We prioritized directly genotyped and imputed SNPs for replication based on statistical significance (P < 10-4), robust QC metrics, and vicinity to plausible candidate genes. In total 96 SNPs (95 autosomal and one on chromosome X) in 66 genomic regions showed nominal evidence for association. We selected 72 independent, uncorrelated variants representing each of the 66 associated genomic regions and added 4 proxies for the most associated SNPs resulting in 76 SNPs for replication. Cluster plots of all prioritized SNPs were examined using Evoker51 in cases and controls separately to minimize the possibility of spurious association due to genotyping error. We included 27 ancestry-informative markers (AIMs) for genotyping in the replication datasets, to guard against population stratification (Supplementary Information).52
