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The two polymorphic alleles of esterase D (ESD), ESD*5 and ESD*7, are specific to Europeans and Asians, respectively. In this study the molecular basis was characterized: ESD*5, arising from ESD*1, has a G to A transition, resulting in Gly257(GGT)VAsp(GAT); and ESD*7, originating from ESD*2, has an A to G transition, resulting in Asp231(GAT)V Gly(GGT). Glycine is also involved in the common ESD*1/ESD*2 polymorphism [Gly190(GGA)VGlu(GAA)]. Haplotype analysis using a few novel intragenic polymorphisms showed strong associations among polymorphic sites, suggesting that recombination has been less frequent in the human ESD gene, although it spans about 25 kb from exon 1 to exon 10. A marked difference was observed in the distribution of haplotype frequencies between Germans and Japanese.