Table 3.
The top ten genes identified in the SMR analysis of CCT in participants of East Asian ancestry
| 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 |
*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
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
FDR was calculated at P = 10− 3 threshold
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