For association tests without PC adjustment, an unbiased evaluation of the over-dispersion factor λ can be obtained using all the 475,116 testing autosomal SNPs. For evaluation after PC adjustment, it is however important to avoid the potential bias that can arise from SNPs highly correlated to the initial structure inference SNP set. Thus, λ is better estimated based on testing statistics measured on a set of genomic control SNPs with no correlation with the set of structure inference SNPs. To remain consistent throughout the analyses, the over-dispersion factor λ for tests with or without PC adjustment was systematically evaluated with the same set of 241,238 genomic control (autosomal) SNPs having r2 less than 0.01 with any nearby (within a distance of 500 kb) structure inference SNP from either the 12,898 or the 7,017 SNP sets. See Figure 1 for a summary of the relationship among the three sets of SNPs.
