We imputed nongenotyped SNPs using two software implementations36,37 that share similar underlying population genetic models38. This methodology facilitates meta-analysis across different marker sets and improves coverage across the genome, and its utility has been empirically shown in several large GWAS. However, the power to detect associations with rare alleles is limited. The loci we report include two relatively infrequent SNPs, GSTCD (rs10516526, minor allele frequency 0.06) and AGER (rs2070600, minor allele frequency 0.05); these SNPs were directly genotyped in the majority of stage 1 subjects (16,514 and 15,386 individuals, respectively).
