Selection of a subset of genes from the top 5% (based on a cutoff of top SNP showing p≤0.0005), identified 51 genes in the EA sample and 98 genes in the AA sample. Results of the set-based analyses using 10,000 permutations showed that the number of genes achieving gene-wise significance was greater than expected. At a significance threshold of 5%, we would have expected 3 significant genes in the EA sample and 5 in the AA sample. However, our analyses demonstrated gene-wise significance in 9/51 genes in the EA sample and 6/98 genes in the AA sample (Table 1). At the more stringent significance cutoff of 0.5%, we would have expected by chance zero or one significant gene in both samples. Instead we observed 5 genes in the EA sample and 3 genes in the AA sample (empirical p<0.005).
