Table 4.
Annotation of genome-wide significant SNPs (P value < 1.58E-06) associated with EN3
| SNP | GGAa | Positionb | ALT/REFc | MAFd | Beta (SE)e | P value | Consequence | Candidate/ Nearest gene |
|---|---|---|---|---|---|---|---|---|
| rs14878430 | 1 | 117,871,938 | C/T | 0.407 | 0.25 (0.05) | 7.96E-07 | Intron | POLA1 |
| rs14878446 | 1 | 117,881,774 | T/C | 0.408 | 0.25 (0.05) | 1.38E-06 | Intron | POLA1 |
| rs313573834 | 1 | 117,885,299 | A/G | 0.408 | 0.25 (0.05) | 1.38E-06 | Intron | POLA1 |
| rs13685872 | 1 | 117,898,459 | A/G | 0.417 | 0.25 (0.05) | 1.04E-06 | Intron | POLA1 |
| rs316686965 | 1 | 117,904,908 | T/A | 0.417 | 0.25 (0.05) | 9.65E-07 | Intron | POLA1 |
| rs314132663 | 1 | 117,907,038 | A/G | 0.408 | 0.25 (0.05) | 1.38E-06 | Intron | POLA1 |
| rs314631582 | 1 | 117,939,090 | C/T | 0.406 | 0.26 (0.05) | 7.05E-07 | Intron | POLA1 |
| rs315777735 | 1 | 117,943,070 | A/G | 0.418 | 0.27 (0.05) | 1.19E-07 | Intron | POLA1 |
| rs13927842 | 1 | 118,028,676 | C/A | 0.426 | 0.26 (0.05) | 4.70E-07 | Intron | POLA1 |
| rs317157084 | 1 | 118,046,119 | C/T | 0.426 | 0.26 (0.05) | 4.70E-07 | Downstream_43.27Kb | PDK3 |
| rs14878614 | 1 | 118,062,286 | C/A | 0.426 | 0.26 (0.05) | 4.70E-07 | Downstream_27.35Kb | PDK3 |
| rs313935473 | 1 | 118,272,993 | A/G | 0.423 | 0.24 (0.05) | 1.45E-06 | Upstream_3.672Kb | APOO |
| rs312874750 | 1 | 118,313,008 | G/A | 0.424 | 0.25 (0.05) | 7.67E-07 | Downstream_5.72Kb | APOO |
| rs312668110 | 1 | 118,340,009 | G/C | 0.433 | 0.25 (0.05) | 6.31E-07 | Intron | ACOT9 |
| rs317511781 | 1 | 118,344,902 | T/G | 0.433 | 0.25 (0.05) | 6.31E-07 | Downstream_86bp | ACOT9 |
| rs313236049 | 1 | 118,364,746 | C/T | 0.451 | 0.26 (0.05) | 1.51E-07 | Upstream_5.44Kb | PRDX4 |
aChicken chromosome; bGallus_gallus-5.0 source; cALT/REF: alternative allele/reference allele; dMinor allele frequency; eEstimated allelic substitution effect per copy of the effect allele based on an inverse-normal transformed scale under an additive model, expressed in SD unit/allele