New ENCODE cCREs track available for human (hg38)
Luis Nassar
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:
- ENCODE4 cCREs: This track presents the ENCODE Registry of 2,348,854 cCREs identified and classified using data from all phases of the ENCODE Project (Phases 1–4). The registry integrates chromatin accessibility and ChIP-seq signals across thousands of biosamples. All cCREs are consolidated into a single, cell type-agnostic annotation track displayed here.
- ENCODE4 Core Collection: This track displays biosample-specific cCREs alongside genome-wide epigenomic signals for the ENCODE4 Core Collection, consisting of 170 biosamples comprehensively profiled using four core assays: DNase-seq, ChIP-seq for H3K4me3 and H3K27ac (histone modifications), and ChIP-seq for CTCF. These data support detailed analysis of regulatory activity in individual biosamples.
The cCREs are colored by their putative functional assignment based on biochemical signatures and genomic context:
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 these 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.