The presence of predicted enhancers and their chromatin environment both affect target gene expression. (A) Cell type-specific genes have significantly more CSPEs in the corresponding cell type. A CSPE is assigned to its nearest gene within +20kb or –20kb outside of the gene region and 500bp outside a promoter. The number of CSPEs from the corresponding cell type associated with cell type-specific genes (top) is significantly higher than the number of CSPEs associated with all genes with RPKM > 0 (bottom) in pRBCs (red), T-cells (green), and B-cells (blue). (B) Genes associated with CSPEs are significantly more highly expressed than predicted (All vs. CSPE p < 2.2 × 10-16). Potential target genes of CSPEs are sorted based on the chromatin environment at CSPEs or association with Brg1, PolII and p300 and their expression levels are compared to all genes. Significant differences are indicated by colored lines. See Additional file 1 for p-values and discussion.