Fig. 1

Experimental and analytical steps used to identify PCa risk-associated regulatory elements involved in chromatin loops. Step (1): The subset of 2,181 fine-mapped PCa-associated SNPs that overlap a DNase hypersensitive site was identified. Step (2): H3K27Ac and CTCF ChIP-seq was performed in duplicate in two normal (PrEC and RWPE-1) and five cancer (RWPE-2, 22Rv1, C4-2B, LNCaP, and VCaP) prostate cell lines; data was collected plus or minus DHT for 22Rv1 and LNCaP cells, for a total of 18 datasets for each mark (36 ChIP-seq samples). The SNPs in open chromatin sites (i.e., those that are contained within a DHS site) were then subdivided into those that overlap a H3K27Ac or a CTCF site in prostate cells; the number of PCa-associated SNPs associated with the H3K27Ac or CTCF sites is shown. Step (3): The PCa risk-associated H3K27Ac and CTCF sites were overlapped with Hi-C looping data, and the subset of each type of site involved in chromatin loops was identified; the number of PCa-associated SNPs associated with the H3K27Ac or CTCF sites involved in looping is shown