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Table 2 EWAS summary statistics in the Discovery, Replication and meta-analyses

From: Altered methylation pattern in EXOC4 is associated with stroke outcome: an epigenome-wide association study

     

Discovery

Replication

Meta-analysis

CpG

CHR

BP

Gene

Feature

COEFF

(UCI,LCI)

P

COEFF

(UCI,LCI)

P

COEFF

(UCI,LCI)

P

Direction

cg00039070

7

133,482,303

EXOC4

Body

− 4.91(− 6.86,− 2.96)

1.14E-06

− 2.58(− 4.62,− 0.54)

1.30E-02

− 5.474(− 5.4738,− 5.4742)

4.44E-08

− −

cg05979619

2

111,947,000

MERTK

Body

− 6.21(− 8.16,− 4.26)

9.72E-10

− 1.26(− 3.24,0.72)

2.15E-01

− 5.250(− 5.2495,− 5.2501)

1.54E-07

− −

cg10977834

4

77,075,687

CCNI

5'UTR

4.85(6.80,2.90)

1.53E-06

1.56(3.55,− 0.43)

1.25E-01

4.875(4.8749,4.8747)

1.11E-06

 +  + 

cg08119231

1

220,747,874

MOSC2

TSS1500

5.01(6.96,3.06)

7.07E-07

0.87(2.83,− 1.09)

3.91E-01

4.871(4.8717,4.8704)

1.11E-06

 +  + 

cg21574204

6

28,081,180

ZNF165

5'UTR

4.72(6.67,2.77)

2.88E-06

1.27(3.24,− 0.70)

2.09E-01

4.847(4.8470,4.8470)

1.21E-06

 +  + 

cg01149259

3

46,979,906

NBEAL2

1stExon

4.68(6.63,2.73)

3.48E-06

1.42(3.41,− 0.57)

1.62E-01

4.768(4.7684,4.7682)

1.86E-06

 +  + 

cg18831371

5

176,610,324

GPRIN1

TSS200

5.35(7.30,3.40)

1.25E-07

0.32(2.17,− 1.53)

7.48E-01

4.752(4.7527,4.7522)

2.02E-06

 +  + 

cg26050512

20

58,981,011

TH1L

TSS1500

4.83(6.78,2.88)

1.71E-06

− 0.09(− 1.93,1.75)

9.30E-01

4.563(4.5626,4.5624)

4.83E-06

− + 

cg21404878

15

72,286,264

BRUNOL6

3'UTR

4.94(6.43,2.51)

1.03E-06

0.02(2.19,− 2.15)

6.69E-01

4.540(4.5407,4.5393)

5.61E-06

 +  + 

cg09548897

16

291,277

AXIN1

Body

− 4.69(− 6.64,− 2.74)

3.37E-06

− 0.73(− 2.67,1.21)

4.69E-01

− 4.499(− 4.4986,− 4.4989)

6.80E-06

− −

cg14659930

3

114,409,454

ZBTB20

5'UTR

4.59(6.48,2.58)

5.24E-06

0.19(2.08,− 1.70)

3.78E-01

4.453(4.4544,4.4511)

8.48E-06

 +  + 

cg00939347

10

606,320

DIP2C

Body

− 5.32(− 7.27,-3.37)

1.45E-07

− 0.5(− 2.42,1.42)

6.22E-01

− 4.450(− 4.4501,− 4.4506)

8.50E-06

− −

cg07925823

16

68,264,601

SLC7A6

5'UTR

4.76(6.71,2.81)

2.43E-06

1.4(3.39,− 0.59)

1.68E-01

4.443(4.4430,4.4428)

8.81E-06

 +  + 

cg20383948

21

45,478,223

COL18A1

Body

5.17(7.12,3.22)

3.15E-07

0.97(2.93,− 0.99)

3.38E-01

4.431(4.4307,4.4305)

9.28E-06

 +  + 

cg09741713

12

62,078,134

FAM19A2

5'UTR

4.66(6.63,2.73)

3.82E-06

− 1.12(− 3.08,0.84)

5.20E-01

4.340(4.3408,4.3393)

1.42E-05

 +  + 

cg12103149

6

30,213,396

TRIM26

TSS200

4.56(6.58,2.68)

6.06E-06

0.08(1.98,− 1.82)

3.79E-01

4.331(4.3312,4.3311)

1.45E-05

 +  + 

cg10156941

17

1,563,002

PITPNA

TSS200

4.67(6.62,2.72)

3.63E-06

0.12(1.90,− 1.66)

9.03E-01

4.349(4.3489,4.3488)

1.46E-05

 +  + 

cg15765398

21

44,990,079

 

IGR

− 5.27(6.51,2.61)

1.92E-07

0.89(2.85,− 1.07)

1.60E-01

− 4.328(− 4.3267,− 4.3288)

1.51E-05

 + -

cg12349416

11

4,184,868

 

IGR

4.58(6.89,2.99)

5.73E-06

0.43(2.32,− 1.46)

4.84E-01

4.321(4.3219,4.3207)

1.55E-05

 +  + 

cg14482313

12

52,233,105

KRT7

TSS200

4.60(6.55,2.65)

5.19E-06

0.62(2.55,− 1.31)

5.40E-01

4.304(4.3047,4.3037)

1.68E-05

 +  + 

cg02996131

6

152,637,463

SYNE1

TSS1500

4.60(6.61,2.71)

5.08E-06

0.65(2.58,− 1.28)

8.63E-01

4.252(4.2532,4.2516)

2.11E-05

 +  + 

cg19935850

4

41,751,422

 

IGR

4.99(6.94,3.04)

7.94E-07

− 0.14(− 1.91,1.63)

8.86E-01

4.182(4.1825,4.1808)

2.90E-05

− + 

cg10363284

4

8,005,411

ABLIM2

Body

− 5.54(-7.49,−  3.59)

4.55E-08

0.29(2.18,− 1.60)

7.76E-01

− 4.179(− 4.1782,− 4.1790)

2.94E-05

 + −

cg18707780

15

99,733,585

LYSMD4

TSS200

4.46(6.41,2.51)

9.75E-06

− 0.41(− 2.31,1.49)

6.85E-01

4.154(4.1539,4.1538)

3.42E-05

− + 

cg20648899

6

93,416,423

EPHA7

Body

4.53(6.60,2.70)

7.17E-06

− 0.2(− 2.03,1.63)

8.54E-01

4.007(4.0083,4.0057)

6.14E-05

 +  + 

cg07987148

20

46,690,251

TP53RK

TSS1500

4.54(6.56,2.66)

6.79E-06

− 0.41(− 2.28,1.46)

9.89E-01

3.980(3.9813,3.9790)

6.88E-05

- + 

cg07475390

1

14,114,109

 

IGR

4.68(6.53,2.63)

3.52E-06

0.7(2.62,− 1.22)

2.67E-01

3.959(3.9593,3.9580)

7.55E-05

- + 

cg00347584

11

47,261,474

NR1H3

Body

4.47(6.47,2.57)

9.50E-06

− 1.26(− 3.24,0.72)

9.87E-01

3.909(3.9098,3.9081)

9.27E-05

 +  + 

cg13114315

21

36,174,169

DOPEY2

Body

4.48(6.43,2.53)

8.92E-06

0.49(2.41,− 1.43)

6.30E-01

3.843(3.8438,3.8418)

1.22E-04

 +  + 

cg14414100

9

19,547,532

SLC24A2

Body

4.63(6.59,2.69)

4.55E-06

− 0.56(− 2.46,1.34)

9.40E-01

3.772(3.7733,3.7717)

1.62E-04

 +  + 

cg18795809

4

10,456,907

ZNF518B

5'UTR

4.68(6.63,2.73)

3.58E-06

0.34(2.22,− 1.54)

7.36E-01

3.771(3.7708,3.7703)

1.64E-04

 +  + 

cg03732020

11

47,261,417

NR1H3

Body

4.64(6.49,2.59)

4.35E-06

− 0.01(− 1.29,1.27)

5.76E-01

3.551(3.5523,3.5506)

3.83E-04

− + 

cg24978805

7

3,687,557

SDK1

Body

− 4.84(− 6.79,− 2.89)

1.67E-06

− 0.35(− 2.24,1.54)

7.30E-01

− 3.184(− 3.1840,− 3.1845)

1.45E-03

− −

cg08526825

16

2,752,228

SRRM2

TSS200

4.65(− 7.22,− 3.32)

4.13E-06

1.43(3.42,-0.56)

8.41E-01

3.051(3.0506,3.0504)

2.28E-03

− + 

cg25354926

4

818,823

CPLX1

Body

− 4.49(− 6.44,− 2.54)

8.52E-06

0.95(2.91,− 1.01)

3.47E-01

− 2.784(− 2.7840,− 2.7844)

5.37E-03

 +−

cg04886221

1

27,343,238

SYTL1

5'UTR

4.61(6.55,2.65)

4.97E-06

0.17(1.97,− 1.63)

6.80E-01

2.532(2.5320,2.5319)

1.14E-02

− + 

cg22363670

7

86,643,853

GRM3

TSS200

4.49(6.44,2.54)

8.55E-06

− 0.3(− 2.16,1.56)

7.65E-01

2.409(2.4095,2.4092)

1.59E-02

- + 

cg06933752

11

65,122,316

FAU

TSS200

5.08(7.03,3.13)

4.90E-07

− 0.06(− 1.80,1.68)

9.51E-01

2.199(2.1995,2.1994)

2.80E-02

− + 

cg04311230

6

159,693,649

SOD2

TSS1500

4.52(6.68,2.78)

7.40E-06

cg04349420

8

48,501,719

 

IGR

4.73(6.66,2.76)

2.79E-06

cg07797073

1

2,051,352

PRKCZ

Body

4.71(− 6.61,− 2.71)

3.02E-06

cg11491381

20

3,082,857

AVP

Body

− 4.66(6.55,2.65)

3.85E-06

cg18862005

2

177,076,135

 

IGR

4.60(6.56,2.66)

5.10E-06

cg25794823

18

63,949,347

HMSD

TSS200

4.61(− 8.16,− 4.26)

4.90E-06

  1. Summary statistics for the 44 CpG sites with nominal association (p value < 10–6) in the Discovery Analysis. Significant CpG sites in the meta-analysis are written in bold letters in the CpG site and p value columns. Numbers in italics in the p value column for the meta-analysis indicate CpG sites with more significant p values in the meta-analysis compared with the Discovery Analysis
  2. CpG: CpG site ID; CHR: chromosome where the CpG site is located; BP: specific chromosomal position for the CpG site; Gene: Gene annotation (from the Illumina Manifest File); Feature: Genomic location of the CpG site. It could reside in the 5’ untranslated region (UTR), between 0 and 200 nucleotides from the transcription start site (TSS), TSS200, or between 200 and 1500 nucleotides from the TSS, TSS1500. It could be also located in the body of the gene, in the 3’UTR or in an intergenic region (IGR); COEFF (UCI,LCI): Effect size for the association of the CpG site with the ∆NIHSS, with information for the upper (UCI) and lower (LCI) 95% confidence intervals; P: p value for the association of the CpG site with the ∆NIHSS
  3. In bold are the significant CpG sites in the meta-analysis