There were 48 associations that did not generalize to African Americans with respect to direction of effect and statistical significance. GWAS associations identified in European descent populations may not generalize in African Americans for several reasons. More often than not, this is due to discordant minor allele frequency differences and linkage disequilibrium (LD) patterns, both of which impact statistical power. On average for SNPs that do not generalize, the MAF in the original population was significantly different compared to the MAF in our study population (p ≤ 0.01). The MAF was lower in African Americans compared to the original study population for 60% of the SNPs that do not generalize (Fig. 1). Low minor allele frequency is directly correlated with power in genetic association studies. We also noticed this correlation in our analysis; 13/79 inadequately powered tests of association had a minor allele frequency < 0.09.
