Table 1 Specific genomic features are characterized by hydroxymethylation in brain

37,145

-

-

65,563

-

-

  Island

120,922 (32.3 %)

2,868 (7.7 %)

0.18 (0.17–0.18)

<2.53E-294

6,524 (10.0 %)

0.23 (0.23–0.24)

<2.53E-294

  Shore

87,312 (23.3 %)

11,934 (32.1 %)

1.55 (1.52–1.59)

2.53E-294

18,544 (28.3 %)

1.30 (1.27–1.32)

1.80E-159

  Shelf

32,912 (8.8 %)

5,434 (14.6 %)

1.78 (1.72–1.83)

3.93E-262

9,958 (15.2 %)

1.86 (1.81–1.90)

<2.53E-294

  Outside

124,010 (33.1 %)

16,565 (44.6 %)

1.62 (1.59–1.66)

<2.53E-294

29,831 (45.5 %)

1.68 (1.66–1.71)

<2.53E-294

  Unannotated

8,938 (2.4 %)

344 (0.9 %)

0.38 (0.34–0.43)

2.99E-91

706 (1.1 %)

0.44 (0.41–0.48)

9.15E-118

  Intergenic

52,325 (14 %)

4,367 (11.8 %)

0.82 (0.79–0.85)

8.46E-34

7,461 (11.4 %)

0.79 (0.77–0.81)

5.13E-75

  Distal promoter

16,990 (4.5 %)

1,986 (5.3 %)

1.19 (1.13–1.25)

5.16E-12

2,897 (4.4 %)

0.97 (0.93–1.01)

0.166

  Proximal promoter

148,029 (39.6 %)

9,693 (26.1 %)

0.54 (0.53–0.55)

<2.53E-294

13,544 (20.7 %)

0.40 (0.39–0.41)

<2.53E-294

  Gene body

140,919 (37.7 %)

19,870 (53.5 %)

1.90 (1.86–1.94)

<2.53E-294

39,335 (60.0 %)

2.48 (2.44–2.52)

<2.53E-294

  Downstream

6,893 (1.8 %)

885 (2.4 %)

1.30 (1.21–1.40)

1.95E-12

1,620 (2.5 %)

1.35 (1.28–1.43)

2.04E-25

  Unannotated

8,938 (2.4 %)

344 (0.9 %)

0.38 (0.34–0.43)

2.99E-91

706 (1.1 %)

0.44 (0.41–0.48)

9.15E-118

 Transcription factor binding site

184,178 (49.2 %)

14,623 (39.4 %)

0.67 (0.66–0.68)

8.40E-291

19,499 (29.7 %)

0.44 (0.43–0.44)

<2.53E-294

 Dnase 1 hypersensitivity site

49,903 (13.3 %)

4,449 (12.0 %)

0.88 (0.86–0.91)

7.49E-14

6,227 (9.5 %)

0.68 (0.66–0.70)

5.80E-174

14,429

-

-

25,582

-

-

  A3SS

3,347 (2.4 %)

330 (2.3 %)

0.95 (0.84–1.06)

0.361

700 (2.7 %)

1.14 (1.05–1.24)

2.63E-03

  A5SS

3,364 (2.4 %)

357 (2.5 %)

1.02 (0.91–1.14)

0.712

710 (2.8 %)

1.15 (1.06–1.25)

1.11E-03

  AFE

57,956 (41.8 %)

4,897 (33.9 %)

0.72 (0.69–0.74)

5.07E-76

7,332 (28.7 %)

0.56 (0.54–0.58)

<2.53E-294

  ALE

9,026 (6.5 %)

1,353 (9.4 %)

1.49 (1.40–1.58)

1.55E-35

2,554 (10.0 %)

1.59 (1.52–1.67)

5.61E-81

  CE

60,203 (43.4 %)

7,783 (53.9 %)

1.53 (1.47–1.58)

2.14E-128

13,980 (54.6 %)

1.57 (1.53–1.61)

1.17E-239

  CNE

20,661 (14.9 %)

1,592 (11.0 %)

0.71 (0.67–0.75)

1.99E-38

3,149 (12.3 %)

0.80 (0.77–0.83)

3.28E-28

  EI

137 (0.1 %)

19 (0.1 %)

1.33 (0.78–2.16)

0.270

45 (0.2 %)

1.78 (1.24–2.51)

1.39E-03

  II

27,746 (20 %)

3,080 (21.3 %)

1.08 (1.04–1.13)

1.60E-04

4,974 (19.4 %)

0.96 (0.93–1.00)

0.036

  IR

16,175 (11.7 %)

1,550 (10.7 %)

0.91 (0.86–0.96)

8.90E-04

3,025 (11.8 %)

1.02 (0.97–1.06)

0.472

  MXE

13,054 (9.4 %)

1,880 (13 %)

1.44 (1.37–1.52)

8.63E-41

3,221 (12.6 %)

1.39 (1.33–1.44)

6.38E-52