Histone modifications and RNA polymerase II (Pol II) have distinct profiles around transcription start sites (TSSs) of transcribed and silent genes. The plots are derived from the K562 cell line. Methylated lysine 4 on histone H3 (H3K4me3) is enriched around TSSs in transcribed genes, H3K36me3 is enriched in gene bodies of transcribed genes and Pol II is enriched at both TSSs and gene bodies of transcribed genes, whereas H3K27me3 is enriched at silent genes. Some H3K4me enrichment was also observed for silent genes. Similar profiles for Gm12878 are shown in Additional file 1, Figure S3.