Our previous data from the human cerebral cortex [2], as well as data from HapMap lymphoblastoid cell lines (LCL) [5] have suggested that SNPs proximal to genes including SNPs upstream of the transcriptional start site (TSS) within the gene and downstream of the transcript end site (TES) have a greater influence on gene expression than those further away. This is presumably because genetic variation around promoter elements, splice sites and 3′ UTR affects transcription, splicing and mRNA stability [19] that results in a relative enrichment of cis over trans eQTLs. To see if this observation generalized to multiple brain regions and also to QTLs linked to CpG methylation, we plotted all significant QTLs by genomic position of the SNP and transcript or SNP and CpG site (Figure 2).
