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 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.
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. For instance, the Core
Collection would have included only 25 biosamples under ENCODE3 criteria. While ENCODE3
tracks are preserved for reproducibility, ENCODE4 tracks are recommended for all
current analyses, as they also incorporate ENCODE3 data.
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