Description

This collection of tracks offers an integrated view of genomic annotations and experimental data from all phases of the ENCODE Project, with a focus on transcriptional regulation. It includes averaged and representative signals from assays that measure chromatin accessibility (DNase-seq and ATAC-seq), transcription factor (TF) binding (ChIP-seq for individual TFs), histone modifications (ChIP-seq for H3K4me3 and H3K27ac), CTCF binding, and transcription (RNA-seq).

Tracks labeled (Layered) show organ-averaged signals as a transparent overlay of multiple organs within a single track. Tracks labeled (Indiv.) show signals from individual experiments in specific biosamples.

• The H3K27ac (Layered) track displays enrichment levels of a histone modification associated with active enhancers and promoters, averaged across 38 organs.
• The DNase (Layered) track displays regions of chromatin that are hypersensitive to DNase I digestion, indicating open and potentially regulatory chromatin. Signal is averaged across biosamples from the same organ for 41 organs.
• The ATAC (Layered) track displays regions of open chromatin identified by ATAC-seq, which uses Tn5 transposase insertion to assay accessibility. Signal is averaged across 26 organs.
• The H3K4me3 (Layered) track displays enrichment levels of a histone modification associated with active or poised promoters, averaged across 38 organs.
• The CTCF (Layered) track displays genomic regions bound by CTCF, a multifunctional DNA-binding protein involved in chromatin organization and gene regulation. Signal is averaged across 36 organs.
• The Transcription (Layered) track displays transcription levels measured by strand-specific total RNA-seq across a large number of biosamples, shown separately for the two genomic strands.
• The TF rPeaks track displays genomic regions bound by TFs and other DNA-associated factors involved in transcriptional regulation, derived from ChIP-seq experiments profiling 912 factors across 1,152 biosamples.
• The TF ChIP-seq (Indiv.), DNase/ATAC/Histone/CTCF (Indiv.), and RNA-seq (Indiv.) tracks display signals from individual experiments in specific biosamples.

These tracks complement one another and collectively provide a resource for interpreting regulatory DNA. Histone marks are broadly informative but have limited resolution (~200 bp) and relatively low functional specificity. DNase-seq assays offer higher resolution and scalability across many cell types, and they reliably indicate regulatory potential, though they lack detailed functional context. ATAC-seq serves a similar role to DNase-seq, with comparable resolution and limitations. Transcription factor ChIP-seq has high positional resolution and, due to the specificity of TFs, often provides more direct functional insight. However, because each TF must be assayed individually, the data are limited in biosample coverage. Despite the individual strengths and limitations of these assays, their independence from one another increases confidence when multiple assays suggest a regulatory function for the same genomic region.

For additional information, click on the hyperlinks for the individual tracks above. Additional histone marks and transcription data are available in other ENCODE tracks. This integrative supertrack presents a curated selection of the most informative and broadly relevant datasets. Further functional annotations of individual regulatory elements are available at SCREEN.

Display Conventions

By default, the DNase (Layered), ATAC (Layered), H3K4me3 (Layered), H3K27ac (Layered), CTCF (Layered), and Transcription (Layered) tracks use a transparent overlay to visualize signals from multiple organs or tissues within a single track. For each organ or tissue, signal values from all associated experiments are averaged. Each organ or tissue is assigned a distinct color, selected to be light and saturated to maintain clarity when overlaid. Initially, each layered track displays an overlay of representative organs: blood, brain, kidney, liver, and muscle (the ATAC track has no kidney data). Clicking on the track opens a details page where you can view and select organs or tissues.

For the TF rPeaks track, each rPeak (representative peak) is colored in grayscale by the maximum ChIP-seq signal for the corresponding TF across all contributing biosamples (darker = higher signal, score 0 to 1,000). The HGNC gene symbol of the TF is displayed to the left when viewed in pack display mode. If the rPeak overlaps a cognate TF motif from a previously curated collection (Andrews et al., 2023), the motif site is colored green using decorators.

The TF ChIP-seq (Indiv.), DNase/ATAC/Histone/CTCF (Indiv.), and RNA-seq (Indiv.) tracks are hidden by default. Clicking on any of these tracks opens a details page where you can select specific biosample-level experiments to display.

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 track data files can be downloaded from our download server or queried using the REST API. Individual regions or the whole genome annotation can be accessed as text using our utilities bigWigToWig and bigBedToBed. Instructions for downloading source code and binaries can be found here. The original data files are also available from the ENCODE portal.

Credits

Data were generated by the ENCODE Consortium. 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, Greg Andrews, Jill Moore, and Zhiping Weng at UMass Chan Medical School, who were part of the ENCODE Data Analysis Center.

Data Use Policy

Users may freely download, analyze, and publish results based on any ENCODE data without restrictions. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional.

Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE production laboratory(s) that generated the datasets used, as described in Citing ENCODE.

References

Andrews G, Fan K, Pratt HE, Phalke N, Zoonomia Consortium, Karlsson EK, Lindblad-Toh K, Weng Z. Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science. 2023;380(6643):eabn7930. PMID: 37104580

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