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Table 2 Significant genes showing pleiotropic association with CCT in participants of European ancestry

From: Mendelian randomization analysis identified genes pleiotropically associated with central corneal thickness

eQTL data

Gene ID

Gene

CHR

Top SNP

PeQTL

PGWAS

Beta

SE

PSMR

PHEIDI

Q value

CAGE

ILMN_1796423

CLIC3

9

rs908839

8.48 × 10−75

6.88 × 10−14

6.171

0.890

4.15 × 10−12

2.59 × 10− 1

6.79 × 10−8

ILMN_1664464

PTGDS

9

rs885070

7.83 × 10−33

3.43 × 10−11

8.474

1.463

6.88 × 10−9

9.97 × 10−4

4.41 × 10−5

ILMN_1761138

C9orf142

9

rs4542025

1.08 × 10−21

4.93 × 10− 13

11.896

2.063

8.09 × 10−9

1.02 × 10− 2

4.41 × 10− 5

ILMN_2198408

MFF

2

rs7560053

~ 0

1.37 × 10−7

−1.834

0.351

1.71 × 10− 7

2.36 × 10−3

6.99 × 10− 4

ILMN_1714108

TP53INP1

8

rs896853

2.29 × 10−33

4.09 × 10− 8

−6.119

1.226

5.96 × 10− 7

1.42 × 10−1

1.95 × 10−3

ILMN_1802894

VKORC1L1

7

rs2460421

4.93 × 10−46

3.57 × 10− 7

− 5.016

1.046

1.64 × 10−6

6.08 × 10− 5

4.46 × 10−3

ILMN_1766859

MSL2

3

rs13433683

2.00 × 10−44

1.17 × 10−6

4.751

1.035

4.40 × 10−6

1.97 × 10− 1

0.010

ILMN_1781560

ST3GAL6

3

rs2439225

1.80 × 10−58

2.04 × 10−6

4.043

0.887

5.23 × 10−6

1.83 × 10−2

0.011

ILMN_1716651

RUNX2

6

rs1200428

8.94 × 10−170

5.21 × 10−6

2.142

0.476

6.92 × 10−6

1.87 × 10−1

0.013

ILMN_1680171

MFF

2

rs7572491

3.84 × 10−16

1.47 × 10−7

−9.712

2.199

1.00 × 10−5

3.13 × 10−1

0.016

ILMN_1785635

BRD3

9

rs457420

5.98 × 10−47

4.23 × 10−6

−4.571

1.043

1.18 × 10−5

8.29 × 10−3

0.018

ILMN_2188204

ATG12

5

rs6872406

4.42 × 10−61

8.61 × 10− 6

3.638

0.847

1.74 × 10−5

8.65 × 10−2

0.024

GTEx

ENSG00000273142.1

RP11-458F8.4

7

rs4718424

3.54 × 10−25

2.02 × 10−12

6.017

1.034

5.89 × 10−9

3.58 × 10−3

5.76 × 10−5

ENSG00000214402.6

LCNL1

9

rs11145951

1.84 × 10−13

9.02 × 10− 16

10.562

1.946

5.67 × 10−8

4.65 × 10−1

2.77 × 10−4

ENSG00000107317.7

PTGDS

9

rs868102

8.79 × 10−20

2.18 × 10−10

9.142

1.756

1.92 × 10−7

8.55 × 10−2

6.24 × 10−4

ENSG00000226824.2

RP4-756H11.3

7

rs6979488

3.99 × 10−30

4.92 × 10−8

2.943

0.598

8.66 × 10−7

9.24 × 10−5

0.002

ENSG00000170175.6

CHRNB1

17

rs12600861

3.47 × 10−17

9.03 × 10−7

4.382

1.033

2.20 × 10−5

1.89 × 10−1

0.037

ENSG00000164938.9

TP53INP1

8

rs2340586

1.17 × 10−10

1.95 × 10−8

− 19.873

4.694

2.30 × 10−5

6.53 × 10− 1

0.037

  1. *The GWAS summarized data were provided by the study of Iglesias et al. and can be downloaded at https://datashare.is.ed.ac.uk/handle/10283/2976. The CAGE and GTEx eQTL data can be downloaded at https://cnsgenomics.com/data/SMR/#eQTLsummarydata
  2. PeQTL is the P-value of the top associated cis-eQTL in the eQTL analysis, and PGWAS is the P-value for the top associated cis-eQTL in the GWAS analysis. Beta is the estimated effect size in SMR analysis, SE is the corresponding standard error, PSMR is the P-value for SMR analysis and PHEIDI is the P-value for the HEIDI test.
  3. FDR was calculated at P = 10− 3 threshold
  4. Bold font means statistical significance after correction for multiple testing using FDR
  5. CAGE Consortium for the Architecture of Gene Expression, CCT central corneal thickness, CHR chromosome, eQTL expression quantitative trait loci, GTEx Genotype-Tissue Expression, HEIDI heterogeneity in dependent instruments, SNP single-nucleotide polymorphism, SMR summary data-based Mendelian randomization, FDR false discovery rate, GWAS genome-wide association studies
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BMC Genomics

ISSN: 1471-2164

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