Imputation was performed for autosomes using MACH (version 1.0.16, http://www.sph.umich.edu/csg/abecasis/MaCH/) to obtain missing genotypes for cohorts 1 and 2 that underwent GWAS. SNPs with minor allele frequency ≥1%, call rate ≥95% and Hardy–Weinberg P-value ≥10−4 were used for imputation. A 1:1 mixture of the HapMap II release 22 (NCBI build 36) CEU:YRI consensus haplotypes (http://mathgen.stats.ox.ac.uk/impute/) were used as a reference panel. Imputation was performed in two steps. For the first step, 484 unrelated African-American samples were randomly selected to calculate recombination and error rate estimates. In the second step, these rates were used to impute all samples across the SNPs in the entire reference panel. Imputation results were filtered at an rsq threshold of ≥0.3 and a minor allele frequency ≥0.05. Among the 46 SNPs examined in this study, 21 SNPs were directly genotyped, whereas 24 SNPs were imputed with a minimum rsq of 0.48, and one SNP (rs4712652) failed for both direct genotyping and imputation and was not analyzed in cohorts 1 and 2.
