We first applied the ALIGATOR program to our EA and AA samples examining 364,069 SNPs covering 22,702 genes in the EA sample and 441,447 SNPs covering 22,902 genes in the AA sample; the results are presented in Table 4. The list of significant SNPs was chosen such that 5% of genes were covered (i.e. the 5% of genes with the most significant single-SNP p-value). For the EA sample, this corresponded to a SNP p-value criterion of 0.0046, and a list of 1135 genes. For the AA sample, the SNP p-value criterion was 0.0030, and the gene list contained 1145 genes.
