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+ + + + ++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 new tracks include:
++The cCREs are colored by their putative functional assignment based on biochemical +signatures and genomic context:
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+
+This results in the following classifications:
+ +| Color | ++ | UCSC label | +ENCODE classification | +Classification criteria | +
|---|---|---|---|---|
| red | +promoter | +promoter-like signature | +within 200 bp of TSS, high chromatin accessibility and H3K4me3 | |
| orange | +proximal enhancer | +TSS-proximal enhancer-like signature | +high chromatin accessibility and H3K27ac, within 2 kb of TSS; if within 200 bp of TSS, must have low H3K4me3 | |
| yellow | +distal enhancer | +TSS-distal enhancer-like signature | +high chromatin accessibility and H3K27ac, >2 kb from TSS | |
| pink | +CA-H3K4me3 | +chromatin accessibility + H3K4me3 | +high chromatin accessibility and H3K4me3, low H3K27ac, not within 200 bp of TSS | |
| blue | +CA-CTCF | +chromatin accessibility + CTCF | +high chromatin accessibility and CTCF, low H3K4me3 and H3K27ac | |
| dark purple | +CA-TF | +chromatin accessibility + transcription factor | +high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF, bound by transcription factor | |
| green | +CA | +chromatin accessibility | +high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF | |
| light purple | +TF | +transcription factor | +low chromatin accessibility, low H3K4me3, H3K27ac, and CTCF, bound by transcription factor |
+This dataset was produced by the ENCODE Data Analysis Center +(Zlab at UMass Medical Center). Thanks +to Mingshi Gao, Zhiping Weng, and Jill Moore for providing this data and +initial version of the track. Thanks also to the ENCODE Consortium, the ENCODE production +laboratories, and the ENCODE Data Coordination Center for generating and processing the datasets +used here.
++For more details on this track and data, see the track description page, as well as +Moore et al. +An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation +. Nature. 2026 January 7. PMID: 39763870; PMC: PMC11703161. +
+We are pleased to announce the release of the EVA SNP Release 8 tracks for 41 assemblies. These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) — collectively Simple Nucleotide Variants (SNVs) — from the European Variation Archive (EVA) Release 8. The full list of assemblies that contain the EVA SNP release 8 track is below: