We identified potential independent genome-wide significant lead variants for each of the broadly defined genome-wide-significant loci of our GWAS meta-analysis results104 using the following approach: For each genome-wide significant SNP we defined the associated LD-region by recording the left and rightmost variant with r2≥0.1, assigning the SNP with the lowest P-value within each LD-clump as the index SNP. Index SNPs were considered independent when r2<0.1 within 3 Mb windows. To define GWAS loci, a 50kb window was added on each side of the LD-region and overlapping LD-regions were combined into a single locus, assigning the index SNP with the lowest P-value as lead SNP. Only a single SNP was kept from within the MHC region, due to extended linkage disequilibrium and a strong association signal of the MHC region (chr 6:25-35 Mb).
