Linkage disequilibrium pattern comparisons showed that INDEL-SNP LD is greater than SNP-SNP LD for mean maximum r
2. Mean max r2 for the CEU population (CHB+JPT and YRI not shown) using common SNP and indel sites from 1000G, OMNI and HapMap, averaged over 1 kb windows. Although indel-SNP LD was higher than SNP-SNP for all SNP panels, this is likely due to ascertainment bias. OMNI LD was the lowest due to its design, and HapMap3 had the highest LD due to the relative reduction in low frequency variants.