Fig. 1.

Schematic of ASM-assisted mQTL mapping. The top three panels show bisulfite sequencing data mapped to a CpG site where methylation level is associated with a nearby SNP, in an AA homozygote (left), an AT heterozygote (middle), and a TT homozygote (right). Note that, while illustrated in the panels, the allele-level methylation information in the two homozygotes is not observed. The bottom three panels depict three methods to detect SNP-CpG association: the standard mQTL mapping approach (left) uses non-allele-specific information from all three individuals to detect an association, the standard ASM analysis (middle) uses allele-level information from the heterozygote only, and the joint analysis approach (right) presented here uses both types of information to achieve a gain in power. mQTL methylation quantitative trait loci, ASM allele-specific methylation