The physical locations of the eight SNPs across the ALDH1A1 gene are schematically presented in Figure 1. Frequencies of the ALDH1A1 genotypes were in general in Hardy-Weinberg equilibrium (HWE), except for rs595958 in intron 1 (p = 0.0008), and are listed in Table 2. Minor allele frequencies within the control sample were similar to those observed in the Centre d'Etude du Polymorphisme Humain (CEPH) sample (data not shown) of the International HapMap Project [22]. The extent of LD between the eight SNPs is presented in Figure 1. LD was strongest between markers rs610529 (intron 8) and rs13959 (exon 3), with one haplotype block structure detected by Haploview [19] between these SNPs. The effective number of independent SNPs was 6.0, as determined by single nucleotide polymorphism spectral decomposition (SNPSpD) [23,24].
