Fig. 4

PCa risk SNPs associated with CTCF sites and chromatin loops. Each row represents one of the 93 SNPs that are associated with both a DHS site and a CTCF peak in normal or tumor prostate cells (Additional file 4: Table S3). The location of each SNP was classified using the Gencode V19 database. “Others” represents mostly intergenic regions. To identify the subset of CTCF-associated risk SNPs located in an anchor point of a loop, chromatin loops were identified using Hi-C data from normal RWPE-1 prostate cells [26] or 22Rv1 and C4-2B prostate tumor cells (Rhie et al., in preparation); Hi-C [25] and cohesin HiChIP data [27] from GM12878 was also used