Two- and three-locus haplotypic association between ALDH1A1 SNP genotypes and the quantitative AUDIT score is graphically presented in Figure 2. Using Qtphase and a sliding window approach, the significance of association increased from p = 0.014 for the single rs610529 SNP analysis to 0.0015 (likelihood ratio statistic [LRS] = 15.47, degrees of freedom [DF] = 3) for rs610529-rs2288087 haplotype analysis, where the two SNPs are in high LD (D' = 0.97, r2 = 0.60). Three common haplotypes (≥1 per cent frequency) were observed, totalling 99.4 per cent of the observed haplotypes. Two common haplotypes, '1-1' (10.4 per cent frequency) and '1-2' (35.9 per cent frequency) had mean AUDIT scores of 23.42 (χ2 = 8.37, p = 0.0038) and 17.64 (χ2 = 7.3, p = 0.0070), respectively. The third common haplotype ('2-1', 53.1 per cent) was not significantly associated (χ2 = 0.4, p = 0.55) with the AUDIT score (mean score = 19.59). The addition of a third neighbouring SNP, rs13959, did not increase the strength of association (p = 0.0024).
