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).

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