In a few genes, a large proportion of the SNPs have modest frequency differences between cases and controls. In 10 out of the 54 genes examined, more than 10% of the SNPs have p<.05 and in 3 genes this portion exceeds 20%. Specifically, the proportion of SNPs in SAGE with p<.05 is 55% (16/29) in GABRA2, 24% (10/29) in BDNF and 44% (4/9) in HTR1A (Table 3). To test whether the large proportion of SNPs with small p values in these genes could be explained by linkage disequilibrium, we performed SNAP analyses.
