Genome-wide methylation profiles were obtained from both the substantia nigra and the frontal cortex of 134 individuals with PD from the Parkinson Disease UK Brain Bank, using the Illumina Infinium HumanMethylation450 BeadChip (Illumina Inc). Cis PD methylation quantitative trait loci were defined as correlations between the target PD SNV genotype and DNA methylation levels of CpG sites within a 500-kb window of the SNV base position. Linear models were fitted to test whether DNA methylation beta values for each CpG site were predicted by SNV genotypes. We included covariates for age at death, sex, population stratification, batch, and postmortem interval. We retained the strongest SNV-CpG pair at a 5% false discovery rate (FDR) to be used in downstream analyses. The CpG sites were mapped to genes if they were within 10 kb of the gene transcription start or end base position according to HG19 (human genome version 19) coordinates. In total, 37 460 CpG sites were included in the final analysis.
