5hmC distribution on genomic elements and histone modifications. The percentage of 5hmC was normalized to the length (bp) of each genomic segment considered. (A) 5hmC was enriched on promoters (± 1 kb) in embryonic stem cells (ESCs) (*P < 0.01).(B) 5hmC was enriched on exons with respect to introns (*P < 0.01).(C) 5hmC was significantly enriched in active enhancers in ESCs and in poised enhancers in differentiated tissues (*P < 0.01; **P < 0.05).(D) Promoters with low and intermediate presence of CpG islands (LCP and ICP, respectively) were preferentially marked by DNA hydroxymethylation with respect to promoters with high CpG (HCP) (*P < 0.01). (E) In ESCs, promoters with both H3K4me3 and H3K27me3 (K4/K27) and promoters with H3K27me3 but not H3K4me3 (K27) were significantly enriched in DNA hydroxymethylation compared with promoters with H3K4me3 but not H3K27me3 (K4) (*P < 0.01). (F) Analysis of correlations between 5hmC and histone modifications in all four cell types (*P < 0.01).