The pattern of LD was examined in each of the regions having SNPs associated with at least one of the three phenotypes (DSM-IV alcohol dependence, early onset DSM-IV alcohol dependence, and COGA alcohol dependence). While there was extensive LD as defined by D’ (Figure 1), differences in allele frequencies mean that the correlation of the SNPs (r2) was much more restricted (Figure 3), such that different groups of SNPs were correlated with each other but much less with other groups. Considering the LD pattern, it appears that there are at least 6 independent regions of association. Several groups of SNPs in LD with each other show similar patterns of association. At the 3′ end of GABRR1, SNPs 8, 10 and 12 are in high LD with each other (Figure 3, inset) and two provide evidence of association with early onset, while the third, less correlated SNP, approaches significance; SNP 9, in that cluster, is also significant. At the 5′ end of GABRR1, 3 SNPs (25, 28, 29) are significantly associated with early onset (and several others are nearly significant), with
