To assess the probability of the same SNV being responsible for both changing PD risk and modulating the expression levels of a gene, we used the Coloc method.11 Both the Braineac and GTEx eQTL data sets were harmonized with the PD GWAS data set to ensure that the regression coefficients were reported with respect to the nonreference alleles in build GRCh37 and that the variants overlapping with the PD GWAS data set were kept for analysis. Coloc uses estimated approximate Bayes factors from summary association data to compute posterior probabilities for the following 5 hypotheses: no shared causal variant in the region, there is a causal PD variant but no eQTL variant, there is a causal eQTL variant but no PD variant, both studies have a different causal variant within the analyzed region, and there is a shared causal variant within the analyzed region.
