We obtained genome-wide genotyping data available from Illumina’s iControl database (iControlDB from Illumina, Inc., San Diego, CA) for 830 African Americans genotyped for 561,466 SNPs on the Illumina HumanHap550v3 BeadChip. Data were downloaded on January 19, 2011. Quality control (QC) was implemented on SNPs and subjects using PLINK [19] unless otherwise stated. The QC criteria were selected to resemble standard criteria used for GWAS. Genotyped SNPs were excluded due to minor allele frequency (MAF) <1%, call rate<95%, or Hardy-Weinberg equilibrium (HWE) p-value<0.0001. There remained 541,860 autosomal SNPs (96.5%), of which 8,101 SNPs from chromosome 22 were used for imputation.
