We first tested the web server using a well-studied locus known to be associated with plasma low-density lipoprotein cholesterol (LDL-C). We collected 17 associated SNPs in 1p13 region (Supplementary Table S2) genotyped in ∼20 000 individuals of European descent and ∼9000 African American individuals with LDL-C (41) and performed GWAS3D pipeline on those variants under HapMap CEU population and HepG2 cell type. We obtained five significant regulatory variants with distinguished GWAS3D signals and identified a leading variant rs12740374, as the top one in the prioritization table. The variant locates between genes CELSR2 and PSRC1, and was scored a more significant CP (7.89E-46) than the original GWAS P-value (1.8E-42). GWAS3D reported that rs12740374 directly connected with two active enhancer marks (H3K27ac and DHS) and located in the conserved region. Importantly, binding affinity between allele G and risk allele T showed substantial difference for C/EBP transcription factors (Supplementary Figure S2). Those results were consistent with previous finding about the role of rs12740374 in the lipoprotein regulatory pathway (41). We also applied same associated SNPs set on YRI and CHB populations, besides the
