehensive view of the expression of exons across a gene using the proportion expression across transcripts, or pext metric, a transcript-level annotation metric which quantifies isoform expression for variants.

This is especially useful for those interested in alternative splicing and clinical assessment of variants. For more information, see the track description page and the associated publication.

We would like to thank the gnomAD team and the UCSC Genome Browser team members Jeltje van Baren, Max Haeussler, Lou Nassar, and Anna Benet-Pages for developing and releasing this track, as well as making the Exon Relevance RTS.

May 5, 2025 VISTA Enhancers track update for Human and Mouse

We are happy to announce an update to the VISTA Enhancers tracks for human (GRCh38/hg38 and

Feb. 24, 2025 enGenome VarChat track for human (hg38 and hg19)

We are happy to announce the release of the enGenome VarChat track for the hg38/GRCh38 and hg19/GRCh37 human assemblies, available in the Variants in Papers superTrack. @@ -2068,31 +2060,31 @@ target="_blank">Dog (canFam6), and Cow (bosTau9) assemblies. This track shows orthologous genes across genomes and allows you to explore gene symbols and orthology information by hovering over or clicking on the track item, with links to the corresponding genome browsers:

This track was created using the latest NCBI files (gene2accession and gene_orthologs). More information on this track can be found on the track description page.

We would like to thank NCBI for making this data available. We would also like to thank Jeltje van Baren, Mark Diekhans, Max Haeussler, and Gerardo Perez for the creation and release of this track.

Oct. 1, 2024 New interactive variant interpretation tutorial

We have a new clinical tutorial showcasing resources that could be useful in variant interpretation. The tutorial is written to educate clinical geneticists with any level of browser experience. It covers topics such as searching for variants and data, recommended track sets, and how to save and share browser configurations.

We would like to thank Jairo Navarro, Chris Lee, Anna Benet-Pages, Maximilian Haeussler and Lou Nassar for their work in creating this tutorial.

Sep. 30, 2024 New gnomAD v4.1 tracks for hg38

We would like to thank Chris Lee, Jairo Navarro, and Lou Nassar for their work on this release.

Aug. 21, 2024 New groups feature for track hubs

We are excited to announce a new grouping feature for track hubs, which allows the structured organization of tracks into distinct groups. This feature can be applied to a UCSC genome, a GenArk assembly, or an assembly hub. These track hub groups are kept separate from other track hubs and the native UCSC Genome Browser track groups, allowing for greater organizational flexibility. For instance, you can add a "genes" group without causing conflicts or confusion. You can define groups with names like "Category 1", "Category 2", and "Category 3".

We would like to thank Brian Joseph Raney, Mark Diekhans, Luis Nassar, and Gerardo Perez for their work on this release.

Aug. 14, 2024 New pop-up dialogue box for item details

We are excited to introduce the new Item Details feature which simplifies the user experience by displaying track item details in a pop-up dialogue box. This feature allows the information to be viewed without the need to navigate away from the current page:

When a track item is clicked in either pack or full mode, the Item Details dialogue box will appear. This box can be resized by clicking and dragging the button located in its lower-right corner. For users who prefer viewing item details on a separate page, clicking the new window button in the upper-right corner will load the information in a new tab. The dialogue box can be closed by clicking the x button, the button, pressing the Escape key, or by clicking outside the box.

If desired, this feature can be disabled by unchecking the "Enable pop-up when clicking items option" on the Configure page. You can access the Configure page by selecting Configure under Genome Browser in the blue bar menu, by clicking the button below the browser graphic, or by using the keyboard shortcut "c f".

We would like to thank Christopher Lee, Lou Nassar, Jairo Navarro, and Gerardo Perez for their work on this release.

Aug. 12, 2024 Illumina SpliceAI tracks for human (hg38 and hg19)

We are pleased to announce the release of the Illumina SpliceAI tracks for the hg38 and hg19 human assemblies. SpliceAI is an open-source deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript @@ -3436,61 +3428,61 @@ other locations of the genome (off-target effects). Efficiency is the frequency of cleavage at the target site (on-target efficiency).

We would like to thank Maximilian Haeussler, Hiram Clawson, and Gerardo Perez for developing and releasing these tracks.

Nov. 08, 2023 New track decorators feature

We are excited to introduce the new track decorators feature which allows highlighting parts of features with colors and/or symbols (glyphs/shapes) within a single track.

The genome browser‘s primary way to annotate the genome uses colored rectangles (“exons” for gene tracks) linked by thin lines (“introns”), often stored as a bigBed. These were originally used for genes but then evolved to cover other types of annotations, e.g. enhancers, chromatin modifications, or single nucleotide variants. We usually call these annotations “features”. Each rectangle (“exon”) of a feature has the same color and individual parts cannot be highlighted. If you wanted to highlight parts of the features, traditionally this required a second track.

Track decorators change this: in your custom track and track hubs, you can now highlight parts of a genome annotation with colors or symbols. Track decorators can be shown in two styles, “block” and “glyph” style, and can either be overlaid onto the feature or shown directly underneath. The “block” style option can be used to color exons and introns and can display a label for them. For example, the “block” track decorator could be used to overlay protein domain boundaries on transcripts where usually one would use an entirely different track for the domains.

The “glyph” style option offers 8 different types of glyphs and the color of choice.

The “glyph” style option can be used to draw entirely new symbols, for example, to indicate insertion positions on the genome with small triangles. For more information, see the Track Decorators help page.

We would like to thank Jonathan Casper, Max Haeussler, Mark Diekhans, and Gerardo Perez for their work on this release. We appreciate user feedback. If you have questions, feedback, suggestions, glyph style requests, or have found new glyph applications, please contact our mailing list. We would appreciate responses on the creative ways of using the new track decorators feature.

Oct. 23, 2023 eMERGE polygenic risk scores for human (hg19)

Aug. 07, 2023 Introducing an interactive tutorial for the UCSC Genome Browser

We are happy to announce the release of a new interactive tutorial for the UCSC Genome Browser. The tutorial is designed to help new users navigate the UCSC Genome Browser. Topics such as navigating around the Genome Browser display, configuring track display settings, searching for tracks, and viewing the negative strand (3' to 5') are covered in the tutorial.

To begin the tutorial, select the Interactive tutorial from the "Help" drop-down menu.

We would like to thank Chris Lee and Jairo Navarro for their work in creating this tutorial.

Aug. 01, 2023 New ability to create duplicate tracks

We are pleased to announce the new Duplicate track feature, which allows a copy of a track to have its own independent settings and be used for multiple display views.

You can have multiple duplicates of the same track where the number will increment by one for each additional duplicate, and each duplicated track is independent of each other. Only tracks that are not inside of composite or supertracks can be duplicated and this feature does not work in hubs.

Duplicate tracks can be helpful when comparing different settings and visibility types on the same data; for instance, displaying all GENCODE genes, including pseudogenes, in dense mode, alongside a more concise gene set, such as the default, in pack mode to see gene symbols and accessions. This is shown in the image below, where duplicated GENCODE track has the additional text "(duplicate #1)" on the label above the track display and "#1" text on the left label of the track display.

@@ -4913,32 +4905,31 @@ href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project for providing these annotations. We would also like to thank Mark Diekhans and Lou Nassar for the development and release of these tracks.

May 5, 2022 Merged Cell Expression on hg38

The Genome Browser already provided single-cell RNA-seq datasets for the human GRCh38/hg38 assembly, but those data have so far been split among a collection of tracks depending on the organ and publication source. We are happy to announce that data from 12 of those papers (and 14 organs) are now available in a combined Merged Cells track that provides normalized RNA-seq values for every cell type in those sets. All components were normalized to show expression in parts per million.

Browser display of merged single-cell RNA-seq expression across cell types

The following tracks were incorporated into this Merged Cells track:

Blood (PBMC) Hao
Colon Wang
Cortex Velmeshev @@ -5468,49 +5459,49 @@
Feb. 22, 2022 Recommended Track Sets paper

We are pleased to announce a new paper about our Recommended Tracks Set feature, available on GRCh37/hg19, which collects related clinical tracks to help investigate variants. The paper, Variant interpretation: UCSC Genome Browser Recommended Track Sets, covers how this new feature can facilitate the interpretation of variants for clinicians.

Track Sets allow a user to quickly swap out the on-screen annotations they may be looking at for a different set of tracks relevant to specific medical scenarios: investigating single nucleotide variants in coding regions (Clinical SNVs), structural copy number variants (Clinical CNVs), and functional aspects of non-coding variants (Non-coding SNVs).

- +

To access Recommended Track Sets, currently available only on the hg19 assembly, go to the top blue bar and under the "Genome Browser" menu click the "Recommended Track Sets" option. This will launch a dialog box offering pre-configured track sets, enabling swapping from one view to another view without changing the current position. Please note this figure does not include a fourth Track Set, Problematic Regions, we added since the release of the paper. Problematic Regions help users evaluate if annotations in the Browser are located in areas of the genome of low confidence due to high homology or other reported concerns. Once displayed, Recommended Track Sets can then be customized, where one can configure tracks in the browser by clicking the grey bar on the left of a track. Or to see more information about displayed items, one can mouseover for an informative pop-up summary, or click on the item to access a details page.

The paper gives an example of using the experimental data in the Clinical SNV Track Set to examine a variant.

- +

This figure from the paper shows a vertical blue highlight for NM_172107.4(KCNQ2):c.635A>G (p.Asp212Gly), the Human Genome Variation Society (HGVS) nomenclature to describe this variant. Located in the KCNQ2 gene, this variant is in a codon for Aspartic acid (D212), and the mutation has been associated with early-onset epileptic encephalopathy, an autosomal dominant inherited disease. The ClinVar Short Variants and SNVs tracks show that all three possible single nucleotide substitutions have been described at this position with pathogenic or likely pathogenic classifications with red blocks (A>C, A>T, A>G). Each described variant leads to a missense change of the Asp residue. The SNV Track Set also includes (discussed in another figure in the paper) computational and predictive components, such as the Rare Exome Variant Ensemble Learner (REVEL) and Combined Annotation Dependent Depletion (CADD) tracks, which calculate impacts of nucleotide changes.

The paper also discusses many of the other features developed with the release of Track Sets, @@ -5658,43 +5649,43 @@ hubs employing new extensive filter settings available for Track Hubs.

The help page is divided into three sections:
- filter.fieldName - Used for numerical data
- filterText.fieldName - Used for text filtering
- filterValues.fieldName - Used for filtering by pre-specified values or categories in data
The filterText.fieldName section discusses settings that allow to filter items in a hub with names as seen with this screenshot of only displaying items starting with BRCA using the wildcard match "BRCA*".

- - + +

The filterValues.fieldName section discusses how to display a drop-down list of options to select items as seen with this screenshot of filtering items that are labeled as either a "DNA-binding region" or "alpha helix" or "beta strand".

- - + +

Each section of the Track Hub Filters Quick Start Guide comes with examples and sessions allowing to quickly click into real interactive demonstration hubs to experiment with how the settings work. The example hubs also provide a starter template for building similar hubs.

Many thanks to Lou Nassar for building this Filters Quick Start Guide and Brian Raney for his work implementing the new filter software.

Dec. 6, 2021 Second of three blog posts about new GenArk hubs

We are pleased to announce the second blog post in a three-part series about @@ -5795,31 +5786,31 @@ tools such as the JSON API, Table Browser, and Data Integrator. We would like to thank the Orphanet team for providing this data. We would also like to thank the UCSC affiliates Chris Lee, Tiana Pereira, and Daniel Schmelter for the creation and release of these tracks.

Nov. 17, 2021 Releasing A New Genome Browser Track Group: Single-Cell RNA-seq

We are excited to release a new Genome Browser track group with single-cell RNA-seq (scRNA-seq) datasets for the hg38 assembly. Data generated by scRNA-seq allows us to study the heterogeneity of cells in organs, explore gene expression at a cellular level, and track cellular states in both development and disease.
-
+

We are starting with 14 scRNA-seq tracks covering different major organs of the body. Each new scRNA-seq track contains anywhere from 2-19 individual mRNA expression tracks in barChart format. By default, tracks display gene expression per individual cell type annotation and are colored according to cell class:

We would like to thank the GTEx investigators, analysts, and portal team for providing this data. We would also like to thank Max Haeussler, Matt Speir, and Jairo Navarro for the creation and release of these tracks.

Oct. 21, 2021 GENCODE Genes V38 for human (hg38)

Color		UCSC label	ENCODE classification	Classification criteria
	red	promoter	promoter-like signature

We are pleased to announce the release of the GENCODE Genes V38 track for the human (GRCh38/hg38) Genome Browser.

Dec. 23, 2020 New ClinVar Interpretations track for human (hg19/hg38)

We are pleased to release a new track, ClinVar Interpretations, for the hg19/GRCh37 and hg38/GRCh38 human assemblies. This track can be found as part of the ClinVar Composite. It is the first track to use our bead graph display, which is a variation of our existing lollipop display.

The ClinVar Interpretations track displays the genomic positions of individual variant submissions and interpretations of the clinical significance, as well as their relationship to disease in the ClinVar database. As seen on the image below, the variants are classified into six categories each on a separate horizontal line:

The size of the bead on the line represents the number of submissions at that genomic position. The color of the beads aids to distinguish the categories further. Hovering on the track items shows the genomic variations which start at that position and the number of individual submissions with that classification. Additional information on the variants @@ -8336,61 +8326,59 @@ Lastly, multiple feature options have been added to both tracks independently:

Below is an example of the filter options available for the ClinVar SNVs track. For additional details on the updated display, see the track description page.

Changes to ClinGen and new tracks

We have created a new composite track, ClinGen, and deprecated the previous ClinGen CNVs track. The ClinGen CNVs track will continue to be available, however, the data will no longer be updated. This was done by request of ClinGen, as all the data, as well as further updates, can be found in the ClinVar Copy Number Variants (ClinVar CNVs) track.

For more information on these tracks, including display conventions, scores, and classifications, see the track description page.

We would like to thank Erin Riggs and May Flowers as well as the rest of the ClinGen team. We would also like to thank ClinVar for making these data available. Track development and release was made possible by Anna Benet-Pages, Christopher Lee, Max Haeussler, and Lou Nassar.

Sept. 25, 2020 New data and visualization types: Covid GWAS (Lollypop) and Family Trios (VCF Trios)

Covid GWAS meta-analysis

@@ -9059,31 +9047,31 @@ We are pleased to announce the ENCODE Registry of candidate cis-Regulatory Elements (cCREs) track for the human and mouse genomes (GRCh38/hg38 and GRCm38/mm10). cCREs are the subset of representative DNase hypersensitive sites across ENCODE and Roadmap Epigenomics samples that are supported by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data. The Registry of cCREs is one of the core components of the integrative level of the ENCODE Encyclopedia of DNA Elements. A total of 926,535 elements for human and 339,815 elements for mouse were identified and classified by the ENCODE Data Analysis Center according to biochemical signatures.

CCREs are colored and labeled according to classification by regulatory signature:

This track features a horizontal bar chart for each GENCODE gene, resulting in colored bars which show median tissue expression values assayed by the GTEx project in RPKM. Mouse over the bar in the graph shows a tissue specific expression value, while clicking on a chart shows a much larger box-and-whiskers graph for that transcript. The complete tissue color legend and filters are shown on the GTEx track configuration page. Below the bar graph, a line is shown indicating the gene extent that was used to generate the annotation, colored by gene class using GENCODE conventions (e.g. blue for protein-coding, green for non-coding).

Thank you Kate Rosenbloom and Daniel Schmelter for developing and releasing these tracks

May 12, 2020 New video: Coronavirus Browser SARS CoV-2

Thanks to Robert Kuhn for production and Max Haeussler and Jason Fernandes for input.

May 6, 2020 Problematic Regions for NGS or Sanger sequencing or very variable regions

@@ -9640,32 +9628,31 @@ Control Only SV's - gnomAD Structural Variants Controls Only

These data can be found as part of the gnomAD super-track. More information on this track can be found in the track description pages, as well as the gnomAD site.

We would like to thank the Genome Aggregation Database Consortium for making these data available. We would also like to thank Christopher Lee, Maximilian Haeussler, Lou Nassar, Jairo Navarro, Robert Kuhn and Anna Benet-Pages for their effort in the creation of these tracks.

Apr. 20, 2020 New video on the Browser's YouTube channel

We would like to thank NCBI and the RefSeq Annotation database for collecting and curating these data. We would also like to thank Hiram Clawson and Daniel Schmelter for their role creating, documenting, and reviewing these tracks.

Feb. 7, 2020 New and updated Variants in Papers tracks: Avada variants (hg19) & Mastermind variants (hg19, hg38)

We are pleased to announce a new track, Avada Variants, now available on hg19. Additionally, we have updated the Mastermind Variants track and expanded it to hg38.

Avada Variants

The Avada Variants track shows the genomic positions of variants in the AVADA database. AVADA is a database of variants built by machine learning software that analyzes full text research articles in PDF format to find genes and variants that look most relevant for genetic diagnosis.

Mastermind Variants

The Mastermind Variants track is now available for the hg38 assembly @@ -13626,31 +13612,31 @@ a color-coded checkbox list of the 53 tissues is an interactive illustration of a human anatomical "body map." Hovering over a tissue in the list will highlight the corresponding anatomical region in the body map image. To show or hide tissues in the GTEx Gene Expression track, tissue selections can be made by either selecting tissues in the list or by clicking on the tissue labels in the body map.

To quickly see which tissues are selected, right-click the bar graph displayed in the browser for the GTEx track and then click the wrench icon to go to the "Configure GTEx" page. To navigate to the new track settings page from the UCSC Genome Browser, go to the hg38 or hg19 browser and click on the track label "GTEx" in the Expression group.

In the coming months, we plan to incorporate the Tissue Body Map into other GTEx resources.

Dec. 7, 2016 New video: Substitute alternate haplotypes into hg38 chromosome

The Genome Reference Consortium has released many alternate haplotypes as part of the most recent human genome assembly, hg38 (GRCh38). Our new video tutorial, shows how to use the Genome Browser's multi-region viewing mode to substitute these sequences, along with their annotations, into the main chromosomes of this assembly, as well as other genome assemblies with alternate haplotypes. The video was produced by Robert Kuhn and David Gibson.

Nov. 7, 2016 New CRISPR track for many assemblies

The data comprising these tracks were generated from hundreds of experiments on multiple cell lines conducted by labs participating in the Encyclopedia of DNA Elements (ENCODE) project, and were submitted to the UCSC ENCODE Data Coordination Center for display on the Genome Browser.

Faced with the problem of how to display such a large amount of data in a manner facilitating analysis, UCSC has developed new visualization methods that cluster and overlay the data, and then display the resulting tracks on a single screen. Each of the cell lines in a track is associated with a particular color. Light, saturated colors are used to produce the best transparent overlay.

The data in the ENCODE Regulation super-track, as with all data from the production phase of the ENCODE project, have genome-wide coverage. In general, Genome Browser tracks that show ENCODE-generated data can be identified by the double-helix icon preceding the name in the track list. Currently, the ENCODE Regulation data are available only on the Mar. 2006 (NCBI Build 36, UCSC version hg18) assembly of the human genome.

For a detailed description of the datasets contained in this super-track and a discussion of how the tracks can be used synergistically to examine regions of regulatory functionality within the genome, see the track description page.

Aug. 18, 2010 Cat Genome Browser available

We have released a Genome Browser for the latest assembly of Cat (Felis catus). The GTB @@ -17457,32 +17442,31 @@ We are pleased to announce the release of a new Conservation track based on the zebrafish (danRer6) assembly. This track shows multiple alignments of 6 vertebrate species and measurements of evolutionary conservation using phastCons from the PHAST package. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are displayed in the companion "Most Conserved" track.

Jul. 7, 2010 Happy 10th birthday, Human Genome

UCSC is pleased to celebrate the 10-year anniversary of the debut of the first assembled human genome sequence and its then-fledgling visualization tool, the UCSC Genome Browser. Released on July 7, 2000, the genome sequence instantly created unprecedented web traffic on the ucsc.edu domain as researchers around the world scrambled to download the data: 0.5 terabytes per day, a record that stood for many years.

David Haussler recounts that day: "Seeing the waterfall of As, Gs, Cs, and Ts pouring off our

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Top graph: total traffic on the UCSC domain during June-July, 2000. Bottom graph: page hit statistics on genome.ucsc.edu in the ensuing years since the Genome Browser was released.

Feb. 24, 2026 Updates to the Genome Browser Gateway Page and Assembly Search