Mach software version 1.0.16 [16] and HapMap CEU phase data (release 22) were used to impute genotypes for ∼2.5 million SNPs. Imputed SNPs were excluded if the linkage disequilibrium r2 values between imputed and known genotypes was less than 0.3, and if their posterior probability averages were less than 0.8 for the most likely imputed genotype. For each of the four tissue regions, SNPs were also excluded if: (a) call rate was less than 95%, (b) Hardy-Weinberg equilibrium (HWE) p-value was less than 0.001, and (c) the SNP had less than 3 minor homozygotes present. Exact numbers of SNPs used per brain tissue and assay type are shown in Table 1.
