Single nucleotide polymorphisms (SNPs) and haplotype structure in the Cholesteryl ester transfer protein ( CETP ) gene. (A) The CETP transcript (GenBank accession NM_000078) is roughly 22 kilobases and contains 16 exons. We obtained good quality genotype data for 14 SNPs in this region. Of these, nine were common SNPs that were included in our haplotype map. In the map, these were assigned to two haplotype blocks, each having three common haplotype patterns. The 5' block includes the Taq1B SNP, rs708272 [28, 29]. (B) We measured linkage disequilibrium, D', for all pairs of SNPs in this interval, using an expectation maximisation (EM) algorithm to determine haplotypes. These data also show two strong blocks of high disequilibrium.