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Table 1 CpGs in vitamin D-related genes with statistically significant (p < 0.05) associations with 25(OH)D; Sister Study subcohort (n = 1270)

From: Vitamin D, DNA methylation, and breast cancer

Rank

CpG

Gene / location type

Chromosome: position

Mean methylation level (SD)

Association with 25(OH)Da

β

p value

1

cg21201924

RXRA / body

9: 137251825

0.76 (0.042)

−0.020

0.0004

2

cg02127980

RXRA / body

9: 137252116

0.40 (0.067)

−0.015

0.0004

3

cg17559402b

NADSYN1 / body

11: 71187890

0.97 (0.006)

−0.017

0.003

4

cg02059519

RXRA / body

9: 137250935

0.83 (0.026)

−0.012

0.003

5

cg09997530

GC / body

4: 72636217

0.91 (0.017)

0.015

0.005

6

cg04329455b

RXRA

9: 137215364

0.96 (0.008)

0.014

0.007

7

cg00268518b

NADSYN1 / TSS200

11: 71164106

0.01 (0.001)

0.011

0.008

8

cg03146219

NADSYN1 / body

11: 71189514

0.47 (0.097)

−0.012

0.009

9

cg13510651b

RXRA / body

9: 137227772

0.94 (0.008)

−0.010

0.01

10

cg03490288b

DHCR7 / body

11: 71146658

0.97 (0.006)

0.015

0.01

11

cg05785753

NADSYN1 / body

11: 71189490

0.59 (0.074)

−0.010

0.01

12

cg13687497

RXRA / body

9: 137249839

0.80 (0.023)

−0.010

0.01

13

cg07793224b

NADSYN1 / body

11: 71183180

0.97 (0.008)

0.017

0.02

14

cg26044621b

DHCR7 / 3´ UTR

11: 71145665

0.94 (0.011)

0.012

002

15

cg04837494

GC / 3´ UTR

4: 72608149

0.85 (0.033)

0.013

0.03

16

cg14236758

RXRA / body

9: 137252129

0.48 (0.066)

−0.009

0.03

17

cg04774822

NADSYN1 / body

11: 71165839

0.78 (0.033)

−0.009

0.03

18

cg16151558b

DHCR7 / TSS1500

11: 71159853

0.02 (0.066)

0.013

0.04

19

cg20372759b

CYP27B1 / TSS1500

12: 58162287

0.97 (0.006)

−0.010

0.04

20

cg24806812

GC / body

4: 72635202

0.93 (0.018)

0.012

0.04

21

cg14154547b

RXRA / body

9: 137293309

0.92 (0.010)

−0.007

0.04

22

cg07099121b

DHCR7 / 3´ UTR

11: 71146096

0.98 (0.004)

−0.010

004

23

cg16910670b

NADSYN1

11: 71215361

0.97 (0.005)

−0.011

0.05

  1. TSS200 within 200 basepairs upstream of the transcription start site, TSS1500 within 1500 basepairs upstream of the transcription start site, UTR untranslated region
  2. aEstimated change in methylation (logit(β)) per 10 ng/mL change in serum 25-hydroxyvitamin D (25(OH)D)
  3. bIntraclass correlation coefficient < 0.5