LD comparisons between cases and controls for AD+DD and AD-only were performed using LD Contrast Test software. Two regions, one around TTC12 exon 3 (SNPs T2 to T5) and another around ANKK1 exon 2 (SNPs T10 to A3), were identified as differing in the standardized composite LD for AD+DD (p = 0.018 and 0.0012, respectively) and AD-only (p = 0.00005 and 0.00013, respectively). The LD difference gradually disappeared as the number of SNPs that were included increased. The differences in pairwise LD matrices are displayed using ellipse plots (Figure 3) in which the shape of an ellipse indicates the magnitude of LD and the direction shows the sign of the disequilibrium. The more circular ellipse reflects a low degree of LD, and the ellipse oriented at 45° suggests a positive value of LD. The two regions, identified by the LD contrast test, are composed of markers in stronger LD among cases than controls. This phenomenon occurs when selection causes transmission of more disease alleles and/or haplotypes in common among cases than controls. The two identified regions of differential LD between
