ENC Chromatin Super-track Settings
ENCODE Chromatin Interactions Tracks   (All Expression tracks)

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GIS ChIA-PET  Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan
UMass 5C  Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass.
Downloads UW 5C  Chromatin Interactions by 5C from ENCODE/University of Washington



These tracks display evidence of chromatin interactions in ENCODE cell types. A chromatin interaction is defined as two regions of the genome that are far apart in terms of genomic distance, but are spatially proximate to each other in the 3-dimensional cellular nucleus. Binding sites are also displayed when a transcription factor is used in the assay. A binding site is defined as a region of the genome that is highly enriched by specific Chromatin Immunoprecipitation (ChIP) against a transcription factor, which indicates that the transcription factor binds specifically to this region.

ChIA-PET: The Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) (Li 2010, Fullwood 2010) track shows the locations of RNA polymerase II-bound (RNAPII-bound) chromatin interactions determined by Paired-End Tag (PET) sequencing using proximity-ligated chromatin extracts from human cell lines. The RNAPII ChIA-PET experiment generates RNAPII binding sites. Generally, a chromatin interaction is more likely to connect two RNAPII binding sites together.

5C: Chromosome Conformation Capture Carbon Copy (5C) (Dostie 2006) maps genomic interactions of a focused set of restriction enzymes. The three-dimensional organization of chromosomes and chromatin domains is obtained by cross-linking, digestion, ligation and then detection (Dekker 2002).

Display Conventions

These are multi-view composite tracks that contains multiple data types controllable using the 'Select view' function as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages.

Further details on display conventions and data interpretation are available in the subtrack descriptions.


These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks.


Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11.

Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309.

Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25.

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.