Genotyping for both phases of MVP was performed using a customized Affymetrix Biobank Array. Imputation and quality control methods for MVP phase1 were described in detail in Kranzler et al. [3]. Similar methods were used for MVP phase2. Before imputation, phase2 subjects or SNPs with genotype call rate < 0.9 or high heterozygosity were removed, leaving 108,416 subjects and 668,324 SNPs. Imputation for MVP phase2 was done separately from phase1; both were performed with EAGLE2 [44] and Minimac3 [45] using 1000 Genomes Project phase 3 data [46] as the reference panel. Imputed genotypes with posterior probability ≥ 0.9 were transferred to best-guess genotypes (the rest were treated as missing genotype calls). A total of 6,635,093 SNPs with INFO scores > 0.7, genotype call rates or best guess rates > 0.95, Hardy-Weinberg Equilibrium (HWE) p value > 1 × 10−6, minor allele frequency (MAF) > 0.001 were remained for GWAS.
