To further evaluate the ability of GWAS3D for detecting and prioritizing regulatory variants in a genome-wide manner, we collected 1370 associated SNPs with prostate cancer from NHGRI GWAS Catalog (6) and GWASdb (39). We detected 195 variants, which have GWAS3D regulatory signals (active promoter/enhancer/insulator marks, TFBS affinity changes, conserved elements), after applying the CEU population and RWPE1 cell type. Seven variants obtained more significant CP than the originals when analyzing top 20 putative regulatory variants in the prioritization table (Supplementary Table S3). Most of these significant variants exert the regulatory function of their associated loci by high linked LD variants other than leading SNPs. However, a noticeable result is a leading SNP rs6983267 that harbors many GWAS3D signals has been successfully validated by many functional studies for affecting enhancer activity (44,45).
