We see that among the genotyped SNPs in Table 2, all are associated with case status with a primary p-value less than 0.05; this is expected since these SNPs are strongly correlated with rs16969968, which we know is associated with cocaine dependence in the EA sample. The key column in Table 2 is the last one, which gives the p-value for the test of the population-by-genotype interaction term and provides a test for heterogeneity of effect in the two population samples. We see that three SNPs (rs9788721, rs8034191, rs1051948) show significantly different effects in the two samples, and two others have p-values of 0.06 (rs2656052, rs1317286). The population-specific odds ratio in the AA group for each of these SNPs is essentially 1. Therefore our method would rule out these SNPs as likely causative variants and assign them lower priority. Of the remaining 5 SNPs, we observe heterogeneity p-values ≤ 0.2 for all except rs16969968, which has a heterogeneity p-value of 0.75 and odds ratios in the EA and AA groups of 0.66 and 0.73 respectively.
