Enhancer candidates overlap multiple transcription factor bound loci. (A) Percentage overlap of Enh, PrL, Unknown and all 1 kb genome bins to TF bound regions in three categories (0, 1–3 or 4+ TFs). Generated by comparison to ChIP-Seq data for 7 ES cell-expressed TFs (excluding OCT4, SOX2, NANOG, MYC and MYCN). The Enh candidates are significantly enriched with MTL in comparison to the PrL and unknown sets as well as whole genome bins with p-values <0.001. (B) Percentage overlap of Enh candidates with TF bound regions using various enhancer probability thresholds. The numbers in brackets beside enhancer probability thresholds show the number of regions predicted to be Enh using the indicated threshold.