Imputed genotype dosage data was analyzed for association with methylation and expression phenotypes using PLINK 20. Linear regression of the phenotype with dosage of the minor allele for each SNP was performed. Cis regions were defined as 4 Mb of the probe site. This definition allowed us to compare our findings in cerebellum to our earlier observations in lymphocytes 7, 21. Trans regions included the rest of the genome. The significance thresholds were based on the estimated number of probes for the cis and trans-analysis. For the cis analysis, the significance threshold was 0.01. For the trans-analysis, 8597 and 25834 probes were analyzed for the methylation and expression data respectively. The trans-analysis significance threshold was set to 0.05 divided by the number of probes.
