Figure 5: Common meQTLs affect most Horvath clock CpGs and vary in frequency across ancestries.

A: The allele frequency distribution of the 29,033 unique variants associated with methylation levels at Horvath clock CpGs. Allele frequencies were computed over the 76,215 genomes in gnomAD version 4.1. Inset: Out of the 353 CpGs in the Horvath clock, 271 (77%) have at least one meQTL, i.e., a genetic variant that is associated with methylation level. B: Clock meQTL have significantly higher alelle frequency in individuals with African genetic ancestry from gnomAD than all other ancestry groups (median 0.068 for African vs. 0.004–0.046; p < 3.85×10⁻²⁵). C: Clock meQTL have significantly higher allele frequency on African local ancestry genomic segments in 7,612 Latino admixed individuals with varying proportions of European, American, and African ancestry from gnomAD. Inset: The distribution of difference in frequencies for each meQTL for each pair of populations.