We annotated variants for genic and intergenic classification using ANNOVAR (hg18, refGene) [37]. Genic variants included all those variants annotated to exons, introns, UTRs and splice sites. Intergenic variants included those not otherwise annotated as genic. Additionally, we annotated directly genotyped and imputed SNPs that we had previously identified as significantly associated with gene expression (p<0.001) in parietal cortex, (GSE35977), cerebellum (GSE35974), and skeletal muscle (GSE40234). Details of the eQTL detection are described in supplementary methods and in previous publications [38]–[45]. Three sets of analyses were conducted using the eQTL annotations. The first analysis simply partitioned the parietal eQTLs and cerebellar eQTLs from their respective complements for all imputed SNPs. The second model included four partitions: 1) brain only eQTLs (those found in cerebellum or parietal tissues but not in muscle), 2) muscle only eQTLs (those found in muscle and not in either brain tissue), 3) eQTLs common to brain and muscle, and 4) a final partition with non-eQTL SNPs. The last analysis included four total partitions to accommodate eQTLs exclusive to each brain tissue (cerebellum and parietal) as well
