We re-analyzed our published mQTL dataset 9 by including imputed genotype data (see Materials and Methods), and extended the cis-region to 4 Mb. Analogous to the traditional classification of eQTLs, we sought to classify methylation QTLs (mQTLs) into cis and trans regulators of methylation phenotypes. SNPs within the cis-region of a variably methylated CpG site were included in our analysis. We identified 5974 distinct genes with cis mQTLs at association p < 0.01, and 4143 distinct genes with cis mQTLs at a more stringent p < 0.001. Supplemental Figure 1 illustrates the genomic locations of the identified cis mQTLs. To further the investigation of these mQTLs, we have deposited this dataset into SCAN (http://www.scandb.org) 6, a publicly available genomic resource containing initially the results of eQTL studies conducted in lymphoblastoid cell lines.
