Description

This track displays genome-wide epigenomic signals and peaks from 589 individual ENCODE experiments, including DNase-seq and ATAC-seq for chromatin accessibility, and ChIP-seq for the histone modifications H3K4me3 and H3K27ac, as well as CTCF binding.

• DNase-seq identifies regions of open chromatin commonly associated with enhancers, promoters, and insulators (shown in green)
• ATAC-seq identifies open chromatin via Tn5 transposase insertion (shown in cyan)
• H3K4me3 ChIP-seq marks active and poised promoters (shown in red)
• H3K27ac ChIP-seq marks active enhancers and promoters (shown in yellow)
• CTCF ChIP-seq identifies binding sites at insulators and chromatin loop anchors (shown in blue)

The track includes two subtrack types:

• Signal - a bigWig track of the experiment's signal
• Peak - a bigBed track of the experiment's peaks

These datasets provide the underlying experimental data used to generate the corresponding layered summary tracks. Additional datasets are available at the ENCODE portal.

Display Conventions and Configuration

Click a specific biosample type and organ/tissue combination to view available datasets. Subtracks can be further filtered by Assay (ATAC, DNase, CTCF, H3K27ac, and H3K4me3), Organ, Biosample Type, and Data Type (Signal or Peak).

Available Organs and Tissues

Data Access

The ENCODE 4 Regulation data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored in bigWig (signal) and bigBed (peak) files that can be downloaded from our download server. The data may also be explored interactively using our REST API. The original data files are also available from the ENCODE portal. Clicking any accession in the track's configuration table links directly to the corresponding file details page on the ENCODE portal.

Signal files may be locally explored using bigWigToWig, e.g.,

bigWigToWig -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/10/16/d60aeb91-36d8-4d24-8d03-4c350a5f5ac3/ENCFF220DSP.bigWig stdout

Peak files may be explored using bigBedToBed, e.g.,

bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/10/16/a1cbfde2-b570-4c32-8b0f-b1557de8849a/ENCFF209SYF.bigBed stdout

Instructions for downloading these tools can be found here.

Credits

Data were generated by the ENCODE Consortium through the following production labs: Drs. Barbara Wold (Caltech), Bing Ren (UCSD), John Stamatoyannopoulos (UW), Michael Snyder (Stanford), Richard Myers (HAIB), and Ross Hardison (PennState).

The data were further processed for visualization through a collaborative effort between the Weng lab and the Moore lab at UMass Chan Medical School (funded by NIH grant HG012343). Integration and visualization were developed by Drs. Mingshi Gao, Jill Moore, and Zhiping Weng at UMass Chan Medical School, who were part of the ENCODE Data Analysis Center.

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