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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