Figure 4.

Linkage disequilibrium between SNPs and INDELs. (A) The r² value was calculated for each SNP within a 1-Mb window of a given INDEL using the SNP genotypes that have been reported for HapMap 3 (http://hapmap.ncbi.nlm.nih.gov/) and our INDEL genotyping data from the same samples. For each population (YRI, CHB), the SNP with the maximum r² value was identified (Supplemental Table 13). INDELs in perfect LD with a SNP have an r² of 1.0. (B) LD also was examined for high-scoring SNPs (with P-values <0.001) that were identified in 118 GWAS studies (Supplemental Table 14; Johnson and O'Donnell 2009). GWAS SNPs that have high levels of LD (r² > 0.8) with INDELs are summarized. (C) Examples of INDELs from B that map to functional regions of genes. The 16 examples were taken from a larger collection of 1102 INDELs that have high levels of LD with GWAS SNPs and also map to genes (Supplemental Table 15).