SNPs occur as a result of mutations during the course of evolution, so each is initially associated with a particular pattern of other SNPs on the chromosome in which it arose. Over many generations, recombination reshuffles the pattern of SNPs, with closer SNPs less likely to be separated. Therefore, SNPs are not randomly sorted along chromosomes; the nonrandom coin-heritance of alleles, which is called LD, tends to be higher among nearby SNPs. There is strong LD between variants in the ADH1B and ADH1C genes, which complicates analyses of the effects of individual coding variations in those genes (Chen et al. 1999a; Osier et al. 1999, 2002b, 2004). The most extensive analysis to date of variations in the ADH gene region showed strong LD across nearly the entire region (Figure 2) (Edenberg et al. 2006). The LD was particularly striking in the regions encompassing the ADH1C–ADH1B and ADH4–ADH5 genes. Conversely, a site of frequent recombination occurs within the ADH7 gene, which means that variations near the start (i.e., in the 5′ portion) of that gene are nearly randomly associated with variations
