We reintroduced the probes on the sex chromosomes and those CpGs that had a variant at the CpG site (as meQTLs to these CpGs would represent biological, and not technical, signal) resulting in 477,636 Illumina 450k probes and 7,426,085 common variants on 520 subjects. Within the adult control subjects, we modeled the additive effect of genotype (number of minor alleles) on DNAm levels, adjusting for the first five MDS components from the genetic data and the first 11 PCs (based on the 100,000 most inter-individual variable probes for computational efficiency) using the MatrixEQTL package63. We allowed for a maximum distance of 20kb between each SNP and CpG analyzed, resulting in 47,675,913 tests, and we adjusted for multiple testing using a false discovery rate (FDR) threshold of 0.01 to call meQTLs significant. Posthoc analyses of the most significant SNP-CpG pair per probe were calculated separately by Caucasians and African Americans, and then within fetal samples.
