Table 1 Genome-wide significant lead variants for the non-IOP-dependent component of POAG

From: GWAS-by-subtraction reveals an IOP-independent component of primary open angle glaucoma

SNP

CHR

POS

MAF

A1

A2

non-IOP-dependent component of POAG

Nearest gene

Previously associated with:

Validation

BETA

SE

P

NTG

IOP

POAG++

rs2790049

1

165743523

0.14

A

G

0.34

0.04

1.42E−21

TMCO1

3.57E−09+

2.16E−42#

1.16E−62

2.05E−23

rs113894504

2

112633092

0.23

C

G

−0.16

0.03

1.99E−08

ANAPC1

NA

5.17E−30#

0.19

3.60E−07

rs13064817

3

85166315

0.37

G

T

0.14

0.03

2.88E−08

CADM2

NA

2.20E−08^

2.88E−14

4.61E−10

rs6845653

4

7899379

0.33

C

T

0.19

0.03

2.63E−13

AFAP1

6.77E−14*

7.04E−22#

7.28E−40

2.25E−15

rs12208086

6

36586070

0.25

G

A

−0.2

0.03

2.17E−11

MIR3925

NA

0.17#

9.74E−13

7.15E−10

rs2771011

6

51477823

0.12

A

T

−0.23

0.04

2.67E−08

RP3-335N17.2;PKH1D

NA

4.26E−10#

5.33E−22

2.80E−11

rs7803764

7

19783351

0.32

G

C

−0.15

0.03

2.92E−08

TMEM196

NA

8.30E−04#

4.63E−07

6.56E−05

rs13298881

9

22012051

0.12

T

C

−0.22

0.04

2.89E−08

RP11-145E5.5:CDKN2B-AS1

3.64E−49±

0.88#

3.01E−09

7.77E−08

rs10217269

9

22016173

0.07

C

T

−0.36

0.06

1.09E−08

RP11-145E5.5:CDKN2B-AS1

3.64E−49±

0.76#

5.61E−09

4.71E−12

rs6475604

9

22052734

0.42

T

C

−0.47

0.03

9.78E−75

CDKN2B-AS1

3.64E−49+

0.31#

1.00E−91

6.87E−62

rs2472494

9

107695539

0.42

T

C

0.22

0.03

7.12E−18

ABCA1-SLC44A1

4.07E−13+

1.32E−29#

2.10E−48

1.66E−20

rs10740731

10

60348886

0.49

G

A

0.16

0.03

5.07E−10

BICC1

1.13E−08*

0.21#

6.79E−16

4.38E−08

rs2667477

12

84023388

0.42

T

C

−0.18

0.03

4.46E−13

TMTC2

6.32E−09*

0.64#

5.10E−16

2.78E−10

rs34935520

14

61091401

0.41

G

A

0.28

0.03

1.12E-27

RPL37P5 - SIX1

1.00E−24+

0.13#

7.16E−39

1.60E−29

rs6117318

20

6507717

0.42

G

A

0.15

0.03

2.58E−09

CASC20

1.75E−14*

0.59#

5.74E−11

1.74E−07

rs7275118

20

18010447

0.34

T

G

0.16

0.03

3.16E−09

OVOL2

NA

0.046#

2.26E−08

2.55E−05

rs737854

22

19860875

0.23

A

G

−0.18

0.03

4.34E−08

TXNRD2

NA

0.014#

5.53E−12

2.33E−08

  1. Beta coefficients correspond to the log odds increased risk of the outcome trait per copy of the A1 allele. Chromosome (CHR) and base pair positions (POS) are reported for human genome build 37. A1 is the effect allele. MAF is the minor allele frequency. Estimates (BETA) correspond to the beta coefficient for the non-IOP-dependent component of POAG in Fig. 1, see “Methods”. P is the two-sided p-value from the GWAS-by-Subtraction analysis. The NTG, IOP and POAG columns show the P-value of lead SNPs or those in high LD (r2 > 0.8) from:
  2. +NTG case and control GWAS reported by Choquet et al.7 or Gharahkhani et al.10 (± represent P value of SNPs located in NTG gene CDKN2B-AS1).
  3. *Multi-ethnic GWAS meta-analysis of NTG by Torres et al.25.
  4. #GWAS of IOPcc reported in this study or ^GWAS of IOP reported by Gao et al.26.
  5. ++GWAS of POAG reported in this study or by Gharahkhani et al.10.
  6. Validation corresponds the smallest P value among the three validation cohorts.
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