Imputation from each array to Hapmap SNPs was done by the program IMPUTE (https://mathgen.stats.ox.ac.uk/impute/impute_v0.5.html) [5]. European Americans were imputed using the CEU reference panel (HapMap release 22 - NCBI Build 36 dbSNP b126). African Americans were imputed separately using the YRI reference panel (HapMap release 22 - NCBI Build 36 dbSNP b126). We omitted sex chromosomes in this study because of the complication of imputation on these chromosomes. The Illumina 1 M array contains a small number of strand-ambiguous A/T C/G SNPs. Although Illumina provides strand information about those SNPs, we still found a few inconsistencies compared with the reference panel. In order to make sure that all SNPs were reported on the same strand, all strand-ambiguous A/T and C/G SNPs (5583 in total, 0.5% of all Illumina 1 M SNPs) were excluded from the comparison.
