Functional enrichment of eQTLs was additionally assessed using ChIP-seq based transcription factor (TF) binding sites (TFBS) from the ENCODE Project 49. Specifically, we used a set of proximal and distal TFBSs, where proximal is defined as a 2,000 bp window centered on Gencode v19 annotated transcription start sites (TSS). These sets were constructed by overlaying TF ChIP-seq peaks from all available cell types with DNase peaks. We limited our analysis to those peaks that overlapped with H1-ESC derived TF peaks. As with chromatin state annotations, we overlapped target and control eQTL variants with binding sites for each individual factor (all sites where the given factor is bound or co-bound). An empirical P-value for the enrichment was derived based on the control sets and adjusted for multiple testing using the Benjamini-Hochberg method. Factors with an adjusted P < 0.05 were considered enriched. Plotted in Fig. 4 are factors with at least 10 observed overlaps.
