Comparison of SNP bins derived from pair-wise measurements of linkage disequilibrium using LDSelect-Comp. SNPs with MAF < 5% do not have a vertical line or arrowhead in the column. A) Scale representation of the ~650 kb region studied, indicating the BRCA1 gene, founder mutations, and genome sequence gap of unknown true size. Anchor lines link to position of the SNP within the region. B-F) LDSelect creates bins of SNPs that have an r2 value of 0.8 or greater with at least one other SNP in the bin. Each vertical line and arrowhead represents a SNP, with dashed lines and shaded background connecting SNPs within the same bin. Down arrowheads indicate Tag SNPs (those with r2 ≥ 0.8 with all other SNPs in a bin). Note that this use of the term Tag-SNP is different from Haploview – with LDSelect, only one Tag-SNP per bin would be required to capture the majority of the nucleotide diversity. Singleton bins (SNPs that did not have r2 ≥ 0.8 with any other SNP) are indicated by solid dots on a single row. SNP number refers to numbering in column 1 of Table 1.