There is significant LD among SNPs within each gene, as well as significant LD across genes in the ADH gene cluster on chromosome 4. Supplementary figures 1–6 show the r2 plots for the SNPs analyzed by chromosome. There were 21 haplotype blocks present, 9 of which are on chromosome 4. No individual haplotypes were associated with either trait at P ≤ 0.01. Two haplotypes in block number three on chromosome 15 (see supplementary figure 1F) in the ALDH1A3 gene, showed the greatest evidence for association to DSM-IV symptom count (P = 0.02). In general, the haplotype association results were less convincing than the individual SNP results within that gene (see table 1). The haplotype association results provide no evidence for untyped, causal loci tagged by our typed markers.
