Next, we identified which predicted associations were supported by ENCODE ChIA-PET (via RNAPII (MMS-126R)) interaction data21 from four ENCODE cell lines (HCT-116, HeLa-S3, K562, MCF-7) by requiring an overlap of both enhancer and promoter in both (and different) sites of a ChIA-PET interaction pair. An association was considered supported if it overlapped in this way with any cell line replicate of interactions.
