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Smaller software changes are not announced here. A summary of the three-weekly release changes can be found here. For the full list of our daily code changes head to our GitHub page. Lastly, see our credits page for acknowledgments of the data we host.

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.

@@ -325,81 +376,30 @@ 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 Denisovian 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.

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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