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Table 3 The top ten genes identified in the SMR analysis of CCT in participants of East Asian 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_1754858

PASK

2

rs16843242

7.23 × 10− 116

6.20 × 10− 5

2.865

0.726

7.98 × 10− 5

3.73 × 10− 1

0.400

ILMN_1667022

PASK

2

rs16843242

1.61 × 10− 102

6.20 × 10−5

3.056

0.776

8.24 × 10− 5

3.90 × 10−1

0.400

ILMN_1670870

ALCAM

3

rs9810954

2.67 × 10−54

6.92 × 10− 5

−5.006

1.299

1.16 × 10−4

4.93 × 10−1

0.400

ILMN_1777906

MAP 7D1

1

rs11263861

3.51 × 10−109

1.05 × 10− 4

−3.348

0.876

1.33 × 10−4

2.01 × 10−5

0.400

ILMN_1778104

ACADM

1

rs2133134

7.36 × 10−72

1.85 × 10−4

6.341

1.733

2.52 × 10−4

1.15 × 10−3

0.575

ILMN_1765578

TIPARP

3

rs344050

1.98 × 10−9

6.46 × 10−6

10.924

3.030

3.12 × 10− 4

3.42 × 10−2

0.575

ILMN_1654065

ATOH8

2

rs10187314

6.31 × 10−93

3.22 × 10−4

3.393

0.958

3.97 × 10−4

1.95 × 10− 1

0.575

ILMN_1696713

POLA2

11

rs487989

1.06 × 10−30

2.03 × 10−4

6.068

1.716

4.07 × 10− 4

1.68 × 10− 3

0.575

ILMN_1703229

HIATL1

9

rs56987829

8.47 × 10−26

1.86 × 10−4

4.510

1.281

4.30 × 10−4

4.26 × 10−2

0.575

ILMN_1737964

HIATL1

9

rs117447155

2.16 × 10−128

5.12 × 10−4

1.601

0.465

5.84 × 10−4

7.80 × 10−3

0.634

GTEx

ENSG00000273142.1

RP11-458F8.4

7

rs4718424

3.54 × 10−25

1.89 × 10−6

5.550

1.282

1.50 × 10−4

2.50 × 10−2

0.103

ENSG00000226824.2

RP4-756H11.3

7

rs6979488

3.99 × 10−30

2.67 × 10−5

3.156

0.801

8.11 × 10−4

3.92 × 10− 4

0.280

ENSG00000116871.11

MAP 7D1

1

rs11263861

3.60 × 10−36

1.05 × 10−4

−7.011

1.892

2.11 × 10−4

4.71 × 10−3

0.484

ENSG00000148110.11

HIATL1

9

rs56074891

3.46 × 10−33

1.95 × 10−4

4.615

1.297

3.73 × 10−4

3.17 × 10−2

0.644

ENSG00000241258.2

CRCP

7

rs1643388

1.34 × 10−34

2.99 × 10−4

−4.654

1.342

5.24 × 10−4

1.81 × 10−10

0.723

ENSG00000238268.2

RP11-229P13.19

9

rs3814499

4.82 × 10−36

4.58 × 10−4

4.691

1.390

7.38 × 10−4

1.65 × 10−1

0.849

ENSG00000014138.4

POLA2

11

rs1858783

3.68 × 10−14

2.52 × 10−4

7.358

2.233

9.82 × 10−4

6.70 × 10−4

0.941

ENSG00000203363.2

AC012454.4

2

rs1561285

1.15 × 10−19

5.29 × 10−4

3.674

1.135

1.21 × 10−3

8.10 × 10−1

0.941

ENSG00000117054.9

ACADM

1

rs61799967

1.32 × 10−12

3.69 × 10−4

14.740

4.631

1.46 × 10−3

4.90 × 10− 3

0.941

ENSG00000168528.7

SERINC2

1

rs7541464

4.49 × 10−25

8.34 × 10−4

3.282

1.032

1.48 × 10−3

7.00 × 10− 2

0.941

  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. 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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