Figure 1

(A) Map of linkage disequilibrium (LD) coefficient |D'| (lower part) and r² (upper part) within the analyzed region on chromosome 20q11.22 (445 kb). A single strong |D'| block (average 0.94) is observed, but broken into small blocks with r². (B) Structure of reference haplotype blocks with three different algorithms (Kamatani's method, Gabriel's method, and four-gamete test) using 725 samples. Each haplotype block is shown as blue (Kamatani's), green (Gabriel's), or red (four-gamete test) horizontal bars. Two gaps of (a) and (b) were observed in the analyzed region ((a) in the four-gamete test, and (b) in Gabriel's method). (C) θ profiles with the maximum number of samples (x = 725), and 3,000 repeats (N = 3,000). θ profiles show values between 0 and 1 based on its definition. The scale of θ profiles is shown on the vertical axis. The physical distance on chromosome 20q is shown on the horizontal axis. SNPs positions are presented as vertical gray bar through (A) to (C). Based on the complete identification of θ profiles, two SNPs intervals of (I) and (II) were selected for further analysis. We also selected four SNPs intervals from (i) to (iv), showing the variations of θ profiles, for further analysis. (A), (B), and (C) are illustrated at the same physical scale.