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Table 2 CpGs associated with CPO compared to CLO in the single-site EWAS analysis after filtering out age-related CpGs

From: Distinct DNA methylation profiles in subtypes of orofacial cleft

Chr

CpG

Regression coefficient

P value

Gene

Relation to CpG island

Relation to gene

19

cg01634146

0.19

9.80 × 10−13

NFIX

S_Shelf

Body

22

cg12899065

0.16

3.98 × 10−8

GP1BB;SEPT5

Island

TSS1500;3′UTR

6

cg14623715

0.14

2.46 × 10−10

PDE7B

 

Body

10

cg02017450

−0.14

5.93 × 10−11

intergenic [SFTA1P]

  

8

cg04364695

−0.13

4.27 × 10−8

ZMAT4

 

Body

7

cg22114489

−0.13

4.60 × 10−8

intergenic [CUX2]

  

1

cg12697139

−0.13

2.23 × 10−11

intergenic [MIR205HG]

  

2

cg19075787

−0.13

8.44 × 10−9

intergenic [LOC284998]

  

11

cg17696044

−0.13

8.61 × 10−8

SHANK2

 

Body

20

cg19592472

−0.12

5.04 × 10−8

OXT

Island

1stExon;5′UTR

4

cg14348967

−0.12

5.12 × 10−9

intergenic [DQ599898]

  

6

cg00257775

−0.12

9.45 × 10−10

ZFAND3

 

Body

3

cg25938530

−0.11

2.04 × 10−8

ITIH1

 

TSS200;Body

11

cg12155547

−0.11

9.96 × 10−12

intergenic [NEAT1]

S_Shelf

 

1

cg18147098

0.11

5.44 × 10−8

intergenic [ATF3]

S_Shore

 

8

cg19496364

0.10

1.16 × 10−8

intergenic [LINC00535]

  

7

cg27508620

0.10

3.67 × 10−8

intergenic [SP4]

  

6

cg25426302

0.10

9.90 × 10−8

PPT2;PRRT1

N_Shore

TSS1500

10

cg20327845

−0.10

6.66 × 10−8

PFKP

 

Body

3

cg05581878

−0.10

2.50 × 10−9

intergenic [AK097161]

  

10

cg19220719

−0.10

7.02 × 10−9

intergenic [C10orf11]

  

22

cg13251842

0.09

6.67 × 10−8

MIRLET7A3;MIRLET7B

 

TSS200; TSS1500

19

cg27392771

0.09

5.25 × 10−15

NFIX

S_Shore

Body

6

cg23279756

−0.09

7.14 × 10−8

intergenic [ARMC2]

  

2

cg07644939

0.09

3.12 × 10−10

SNED1

S_Shore

Body

  1. The top 25 CpGs with the largest effect sizes and P values <1 × 10−7 are shown. For intergenic regions, the closest annotated gene is shown in square brackets
  2. S_Shore South shore, S_Shelf South shelf, N_Shore North shore, TSS1500 1500 base pairs from a transcription start site; TSS200 200 base pairs from a transcription start site, UTR untranslated region