statistic of each SNP by λ, where λ is the genomic control inflation factor, estimated to be the median of all 276 122 test statistics divided by 0.456.14 Because SNPs that are near to each other can show correlated association signals (due to linkage disequilibrium) we filtered that set of association signals from each analysis to remove non-independent SNPs using the clumping facility within PLINK.13 (The non-independent SNPs lie within 250 kb and are in linkage disequilibrium at r2>0.2 with the index SNP.) For each such genome-wide analysis we used the number of (λ-corrected) independent SNPs showing an association signal at P<10–5 (number of ‘hits’) as a summary measure of the genome-wide analysis.
