We also found that the best associated SNP for each gene expression trait was frequently immediately upstream or downstream from the transcription start site (TSS) (Figure 2C, [37]). Replication rate of significant cis-eQTLs was associated with absolute SNP to TSS distance (logistic regression chi-squared p-value = 5.35×10−3). 74.5% of cis-eQTLs within 5 kb of the TSS replicated, compared with only 60.6% located more than 100 kb from the TSS. Thus while distal regulatory elements are clearly important for human gene expression regulation, robustly quantifiable, segregating expression polymorphism was more likely to be found in SNPs very close to the TSS of genes.
