It is important to note that it is possible for a significant difference in odds ratio to occur not because the effect is lacking in the second population, but because it is significantly stronger. Therefore, significant results from the cross-population heterogeneity tests should be reviewed to check for such cases, and such SNPs for which there is a clear genetic effect in both populations should not be filtered from further study. For the 10 SNPs studied in our sample, this situation does not occur: the point estimate for the population-specific odds ratio in the AA sample is essentially one for all SNPs except rs16969968, as we had hoped to demonstrate for at least some SNPs. The direction of effect for rs16969968 in the AA sample also matches the direction in the EA sample (allele A is "protective").
