A primary aim underlying these experiments was to examine the extent of genetic control of DNA methylation and expression within brain tissues. To investigate this process, we undertook a series of QTL analyses. From the 537,411 genotyped SNPs that passed quality control filtering we then imputed genotypes for 2,545,178 SNPs using MACH [16] and HapMap CEU phase data. After additional quality and analysis specifications filtering of the imputed genotypes 1,629,853 SNPs (average) were used for analysis. The QTL analysis of each tissue region was performed separately so we expanded our trait selection from those that were detected in 95% of samples across all four brain regions to those that were detected in 95% of samples within a specific brain region. Changing this trait selection threshold based on what is present within a specific brain region allowed us to analyze additional mRNA transcripts that are well detected within one or more brain regions but not all four tissue regions. The number of SNPs, CpG sites and mRNA transcripts tested for each brain tissue can be found in Table 1. With these
