Figure 1.

Number of variants included in TOP-LD

(A) Comparison of autosomal variants with HaploReg 4.0 by population. Blue bars on the left show total number of autosomal variants in HaploReg4.0. Green and red indicate common (MAF ≥ 1%) and uncommon (MAF < 1%) autosomal variants in TOP-LD. Note that HaploReg4.0 provides LD for ASN (Asian) with no separate information for EAS and SAS. Therefore, we used the same 13.7 million ASN variants for comparison in both EAS and SAS.

(B) Number of autosomal variants in TOP-LD breaking down by LD R² threshold. The majority of the variants have at least one LD proxy with R² ≥ 0.8.

(C) Number of chrX variants in TOP-LD breaking down by LD R² threshold.

(Note: LD information downloaded from HaploReg4.0 does not contain chromosome X. Therefore, we compared TOP-LD with HaploReg4.0 only for autosomal variants).