Indels and SNPs show similar tag SNP patterns. (a) We evaluated the percentage of common indels or SNPs with at least one pairwise r2 greater than 0.5 (medium LD), 0.8 (high LD) or equal to 1 (perfect LD) using 1000G SNPs. Our results suggest that indels and SNPs are similarly tagged by nearby SNPs. (b) The percentage of low frequency and common indels that are in high LD with low frequency or common 1000G SNPs for CEU, CHBJPT and YRI populations. Low frequency and common indels are best tagged by frequency matching SNPs. (c) We evaluated tagging of LOF and non-LOF indels. The percentage of LOF that are in medium, high and perfect LD is slightly lower than non-LOF variants for all populations.