Pair-wise measures of linkage disequilibrium and the two founder mutation-containing haplotypes. SNP number refers to numbering in column 1 of Table 1; only the 70 with MAF ≥ 0.05 in Ashkenazi Jews are shown in B-D. A) Scale representation of the ~650 kb region studied, indicating the BRCA1 gene, founder mutations, and genome sequence gap of unknown true size. B) LDSelect-Comp output showing a total of 22 bins for Ashkenazi Jews, with 17 "singleton" bins indicated by solid dots on a single row. C) Haploview output showing three block structures and related ht-SNPs (indicated with up arrowheads). D) Haplotypes estimated for 85 unrelated Ashkenazi Jews using SNPHAP as implemented in HapScope. The block boundaries were calculated in Haploview and overlaid on this figure. All haplotypes with an estimated frequency of at least 1% are displayed (h1 to h11), with individual frequencies and sums indicated to the right of the blocks. The common allele is designated "1" and the minor allele "2". The 185delAG and 5382insC containing haplotypes, determined from the family based genotypes, are indicated with gray (haplotype 2) and blue background (haplotype 1), respectively. Black arrows indicate the relative position of these two founder mutations.