Table 3 CCT-associated variants from the conditional and joint analysis of the meta-analysis of European studies and replication in Asians

From: Cross-ancestry genome-wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

SNP

Chr:bp

Nearest gene

Annotation

Previously reported SNP (ref)a

A1/A2

Meta-analysis in Europeans

CoJo analysis in Europeans

Meta-analysis in Asians

A1F

β (SE)

P

A1F

β (SE)

P COJO

LD_r

A1F

β (SE)

P

rs1309531

5:64306311

CWC27

Intronic

 

a/t

0.55

−2.4 (0.379)

2.439E-10

0.56

−2.096 (0.383)

4.28E-08

0.130

0.63

−1.184 (0.547)

3.03E-02

rs10064391

5:64686659

ADAMTS6

Intronic

rs230712117

a/g

0.63

−2.765 (0.397)

3.182E-12

0.62

−2.484 (0.4)

5.53E-10

0.000

0.70

−0.889 (0.601)

1.39E-01

rs1931656

6:82610188

148 kb 5’ of FAM46A

Intronic

 

a/t

0.45

2.172 (0.391)

2.749E-08

0.45

2.383 (0.393)

1.31E-09

−0.104

0.47

2.965 (0.529)

2.13E-08

rs9361886

6:82778502

101 kb 3’ of IBTK

Intergenic

rs153813817

t/c

0.54

2.391 (0.445)

7.665E-08

0.56

2.637 (0.447)

3.66E-09

0.000

0.57

2.35 (0.66)

3.67E-04

rs3094339

9:136884738

VAV2-BRD3

Intergenic

 

a/g

0.71

−2.804 (0.426)

4.682E-11

0.72

−3.042 (0.427)

1.01E-12

−0.008

0.53

0.671 (0.559)

2.30E-01

rs4841899

9:137424412

92 kb 3’ of RXRA

Intergenic

rs4842044, rs153647866,67

t/c

0.67

−2.993 (0.405)

1.413E-13

0.67

−2.289 (0.416)

3.60E-08

−0.037

0.63

−2.383 (0.596)

6.32E-05

rs1536482

9:137440528

93 kb 5’ of COL5A1

Intergenic

rs3132306, rs3118516, rs311852017,68

g/a

0.66

4.569 (0.399)

1.95E-30

0.66

3.455 (0.425)

4.60E-16

0.388

0.68

2.864 (0.601)

1.85E-06

rs3132303

9:137444298

89 kb 5’ of COL5A1

Intergenic

 

c/g

0.26

5.236 (0.497)

6.11E-26

0.26

3.55 (0.544)

6.86E-11

−0.039

0.26

5.912 (0.714)

1.21E-16

rs7032489

9:137559775

COL5A1

Intronic

rs704452917

c/g

0.86

4.033 (0.547)

1.637E-13

0.86

4.296 (0.548)

4.64E-15

−0.008

0.81

1.845 (0.685)

7.08E-03

rs116878472

12:104210992

NT5DC3

Intronic

 

t/c

0.97

−8.392 (1.506)

2.523E-08

0.97

−8.829 (1.509)

4.95E-09

−0.058

NA

NA

NA

rs11111869

12:104402485

GLT8D2

Intronic

rs156489217

g/a

0.83

−3.174 (0.51)

4.77E-10

0.83

−3.308 (0.511)

9.40E-11

0.000

0.78

−3.479 (0.636)

4.38E-08

rs2034809

15:101555399

LRRK1

Intronic

rs4965359

g/a

0.51

1.844 (0.4)

4.047E-06

0.51

2.545 (0.407)

3.82E-10

−0.177

0.34

2.161 (0.579)

1.88E-04

rs930847

15:101558562

LRRK1

Intronic

rs93084717

g/t

0.23

3.573 (0.453)

3.194E-15

0.22

3.955 (0.461)

9.17E-18

−0.042

0.27

3.793 (0.617)

7.82E-10

rs752092

15:101781934

CHSY1

Intronic

 

a/g

0.66

−2.205 (0.396)

2.554E-08

0.67

−2.19 (0.397)

3.46E-08

0.000

0.79

−1.745 (0.652)

7.40E-03

rs35193497

16:88324821

169 kb 5’ of ZNF469

Intergenic

rs654022317

t/g

0.36

−6.238 (0.434)

8.637E-47

0.34

−4.654 (0.495)

4.90E-21

0.653

0.29

−4.928 (0.622)

2.34E-15

rs28687756

16:88328928

165 kb 5’ of ZNF469

Intergenic

 

t/g

0.57

−7.507 (0.584)

8.418E-38

0.53

−4.566 (0.667)

7.84E-12

0.000

NA

NA

NA

  1. Results from the conditional and joint analysis, genotype data from BMES cohort was used (N = 2582)
  2. Nearest gene, (reference NCBI build37) is given as locus label, but this should not be interpreted as providing support that the nearest gene is the best candidate, a list including all the genes +/− 200 kb of the lead SNP is presented in Supplementary Table 12
  3. SNP rsID, Chr:bp chromosome: base pair, A1 risk allele, A2 other allele, A1F frequency of allele A1, β effect size on CCT based on allele A1, SE standard error of the effect size, i insertion, d deletion, r reference, PCOJO = P-value after CoJo analyses
  4. aSNPs in LD (r2 > 0.5) with SNP from CoJo analyses. In bold novel independent CCT-associated SNPs
Back to article page