A total of 704,588 autosomal genotyped SNPs remained after exclusions for call rate<95%, MAF<1%, Hardy-Weinberg equilibrium (HWE) P<10−5, or lacking strand annotation. MACH (version 1.00.16)65 was used to impute all autosomal SNPs with reference to HapMap CEU (release 21, build 35)70 from these 704,588 SNPs. Imputed SNPs failing additional quality control criteria (monomorphism, HWE P<10−6, or genotype frequencies between two genotyping phases differed by P<10−6) were excluded, leaving 2,515,866 genotyped or imputed SNPs for analysis.
