Insights into potential mechanisms involved in MD genetic effects. (A) One potential mechanism leading to MD genetic effects wherein TFs distinguish between alleles in one condition but not the other with an example site showing allelic imbalance (the ratio of reference allele to total counts) in the methylated versus unmethylated condition and a pie chart showing the percentage of MD genetic effect sites following this pattern. (B) Another potential mechanism leading to MD genetic effects wherein TFs bind to different alleles in alternate conditions with an example site and a pie chart showing the percentage of MD genetic effect sites following this pattern. (C) TF motifs that are enriched within ±200 bp of MD genetic sites that display increased ASE in the unmethylated condition (top) or methylated condition (bottom) colored by TF family. (D) Example of a MD genetic effect site that directly overlaps with a GWAS hit and is 60 bp away from an EWAS hit, which are associated with hemoglobin concentration and MetS, respectively. Created with bioRender (https://www.biorender.com/).