Table 2 Results of the hypospadias case–control and case-only epigenome-wide association studies (EWAS) and two-stage least squares Mendelian randomization (2SLS MR) using methylation quantitative trait loci as instrumental variables for causal association of the CpG with hypospadias characteristics.

From: Altered mechanisms of genital development identified through integration of DNA methylation and genomic measures in hypospadias

EWAS

CpG

Chr

Pos

UCSC Gene

Casea mean beta

Comparisonb mean beta

Delta beta

EWAS P-value

EWAS FDR Q-value

n meQTLs

2SLS MR P-value

Hypospadias

cg04714159

1

47,301,259

CYP4B1-CYP4Z2P

0.875

0.913

0.038

9.3E−07

0.109

13

3.9E−06

cg14436889

1

108,231,706

VAV3

0.591

0.748

0.157

5.4E−07

0.109

4

9.8E−15

cg26143053

2

3,718,125

ALLC

0.905

0.927

0.023

7.5E−07

0.109

12

0.003

cg03368481

2

76,014,479

EVA1A-MRPL19-GCFC2

0.773

0.847

0.074

8.8E−07

0.109

12

0.191

cg25918138

3

38,408,147

XYLB

0.926

0.944

0.018

1.3E−06

0.132

12

0.001

cg14906547

9

33,908,335

UBE2R2

0.920

0.944

0.025

7.4E−07

0.109

13

8.8E−06

cg25196688

12

3,421,025

TSPAN9-PRMT8-EFCAB4B

0.392

0.506

0.114

1.7E−07

0.109

13

5.5E−10

cg00752630

12

125,591,239

AACS

0.884

0.920

0.037

2.1E−06

0.175

11

0.159

cg08539758

17

57,638,482

YPEL2-DHX40-PTRH2

0.732

0.701

− 0.031

6.0E−07

0.109

5

1.7E−05

cg26638975

19

51,876,721

NKG7

0.780

0.754

− 0.026

2.1E−06

0.175

8

0.025

Chordee

cg07999371

1

26,847,004

DHDDS-HMGN2-RPS6KA1

0.558

0.576

0.018

8.5E−07

0.148

20

0.093

cg05045951

2

70,485,377

PCYOX1

0.024

0.021

− 0.003

1.6E−06

0.148

10

5.2E−04

cg15945209

2

133,039,143

ANKRD30BL-GPR39

0.575

0.544

-0.031

5.5E-07

0.148

21

1.3E-07

cg24241688

3

13,036,636

IQSEC1

0.097

0.085

− 0.012

3.3E-07

0.135

15

0.004

cg06484075

4

184,393,241

CDKN2AIP-ING2

0.552

0.592

0.040

1.4E−06

0.148

12

0.011

cg19445285

12

32,480,897

BICD1

0.907

0.886

− 0.020

1.6E-06

0.148

4

1.2E-08

cg07509211

14

54,950,145

GMFB

0.745

0.708

− 0.038

1.4E−07

0.114

2

1.3E−05

cg16752029

16

27,214,750

JMJD5 (currently KMD8)

0.039

0.043

0.004

1.2E−06

0.148

4

0.041

cg15014976

19

52,101,661

SIGLEC6-ZNF175

0.875

0.862

− 0.013

1.4E−06

0.148

3

0.002

Degree

cg15231374

1

160,132,381

ATP1A4

0.663

0.684

0.022

7.0E−07

0.119

13

0.079

cg22788109

1

225,867,346

ENAH-SRP9

0.814

0.747

− 0.067

8.9E−08

0.041

23

6.3E−10

cg21454600

3

18,772,063

SATB1-KCNH8

0.875

0.894

0.020

9.4E−07

0.128

7

3.8E−04

cg15242360

6

39,854,530

DAAM2

0.841

0.872

0.031

7.3E−07

0.119

5

1.0E−04

cg01749436

8

9,756,178

TNKS-MSRA

0.056

0.039

− 0.017

4.2E−07

0.114

14

0.001

cg10817615

11

45,687,277

CHST1

0.523

0.461

− 0.062

1.0E−07

0.041

5

1.9E−09

  1. 2SLS MR two-stage least squares Mendelian randomization; Chr chromosome; CpG cytosine-guanine dinucleotide; EWAS epigenome-wide association study; FDR false discovery rate; meQTLs methylation quantitative trait loci; Pos genomic position in build 37.
  2. aThe case groups are: 45 hypospadias cases for the hypospadias case–control study, 21 hypospadias cases with chordee for the chordee case-only study, and 9 severe hypospadias cases for the degree case-only study.
  3. bThe comparison groups are: 46 boys without hypospadias for the hypospadias case–control study, 24 hypospadias cases without chordee for the chordee case-only study, and 36 moderate hypospadias cases for the degree case-only study.
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