The chi-square tests show that genotype and allele frequencies of all selected SNPs did not differ between the AD and control groups (Table 1). In the single marker association analysis, in the subset of the sample with AIM information, when the covariates of ancestry proportion and subject recruitment site were included as covariates, there was no significant single SNP association signal. A site effect for MUSC (p-value <0.0001) is likely due to the fact that the smallest proportion of AD subjects (6.1%) and the largest proportion of control subjects (36%) were recruited at that site. To gauge the contribution of each gene to AD risk, we tested differences in estimated haplotype frequency based on 3-SNP haplotypes spanning either GABRG1 or GABRA2. We designated GABRG1 haplotypes “G---” and GABRA2 haplotypes, “A---” (Tables 2 and 3). Notable significant differences were observed in 3-SNP haplotypes mapped to the GABRA2 gene, where significant differences were shown in 2 of 5 haplotypes, including the G-T-A and A-G-G (A2-4, and A2-5) haplotypes, which accounted for 10.6% and 3.2% in the case and control groups, respectively (Table
