We found that 31% (1113/3591) of the cancer-specific enhancers that are involved in enhancer–promoter loops in C42B prostate cancer cells are bound by FOXA1, suggesting that FOXA1 is a major regulator of the cancer transcriptome (see Fig. 5d which shows enhancers and loops for an example chromosome, chrX). Here, FOXA1 is linked to prostate cancer.