If the Fisher’s combined probability test from GWAS3D provided increased evidence based on potential function of the test SNP or a SNP in LD with the test SNP, the combined p-value is also shown in Table 1. Of the 28 SNPs with q<0.1 input to GWAS3D, 14 showed more significant combined p-values after incorporating evidence of function. Of these 14 results, 12 were based on evidence of functional impact for the GWAS target SNP itself. For the two sites where the increased evidence was based on putative functional impact of a variant in LD with the GWAS signal, the LD SNP rsID, r2 with the GWAS target and functional evidence are shown. GWAS3D analysis yields strongly enhanced signals in COL6A3 (rs2646265: p=1.47×10−8, combined p=1.40×10−12; rs2256485: r2=1 with rs2646265, p=6.17×10−9, combined p=6.18×10−13) and RYR3 (rs4780153: r2=0.867 with rs2076954, p=1.47×10−7, combined p=7.92×10−10).
