Our methylome profiling revealed hotspots of DNA methylation on chromosomes 2, 16 and 18. Association of these chromosomes with alcohol dependence has been reported (Dick et al., 2010; Foroud et al., 1998; Treutlein et al., 2009; Wang et al., 2005). Thus, using earlier findings that chromosome 2, especially 2p14-2q14.3, is associated with phenotypes of alcohol dependence, suicide attempts, and conduct disorder, a systematic screen of SNPs with the three comorbid phenotypes yielded evidence of association with 23 genes, likely contributing to the preponderance of reported linkages with alcohol dependence and related phenotypes across chromosome 2 (Dick et al., 2010). Another study utilized a genome-wide association study, discovering 15 SNPs significantly associated with same allele that had shown expression changes in rat brains after long-term alcohol consumption. In the combined analysis, 2 closely linked intergenic SNPs are located on chromosome region 2q35, which has been implicated in linkage studies for alcohol phenotypes, including the CDH13 and ADH1C genes that have been reported to be associated with alcohol dependence (Treutlein et al., 2009). Linkage analysis also detected loci underlying moderate and severe
