The SNVs detected by GWAS are associated with the disease/trait, but may not be the one with function implications. GWAS3D can find functional SNVs from GWAS SNVs through LD and other information. To assess this capability, we used GWAS3D pipeline to find functional SNV for each of the selected GWAS SNVs (118 top GWAS significant variants in intergenic and promoter regions from GWAS Catalog database). We found there were no significant differences between the GWAS SNVs and any of the three random data sets (all P > 0.05, Wilcoxon rank-sum test). However, the functional SNVs found by GWAS3D are significantly highly scored with P-values of 2.966E-05, 9.591E-08 and 3.034E-07 compared with the three random sets (Wilcoxon rank-sum test), respectively. Those results further confirmed the capability of GWAS3D in identifying functional regulatory variants (Supplementary Figure S6).
