Table 2 haploReg results

Total number

31,482

246,758

6850

150,000

–

–

–

–

–

–

–

–

Conservation

GERP

1049 (3.66%)

8112 (3.59%)

148 (2.35%)

6349 (4.65%)

5.04e−14

2.36e−55

8.57e−21

–

–

–

–

–

Siphy

716 (2.5%)

5305 (2.35%)

116 (1.84%)

3619 (2.65%)

1.43e−01

1.29e−08

4.42e−05

–

–

–

–

–

Chromatin states

1_TssA

195 (0.68%)

1057 (0.47%)

32 (0.51%)

222 (0.16%)

1.03e−43

8.55e−57

1.19e−07

1.74e−42

1.45e−55

2.03e−06

Promoter-associated

Active transcription start site

2_PromU

203 (0.71%)

1598 (0.71%)

62 (0.98%)

766 (0.56%)

3.78e−03

9.90e−08

8.23e−05

6.42e−02

1.68e−06

1.40e−03

Promoter-associated

Promoter upstream transcription start site

3_PromD1

138 (0.48%)

841 (0.37%)

68 (1.08%)

375 (0.27%)

6.39e−08

7.11e−07

5.56e−19

1.09e−06

1.21e−05

9.46e−18

Promoter-associated

Promoter downstream transcription start site 1

4_PromD2

129 (0.45%)

1195 (0.53%)

31 (0.49%)

300 (0.22%)

1.01e−10

5.71e−49

1.23e−04

1.72e−09

9.71e−48

2.10e−03

Promoter-associated

Promoter downstream transcription start site 2

22_PromP

90 (0.31%)

924 (0.41%)

29 (0.46%)

306 (0.22%)

6.32e−03

1.71e−21

6.99e−04

1.08e−01

2.91e−20

1.19e−02

Promoter-associated

Poised promoter

23_PromBiv

218 (0.76%)

2482 (1.1%)

47 (0.75%)

1227 (0.9%)

2.33e−02

5.59e−09

2.18e−01

3.96e−01

9.51e−08

1.00e + 00

Promoter-associated

Bivalent promoter

10_TxEnh5

299 (1.04%)

2394 (1.06%)

83 (1.32%)

542 (0.4%)

1.08e−36

4.22e−114

8.44e−19

1.83e−35

7.17e−113

1.44e−17

Enhancer-associated

Transcribed 5′preferential and enhancer

11_TxEnh3

417 (1.46%)

2332 (1.03%)

92 (1.46%)

474 (0.35%)

7.80e−92

5.23e−129

5.68e−27

1.33e−90

8.89e−128

9.66e−26

Enhancer-associated

Transcribed 3′preferential and enhancer

12_TxEnhW

171 (0.6%)

840 (0.37%)

21 (0.33%)

259 (0.19%)

5.81e−28

2.28e−23

1.86e−02

9.87e−27

3.87e−22

3.15e−01

enhancer-associated

Transcribed and weak enhancer

13_EnhA1

219 (0.76%)

1165 (0.52%)

111 (1.76%)

365 (0.27%)

4.68e−31

9.22e−31

1.30e−47

7.96e−30

1.57e−29

2.21e−46

Enhancer-associated

Active enhancer 1

14_EnhA2

124 (0.43%)

1554 (0.69%)

54 (0.86%)

388 (0.28%)

8.46e−05

6.00e−64

2.32e−11

1.44e−03

1.02e−62

3.95e−10

Enhancer-associated

Active enhancer 2

15_EnhAF

139 (0.49%)

1421 (0.63%)

30 (0.48%)

434 (0.32%)

3.16e−05

1.78e−39

4.04e−02

5.38e−04

3.02e−38

6.87e−01

enhancer-associated

Active enhancer flank

16_EnhW1

155 (0.54%)

1136 (0.5%)

23 (0.37%)

271 (0.2%)

7.73e−21

9.90e−51

9.47e−03

1.31e−19

1.68e−49

1.61e−01

Enhancer-associated

Weak enhancer 1

17_EnhW2

247 (0.86%)

1963 (0.87%)

26 (0.41%)

580 (0.43%)

8.48e−19

3.79e−58

1.00e + 00

1.44e−17

6.44e−57

1.00e + 00

Enhancer-associated

Weak enhancer 2

18_EnhAc

110 (0.38%)

767 (0.34%)

32 (0.51%)

284 (0.21%)

2.27e−07

3.67e−13

1.43e−05

3.86e−06

6.24e−12

2.43e−04

Enhancer-associated

Primary H3K27ac–possible enhancer

9_TxReg

129 (0.45%)

1274 (0.56%)

21 (0.33%)

807 (0.59%)

3.24e−03

2.97e−01

6.42e−03

5.50e−02

1.00e + 00

1.09e−01

Promoter/enhancer associated

Transcribed and regulatory

19_DNase

110 (0.38%)

948 (0.42%)

38 (0.6%)

404 (0.3%)

1.68e−02

2.31e−09

1.06e−04

2.85e−01

3.93e−08

1.80e−03

Promoter/enhancer associated

Primary DNase

Histone marks

H3K4me3_Pro

3322 (11.6%)

27,570 (12.21%)

775 (12.3%)

7896 (5.79%)

7.20e−242

0.00e + 00

2.25e−79

2.88e−241

0.00e + 00

9.00e−79

Promoter-associated

Histone H3 lysine 4 trimethylation

H3K9ac_Pro

4356 (15.21%)

30,036 (13.3%)

1207 (19.16%)

10,517 (7.71%)

7.45e−313

0.00e + 00

1.21e−175

2.98e−312

0.00e + 00

4.83e−175

Promoter-associated

Histone H3 lysine 9 acetylation

H3K4me1_Enh

3019 (10.54%)

22,816 (10.1%)

794 (12.6%)

5877 (4.31%)

0.00e + 00

0.00e + 00

7.46e−146

0.00e + 00

0.00e + 00

2.98e−145

Enhancer-associated

Histone H3 lysine 4 monomethylation

H3K27ac_Enh

5179 (18.08%)

43,529 (19.27%)

1097 (17.41%)

14,640 (10.73%)

1.83e−241

0.00e + 00

5.42e−54

7.31e−241

0.00e + 00

2.17e−53

Enhancer-associated

Histone H3 lysine 27 acetylation

eQTLs

eQTLs

20,199 (70.53%)

52,029 (23.04%)

5370 (85.22%)

6452 (4.73%)

0.00e + 00

0.00e + 00

0.00e + 00

–

–

–

–

–