Two CNV regions were significantly associated with alcohol dependence (Table 3): chromosome 6q14.1 (OR=2.86, P= 1.04 × 10−6, n=121 subjects with the duplication) and chromosome 5q13.2 (OR=1.99, P= 3.37 × 10−4, n=59 subjects with the duplication, and n=58 subjects with deletions). The P values for each probe in these two regions are listed in Supplementary Tables 2 & 3. There were significant differences in the distribution of males and females across cases and controls. While all analyses modeled sex as a covariate, we also conducted secondary analyses separately in males and females. Significant results for SNPs in the region of the CNV on 5q13.2 and 6q14.1 was replicated with the same direction of effect (albeit at less significant p-values, see Supplemental Tables 4A, 4B, 5A and 5B).
