Association of the SNPs with alcohol dependence was carried out employing an additive model, with sex as a covariate. The λ value (inflation factor) after these adjustments was 1.049; the Q-Q plot for this analysis is shown in Figure 1. None of the SNPs analyzed met conventional criteria for genome-wide significance. However, eleven SNPs had p-values <10−5, and a total of 93 SNPs had p-values ≤10−4 (Supplemental Table 1 shows data from all SNPs with p≤10−3). There were many genes or regions in which surrounding SNPs provided additional support for association (Supplemental Table 1). A region of chromosome 11 (Figure 2A) had many SNPs among those with lowest p values. This was not due to a single SNP in high LD with other SNPs; including the most significant SNP (rs4758533) as a covariate in the logistic regression model decreased the evidence of association with several SNPs near the right end but did not substantially alter the evidence of association with most of the SNPs in the region (see also Figure 2B, which shows that most of the significant SNPs in the chromosome 11 region are not in high LD with rs4758533).
