A set of 306,655 autosomal genotyped SNPs remained after exclusions for call rate<97%, HWE P<10−5, more than two duplicate errors or Mendelian inconsistency (for reference HapMap CEU trios)70, heterozygote frequency>0, or no mapping in dbSNP. Imputation of autosomal SNPs was based on these 306,655 SNPs using BIMBAM (version 0.99)66 with reference to HapMap CEU (release 22, build 36)70. The analysis data set included 2,543,887 genotyped or imputed SNPs.
