Table 3.
Annotation of SNP with significant (P < 0.001) buffering epistatic effect in both populations (BB and TC) including genome position, distance to nearest gene, gene (according to the bovine reference genome assembly ARS-UCS1.2), reference allele frequency (RAF), estimated effect, and significance (−Log(P))
| SNP | Chr | Bp | Distance | Gene | Brahman | Tropical Composite | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| RAF | Effect | −Log(P) | RAF | Effect | −Log(P) | |||||
| BovineHD0200001651 | 2 | 5,747,611 | 38,487 | NEMP2 | 0.0263 | −0.5406 | 3.0404 | 0.0729 | 0.3258 | 3.5760 |
| BovineHD0200001652 | 2 | 5,748,515 | 37,583 | NEMP2 | 0.0263 | −0.5406 | 3.0404 | 0.0727 | 0.3237 | 3.5065 |
| BovineHD0200001654 | 2 | 5,757,112 | 28,986 | NEMP2 | 0.9737 | 0.5433 | 3.0404 | 0.9272 | −0.3234 | 3.5297 |
| ARS-BFGL-NGS-100083 | 8 | 11,133,497 | 0 | SCARA3 | 0.9528 | −0.5113 | 3.4369 | 0.6920 | 0.1975 | 4.1983 |
| BovineHD0800014800 | 8 | 49,143,207 | 36,501 | ALDH1A1 | 0.9820 | 0.7474 | 3.5992 | 0.7831 | 0.2002 | 3.9915 |
| BovineHD0800015819 | 8 | 52,427,816 | 8,480 | PCSK5 | 0.0452 | −0.4416 | 3.3439 | 0.2349 | −0.1963 | 3.6686 |
| Hapmap48089-BTA-81187 | 8 | 52,524,895 | 0 | GCNT1 | 0.9403 | 0.3760 | 3.0638 | 0.6829 | 0.1562 | 3.2041 |
| BovineHD1000026980 | 10 | 92,312,649 | 0 | TSHR | 0.6054 | 0.2160 | 3.5761 | 0.4686 | −0.1712 | 4.0605 |
| BovineHD1000026985 | 10 | 92,331,573 | 0 | TSHR | 0.3946 | −0.2140 | 3.5761 | 0.5317 | 0.1779 | 4.1064 |
| BovineHD1000030828 | 10 | 92,335,071 | 0 | TSHR | 0.4216 | −0.2017 | 3.2507 | 0.7002 | 0.1623 | 3.2973 |
| BovineHD1200025989 | 12 | 84,830,432 | 15,785 | 5S_rRNA | 0.7141 | 0.2066 | 3.2041 | 0.6998 | −0.1603 | 3.0872 |
| BovineHD1400011237 | 14 | 37,055,691 | 0 | ENSBTAG00000002076 | 0.1033 | −0.3042 | 3.0404 | 0.5288 | −0.1442 | 3.0872 |
| BovineHD1400011280 | 14 | 37,211,716 | 0 | ENSBTAG00000050514 | 0.9095 | 0.3733 | 3.9915 | 0.6543 | 0.2204 | 5.9710 |
| BovineHD1400013234 | 14 | 44,638,868 | 5,792 | PMP2 | 0.6080 | 0.1951 | 3.0169 | 0.6512 | −0.1791 | 3.9225 |
| BovineHD1600016214 | 16 | 56,665,443 | 0 | TNR | 0.1409 | 0.2618 | 3.0872 | 0.6231 | −0.1635 | 3.6917 |
| BovineHD1700009805 | 17 | 35,070,459 | 0 | IL21 | 0.9377 | 0.4452 | 3.7841 | 0.7129 | −0.1633 | 3.2973 |
| BovineHD1700009807 | 17 | 35,079,284 | 8,519 | IL21 | 0.0623 | −0.4429 | 3.7610 | 0.2859 | 0.1659 | 3.2274 |
| BovineHD1700009808 | 17 | 35,083,771 | 13,006 | IL21 | 0.0623 | −0.4429 | 3.7610 | 0.2859 | 0.1659 | 3.2274 |
| BovineHD1700009811 | 17 | 35,094,499 | 23,734 | IL21 | 0.9377 | 0.4452 | 3.7841 | 0.7131 | −0.1626 | 3.2740 |
| BovineHD1900012991 | 19 | 45,742,542 | 18,774 | ENSBTAG00000053203 | 0.2399 | 0.2629 | 3.5297 | 0.3921 | −0.1908 | 4.5416 |
| BovineHD4100015365 | 21 | 65,988,493 | 33,080 | bta-mir-656 | 0.0559 | 0.4343 | 3.1340 | 0.0502 | −0.4564 | 5.9259 |
| BovineHD2500009619 | 25 | 34,418,988 | 0 | SSC4D | 0.1843 | 0.3028 | 3.6455 | 0.4378 | −0.1702 | 3.8764 |
| BovineHD2500009621 | 25 | 34,427,964 | 0 | SSC4D | 0.1831 | 0.3168 | 3.8764 | 0.3959 | −0.2030 | 4.9974 |
| BovineHD2800005959 | 28 | 22,571,976 | 0 | CTNNA3 | 0.1338 | 0.3147 | 3.1807 | 0.3500 | 0.1516 | 3.2973 |