Table 3. Significantly associated SNPs for birth weight (BW), weaning weight (WW), and long-yearling weight (LYW) obtained by the Generalized Quasi-Likelihood Score method (GQLS).
| Trait | SNP Reference | BTA | Position (bp) | Alleles | Genes | Region | MAF | p-value | FDR | Allele substitution effect* |
| BW | rs43421095 | 4 | 117,400,491 | A,C | DPP6 | Intron | 0.2957 | 1.39E-06 | 5% | −0.5929 |
| BW | rs135754703 | 9 | 55,075,535 | A,C | LOC783932, MANEA | Intergenic | 0.4552 | 8.22E-06 | 10% | −0.41612 |
| BW | rs136146400 | 9 | 55,078,557 | A,G | LOC783932, MANEA | Intergenic | 0.4563 | 7.23E-06 | 10% | −0.41976 |
| BW | rs109313268 | 9 | 55,103,057 | T,C | LOC783932, MANEA | Intergenic | 0.4962 | 3.98E-06 | 10% | −0.44946 |
| WW | rs43421095 | 4 | 117,400,491 | A,C | DPP6 | Intron | 0.2957 | 1.91E-07 | 1% | −2.84898 |
| WW | rs135156506 | 6 | 35,008,291 | T,C | FARSB | Upstream | 0.1582 | 7.32E-07 | 5% | −2.17934 |
| WW | rs135591504 | 6 | 41,978,318 | T,C | KCNIP4 | Intron | 0.2273 | 2.74E-06 | 5% | 1.55340 |
| WW | rs136337296 | 11 | 103,096,174 | T,C | GTF3C5 | Intron | 0.365 | 1.81E-05 | 10% | 1.82227 |
| WW | rs109348820 | 11 | 103,154,983 | T,C | RALGDS | Intron | 0.3916 | 2.02E-05 | 10% | 1.76133 |
| WW | rs133132366 | 11 | 103,157,389 | T,C | RALGDS | Intron | 0.4077 | 1.28E-05 | 10% | 1.81074 |
| WW | rs134657108 | 11 | 103,162,503 | A,G | RALGDS | Intron | 0.4177 | 1.26E-05 | 10% | 1.90613 |
| WW | rs136054783 | 11 | 103,167,055 | A,G | RALGDS | Intron | 0.4066 | 8.40E-06 | 10% | 1.79279 |
| WW | rs136961684 | 11 | 103,170,500 | A,G | RALGDS | Intron | 0.4076 | 1.08E-05 | 10% | −1.80009 |
| WW | rs109945520 | 11 | 103,171,584 | G,T | RALGDS | Intron | 0.4047 | 1.17E-05 | 10% | 1.80350 |
| WW | rs109524492 | 11 | 103,172,572 | C,T | RALGDS | Intron | 0.4099 | 5.74E-06 | 10% | 1.63200 |
| WW | rs110048168 | 11 | 103,174,303 | A,C | RALGDS | Intron | 0.3886 | 3.05E-06 | 10% | −1.66682 |
| LYW | rs29011435 | 7 | 28,515,652 | T,C | MARCH3, LMNB1, PHAX, ALDH7A1, C7H5orf48, GRAMD3, MIR2458, LOC100848523 | Intergenic | 0.374 | 4.62E-06 | 10% | 3.59660 |
| LYW | rs134201365 | 7 | 28,522,539 | T,G | MARCH3, LMNB1, PHAX, ALDH7A1, C7H5orf48, GRAMD3, MIR2458, LOC100848523 | Intergenic | 0.375 | 4.62E-06 | 10% | −3.59660 |
| LYW | rs109581958 | 22 | 54,624,190 | T,C | LARS2, LOC101907967, TMEM158, LOC101908013, CDCP1, LOC614114, LOC101908094, LOC101901958, ZDHHC3, EXOSC7, LOC100847326, CLEC3B | Intergenic | 0.2335 | 1.09E-05 | 10% | −3.61775 |
| LYW | rs110246286 | 22 | 54,625,467 | T,C | LARS2, LOC101907967, TMEM158, LOC101908013, CDCP1, LOC614114, LOC101908094, LOC101901958, ZDHHC3, EXOSC7, LOC100847326, CLEC3B | Intergenic | 0.2348 | 1.09E-05 | 10% | −3.61775 |
| LYW | rs109242147 | 25 | 15,697,543 | A,G | XYLT1 | Intron | 0.1192 | 1.26E-06 | 5% | 3.24823 |
| LYW | rs109646351 | 27 | 2,614,991 | A,G | LOC101904868 | Intron | 0.4456 | 3.05E-05 | 10% | −3.91546 |
| LYW | rs109822265 | 27 | 2,619,242 | A,C | LOC101904868 | Intron | 0.4454 | 3.05E-05 | 10% | 3.91546 |
| LYW | rs110603636 | 27 | 2,620,088 | A,C | LOC101904868 | Intron | 0.4456 | 3.05E-05 | 10% | 3.91546 |
| LYW | rs110994026 | 27 | 2,620,961 | T,C | LOC101904868 | Intron | 0.4494 | 3.46E-05 | 10% | −3.85715 |
| LYW | rs134791735 | 27 | 2,623,000 | T,G | LOC101904868 | Intron | 0.4443 | 3.05E-05 | 10% | 3.91546 |
Single locus regression was carried out to estimate allele substitution effects for significant SNPs.
*Coefficient of regression (P<0.001); FDR = False discovery rate; MAF = Minor allele frequency; bp = base pairs; BTA = Bos taurus autosome.