Description

This track collection displays candidate Cis-Regulatory Elements (cCREs) generated by the ENCODE Consortium during Phase 4 (ENCODE4) and Phase 3 (ENCODE3), with the ENCODE3 track retained for archival purposes. The tracks include both integrated (biosample-agnostic) and biosample-specific annotations derived from core epigenomic assays.

• ENCODE4 cCREs: This track presents the ENCODE Registry of 926,843 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 hundreds 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 18 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.


• ENCODE3 cCREs: This track provides the version of the cCRE Registry generated at the end of ENCODE3, using data available up to that phase. The methodology was refined and the dataset greatly expanded during ENCODE4. While ENCODE3 tracks are preserved for reproducibility, ENCODE4 tracks are recommended for all current analyses, as they also incorporate ENCODE3 data.

The Registry and Core Collection tracks both annotate the same 926,843 cCREs. The Registry classifies each element cell type-agnostically using the maximum Z-score (max-Z) for each mark across all biosamples. The Core Collection evaluates each element in specific cell types using biosample-specific Z-scores.

Display Conventions, Data Access, and Credits

For information on track configuration, data description, data access, methods, and data provenance, see the individual track description pages via their links above.

References

ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. PMID: 32728249; PMC: PMC7410828

Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y et al. An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation. Nature. 2026 January 7. PMID: 39763870; PMC: PMC11703161