Figure 4.

eQTN enrichment in regulatory elements of the core promoter. (a) The fold enrichments of eQTNs in a variety of predicted regulatory elements based on published methods, sequence motifs and evolutionary conservation. See main text for further details. Only SNPs occurring within 50 bp of the TSS were considered. The confidence intervals for the estimates of enrichment in other core motifs (TATA, SP1, Initiator (Inr) and the TFIIB recognition element (BRE)) were (-∞, > 0) and are not shown. (b) The QQ-plots of expected versus observed quantiles of the -log10(P-value) for SNPs located in several known core promoter motifs, including the TATA box, the SP1 binding site (or GC-box), the Inr element, the BRE and the downstream promoter element (DPE), as well as in 1,000 6-mer sequences that are highly overrepresented in core promoters.

Gaffney et al. Genome Biology 2012 13:R7   doi:10.1186/gb-2012-13-1-r7
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