The LD pattern as computed with Haploview (Fig. 1) indicates that all 9 SNPs are in fairly strong LD with each other. The positive SNP associations extend over both blocks; however, the LD figure displays two blocks based on a more conservative definition. Therefore, for haplotype analysis, we have derived haplotypes from all 9 SNPs as they appear to be within one haplotype block. Table 4 summarizes the haplotype frequencies (of those 8 haplotypes with frequency greater than 0.01) and the respective p-values resulted from the haplotype analyses with the continuous phenotypes of P3 amplitude in the seven posterior electrodes and with the dichotomous diagnostic phenotype of alcohol dependence by DSM-IV. The most common haplotype, H1 (121111112), is over-transmitted to individuals with reduced P3 amplitude (Table 4 and Fig. 2).
