Using a sliding window method, a series of two- and three-SNP haplotypes were analyzed in three quantitative phenotypes: factAD4, factAD3r, sumAbuse (the 1177 DZ families were used for this analysis). For factAD4, the smallest p-value for any 2-SNP haplotype was between rs279858 and rs279845 (p = 0.01, uncorrected for multiple testing). This is no better than the best single marker result (p = 0.007). Haplotypes for the other variables all produced less significant results than for the single markers. Haplotype association analysis between sumAD3r and the LD block spanning SNPs 1−7 (Table 2) was not significant, with two complementary common (>5%) haplotypes observed: T-T-A-A-T-T-T (59.1%), C-C-G-T-C-C-C (36.5%) where the rs279858 and rs279845 alleles are highlighted in bold.
