eLD: entropy-based linkage disequilibrium index between multiallelic sites.

Quantification of linkage disequilibrium (LD) is a critical step in studies investigating human genome variations. Commonly used LD indices such as handle LD of biallelic variants for two sites. As shown in a previously introduced LD index of , normalized entropy difference of the haplotype frequency between LD and linkage equilibrium (LE) could be utilized to estimate LD of biallelic variants for multiple sites. Here, we developed eLD (ntropy-based inkage isequilibrium index between multiallelic sites) as publicly available software to calculate of multiallelic variants for two sites. Application of eLD could dissect complex LD structures among multiple HLA genes (e.g., strong LD among , , and in East Asians). Use of eLD is not restricted to haplotype-based LD; it is also applicable to genotype-based LD. Therefore, eLD enables estimation of -regional LD of SNP genotypes at two unlinked loci, such as the nonlinear LD between functional missense variants of (rs1229984 [Arg47His]) and (rs671 [Glu504Lys]).