Table 2.
Top 10 most significant cis-eQTL found in the SMR analyses (P-value ≤ 0.05) using GWAS data from a case–control study where cows with multifocal lesions (N = 33) and without lesions (N = 373) were compared
| Sample | Chr | Position | Gene ID | Gene symbol | SNP ID | SNP effect | P-value | FDR |
|---|---|---|---|---|---|---|---|---|
| ICV | 23 | 27,146,264 | ENSBTAG00000049699 | U6 | rs382341668 | 0.27394 | 0.00052194 | 0.134 |
| 24 | 60,894,426 | ENSBTAG00000035171 | SERPINB12 | rs477516898 | 0.13948 | 0.00171221 | 0.22 | |
| 18 | 63,798,265 | ENSBTAG00000053810 | rs432670715 | 0.220168 | 0.00404204 | 0.346 | ||
| 5 | 106,389,826 | ENSBTAG00000042924 | SNORA70 | rs464151990 | -0.0624398 | 0.01562814 | 0.963 | |
| 29 | 1,195,578 | ENSBTAG00000054019 | rs379620385 | 0.0697581 | 0.02785573 | 0.963 | ||
| 3 | 17,894,282 | ENSBTAG00000053103 | rs109701681 | 0.00163663 | 0.03640438 | 0.963 | ||
| 3 | 20,098,666 | ENSBTAG00000022741 | MGC134040 | rs478694916 | 0.055018 | 0.03735433 | 0.963 | |
| 14 | 63,608,763 | ENSBTAG00000042171 | SNORA70 | rs441304008 | -0.0235147 | 0.03771466 | 0.963 | |
| 6 | 94,896,092 | ENSBTAG00000035776 | CFAP299 | rs459014612 | 0.0827706 | 0.04253706 | 0.963 | |
| 22 | 55,021,464 | ENSBTAG00000043073 | U6 | rs443419569 | 0.0815626 | 0.04585341 | 0.963 | |
| PB | 11 | 10,810,645 | ENSBTAG00000024058 | EGR4 | rs383097118 | 0.222932 | 4.75E-06 | 0.002 |
| 3 | 47,966,652 | ENSBTAG00000007101 | F3 | rs380850681 | 0.00536243 | 0.00193635 | 0.207 | |
| 23 | 16,744,416 | ENSBTAG00000015131 | SLC29A1 | rs137606813 | 0.00021436 | 0.00189969 | 0.207 | |
| 1 | 38,894,238 | ENSBTAG00000023652 | PROS1 | rs385387727 | 0.00120501 | 0.00103787 | 0.207 | |
| 19 | 18,988,823 | ENSBTAG00000008788 | SLC13A2 | rs478589506 | 0.24342 | 0.00511518 | 0.365 | |
| 22 | 6,288,529 | ENSBTAG00000022744 | TRIM71 | rs136689901 | 0.0169698 | 0.00434811 | 0.365 | |
| 2 | 128,473,027 | ENSBTAG00000038865 | TCEA3 | rs482027819 | 0.0143887 | 0.00868258 | 0.532 | |
| 3 | 94,262,264 | ENSBTAG00000009674 | C3H1orf185 | rs466365210 | 0.216626 | 0.01357773 | 0.677 | |
| 1 | 72,577,888 | ENSBTAG00000048826 | rs109233921 | -0.0774901 | 0.0142077 | 0.677 | ||
| 5 | 106,654,304 | ENSBTAG00000008553 | B4GALNT3 | -0.0420428 | 0.02157095 | 0.74 |
SNP effect- the effect size of a SNP on the phenotype that is mediated by gene expression.
ICV Ileocecal valve, PB Peripheral blood, Chr Chromosome, SNP single nucleotide polymorphism, FDR false discovery rate, ID identification code