Table 1 Summary of significant SV loci in 36 traits
Phenotype | Chr | Position | Gene name | SV location | Type | Length | P-value |
|---|---|---|---|---|---|---|---|
Abdominal circumference | 1 | 260,511,205 | CDK5RAP2 | Intron | DEL | 283 | 4.24E-07 |
1 | 271,010,710 | LAMC3 | Intron | DEL | 284 | 5.41E-07 | |
Body height | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 8.75128E-08 |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 3.3894E-07 | |
7 | 26,286,305 | - | Intergenic | DEL | 291 | 8.85504E-07 | |
7 | 27,338,884 | - | Intergenic | DEL | 2,446 | 1.23795E-06 | |
Body length | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 3.78792E-15 |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 7.1424E-10 | |
7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 8.99621E-10 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 1.05991E-09 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 8.61888E-09 | |
7 | 24,883,903 | ENSSSCG00000061569, ENSSSCG00000001455 | Coverage | DUP | 19,228 | 5.58603E-08 | |
7 | 31,311,879 | FANCE | Gene upstream | DEL | 288 | 5.9659E-08 | |
7 | 27,338,884 | - | Intergenic | DEL | 2,446 | 8.84893E-08 | |
7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 1.61736E-07 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 2.19766E-07 | |
7 | 19,232,872 | ENSSSCG00000057632 | Gene upstream | MEI | 292 | 2.62207E-07 | |
7 | 43,989,593 | DEFB114 | Intron | DEL | 1,677 | 4.49759E-07 | |
7 | 26,286,305 | - | Intergenic | DEL | 291 | 1.53065E-06 | |
Bone ratio | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 1.04559E-12 |
7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 4.02735E-10 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 7.68871E-09 | |
7 | 28,324,725 | PRIM2 | Intron | INV | 388 | 2.68482E-08 | |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 4.31208E-08 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 5.94847E-08 | |
7 | 40,599,238 | - | Intergenic | DUP | 309 | 6.52153E-08 | |
7 | 38,794,225 | - | Intergenic | DEL | 357 | 1.46567E-07 | |
7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 3.36078E-07 | |
7 | 24,883,903 | ENSSSCG00000061569, ENSSSCG00000001455 | Coverage | DUP | 19,228 | 5.02475E-07 | |
7 | 39,605,564 | - | Intergenic | DEL | 694 | 5.9881E-07 | |
7 | 31,311,879 | FANCE | Gene upstream | DEL | 288 | 6.393E-07 | |
7 | 30,962,999 | ANKS1A | Intron | DEL | 92 | 9.76289E-07 | |
7 | 27,336,953 | - | Intergenic | DUP | 5,095 | 1.18774E-06 | |
7 | 33,582,502 | ZFAND3 | Intron | DEL | 65 | 1.49752E-06 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 1.54425E-06 | |
7 | 40,599,295 | - | Intergenic | DEL | 267 | 1.70419E-06 | |
Calf bone length | 7 | 38,794,225 | - | Intergenic | DEL | 357 | 1.54116E-10 |
7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 2.16357E-08 | |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 2.68006E-08 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 3.68605E-08 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 7.87112E-08 | |
7 | 19,232,872 | ENSSSCG00000057632 | Gene upstream | MEI | 292 | 4.2437E-07 | |
7 | 33,093,365 | - | Intergenic | DEL | 1,547 | 4.70256E-07 | |
7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 6.1988E-07 | |
Cannon circumference | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 6.71872E-18 |
7 | 28,324,725 | PRIM2 | Intron | INV | 388 | 7.63587E-12 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 1.14929E-11 | |
7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 1.41436E-11 | |
7 | 38,794,225 | - | Intergenic | DEL | 357 | 3.23829E-11 | |
7 | 41,553,724 | ANKRD66 | Intron | DEL | 673 | 7.02795E-11 | |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 1.56476E-10 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 5.70722E-10 | |
7 | 28,324,716 | PRIM2 | Intron | DEL | 130 | 6.7774E-10 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 1.62437E-09 | |
7 | 24,883,903 | ENSSSCG00000061569, ENSSSCG00000001455 | Coverage | DUP | 19,228 | 1.80288E-09 | |
7 | 38,094,955 | RRP36 | Gene downstream | DEL | 309 | 3.80358E-09 | |
7 | 19,232,872 | ENSSSCG00000057632 | Gene upstream | MEI | 292 | 5.08074E-09 | |
7 | 41,553,727 | ANKRD66 | Intron | INV | 721 | 1.0657E-08 | |
7 | 19,239,684 | MRS2 | Gene upstream | DEL | 278 | 1.77718E-08 | |
7 | 26,286,305 | - | Intergenic | DEL | 291 | 1.80886E-08 | |
7 | 30,962,999 | ANKS1A | Intron | DEL | 92 | 2.25339E-08 | |
7 | 41,078,897 | RCAN2 | Intron | DEL | 314 | 3.8015E-08 | |
7 | 34,536,073 | GLP1R | Gene downstream | DEL | 221 | 4.84358E-08 | |
7 | 41,288,870 | - | Intergenic | DEL | 327 | 5.08201E-08 | |
7 | 31,311,879 | FANCE | Gene upstream | DEL | 288 | 1.01069E-07 | |
7 | 36,811,392 | - | Intergenic | DEL | 53 | 2.35974E-07 | |
7 | 19,463,307 | KIAA0319 | Intron | DEL | 309 | 2.56879E-07 | |
7 | 37,476,936 | TRERF1 | Intron | DEL | 294 | 3.72867E-07 | |
7 | 37,055,115 | USP49 | Gene upstream | DEL | 304 | 3.76061E-07 | |
7 | 19,678,493 | RIPOR2 | Intron | DEL | 308 | 4.41254E-07 | |
7 | 36,074,049 | - | Intergenic | DEL | 268 | 6.33459E-07 | |
7 | 31,084,916 | TCP11 | Intron | DEL | 289 | 6.50236E-07 | |
7 | 31,757,248 | SLC26A8 | Intron | DEL | 2,450 | 6.78635E-07 | |
7 | 29,593,390 | COL21A1 | Intron | DEL | 316 | 7.1008E-07 | |
7 | 43,989,593 | DEFB114 | Intron | DEL | 1677 | 1.00074E-06 | |
7 | 24,311,068 | ENSSSCG00000030901 | Coverage | DUP | 31,737 | 1.05293E-06 | |
7 | 39,605,564 | - | Intergenic | DEL | 694 | 1.22437E-06 | |
7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 1.70098E-06 | |
Carcass length | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 1.65E-13 |
7 | 19,232,872 | ENSSSCG00000057632 | Gene upstream | MEI | 292 | 4.82488E-09 | |
7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 7.31789E-09 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 1.22581E-08 | |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 1.74936E-08 | |
7 | 34,536,073 | GLP1R | Gene downstream | DEL | 221 | 2.34715E-08 | |
7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 5.21348E-08 | |
7 | 24,883,903 | ENSSSCG00000061569, ENSSSCG00000001455 | Coverage | DUP | 19,228 | 1.51579E-07 | |
7 | 38,794,225 | - | Intergenic | DEL | 357 | 2.21327E-07 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 2.41208E-07 | |
7 | 34,419,953 | DNAH8 | Intron | DEL | 302 | 2.72373E-07 | |
7 | 31,311,879 | FANCE | Gene upstream | DEL | 288 | 3.10433E-07 | |
7 | 26,286,305 | - | Intergenic | DEL | 291 | 3.37836E-07 | |
7 | 30,002,117 | MLN | Gene downstream | DEL | 396 | 4.64132E-07 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 4.78724E-07 | |
7 | 37,055,115 | USP49 | Gene upstream | DEL | 304 | 8.04377E-07 | |
7 | 31,757,248 | SLC26A8 | Intron | DEL | 2,450 | 1.5249E-06 | |
7 | 24,311,068 | ENSSSCG00000030901 | Coverage | DUP | 31,737 | 1.6098E-06 | |
7 | 27,489,396 | KHDRBS2 | Intron | DEL | 879 | 1.79273E-06 | |
Femur length | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 1.69288E-11 |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 4.4582E-09 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 1.41047E-08 | |
7 | 30,962,999 | ANKS1A | Intron | DEL | 92 | 1.74416E-08 | |
7 | 38,794,225 | - | Intergenic | DEL | 357 | 3.2897E-08 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 7.98636E-08 | |
3 | 125,943,216 | NOL10 | Intron* | DEL | 252 | 2.17341E-07 | |
7 | 38,094,955 | RRP36 | Gene downstream | DEL | 309 | 6.88085E-07 | |
7 | 37,055,115 | USP49 | Gene Upstream | DEL | 304 | 7.03532E-07 | |
7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 7.45747E-07 | |
3 | 125,953,211 | NOL10 | Intron* | DEL | 2,681 | 7.80005E-07 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 8.90967E-07 | |
Forearm bone length | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 7.15594E-12 |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 1.46387E-10 | |
7 | 30,962,999 | ANKS1A | Intron | DEL | 92 | 3.50128E-10 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 1.4709E-09 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 2.61096E-09 | |
7 | 37,488,354 | TRERF1 | Intron | DEL | 300 | 3.35499E-09 | |
7 | 38,794,225 | - | Intergenic | DEL | 357 | 3.63713E-09 | |
7 | 19,232,872 | ENSSSCG00000057632 | Gene upstream | MEI | 292 | 4.92423E-09 | |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 2.78437E-08 | |
7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 1.06476E-07 | |
7 | 30,002,117 | MLN | Gene downstream | DEL | 396 | 2.4688E-07 | |
7 | 19,239,684 | MRS2 | Gene upstream | DEL | 278 | 3.66744E-07 | |
7 | 37,261,717 | C6orf132 | Gene upstream | DEL | 297 | 4.22894E-07 | |
7 | 34,536,073 | GLP1R | Gene downstream | DEL | 221 | 6.18251E-07 | |
7 | 28,324,716 | PRIM2 | Intron | DEL | 130 | 1.04137E-06 | |
7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 1.09207E-06 | |
7 | 24,883,903 | ENSSSCG00000061569, ENSSSCG00000001455 | Coverage | DUP | 19,228 | 1.19239E-06 | |
7 | 36,074,049 | - | Intergenic | DEL | 268 | 1.19749E-06 | |
7 | 37,055,115 | USP49 | Gene upstream | DEL | 304 | 1.76888E-06 | |
Heart weight | 3 | 125,953,211 | NOL10 | Intron* | DEL | 2,681 | 5.99072E-07 |
Hip bone length | 7 | 31,757,248 | SLC26A8 | Intron | DEL | 2,450 | 6.10178E-07 |
7 | 24,311,068 | ENSSSCG00000030901 | Coverage | DUP | 31,737 | 7.92587E-07 | |
Humerus length | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 1.35763E-08 |
7 | 34,536,073 | GLP1R | Gene downstream | DEL | 221 | 4.81907E-08 | |
7 | 19,232,872 | ENSSSCG00000057632 | Gene upstream | MEI | 292 | 1.04481E-07 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 2.51234E-07 | |
1 | 264,535,617 | DENND1A | Intron | DEL | 311 | 5.70534E-07 | |
Intramuscular fat | 12 | 57,675,134 | HS3ST3A1 | Intron | DEL | 122 | 8.67028E-07 |
12 | 54,564,984 | CFAP52 | Intron | MEI | 291 | 9.75823E-07 | |
12 | 54,407,453 | STX8 | Intron | DEL | 302 | 1.19263E-06 | |
Liver weight | 7 | 19,239,684 | MRS2 | Gene upstream | DEL | 278 | 1.50207E-06 |
Scapula length | 7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 2.38035E-07 |
Total weight of front bone | 7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 2.25255E-12 |
7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 5.21713E-12 | |
7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 3.8738E-11 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 1.47312E-10 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 5.58282E-10 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 1.06535E-09 | |
7 | 38,794,225 | - | Intergenic | DEL | 357 | 2.91302E-09 | |
7 | 24,311,068 | ENSSSCG00000030901 | Coverage | DUP | 31,737 | 4.48617E-09 | |
7 | 37,055,115 | USP49 | Gene upstream | DEL | 304 | 1.64413E-08 | |
7 | 24,883,903 | ENSSSCG00000061569, ENSSSCG00000001455 | Coverage | DUP | 19,228 | 1.70589E-08 | |
7 | 28,324,725 | PRIM2 | Intron | INV | 388 | 2.21799E-08 | |
7 | 19,232,872 | ENSSSCG00000057632 | Gene upstream | MEI | 292 | 2.60468E-08 | |
7 | 34,419,953 | DNAH8 | Intron | DEL | 302 | 6.0505E-08 | |
7 | 36,074,049 | - | Intergenic | DEL | 268 | 7.33407E-08 | |
7 | 30,962,999 | ANKS1A | Intron | DEL | 92 | 1.05105E-07 | |
7 | 38,094,955 | RRP36 | Gene downstream | DEL | 309 | 1.45388E-07 | |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 2.07241E-07 | |
7 | 37,261,717 | C6orf132 | Gene upstream | DEL | 297 | 2.68119E-07 | |
7 | 37,488,354 | TRERF1 | Intron | DEL | 300 | 4.77823E-07 | |
7 | 34,536,073 | GLP1R | Gene downstream | DEL | 221 | 7.19729E-07 | |
7 | 28,324,716 | PRIM2 | Intron | DEL | 130 | 7.81429E-07 | |
7 | 30,002,117 | MLN | Gene downstream | DEL | 396 | 7.89703E-07 | |
7 | 40,599,295 | - | Intergenic | DEL | 267 | 1.01179E-06 | |
7 | 43,989,593 | DEFB114 | Intron | DEL | 1,677 | 1.17865E-06 | |
7 | 39,605,564 | - | Intergenic | DEL | 694 | 1.31736E-06 | |
7 | 27,489,396 | KHDRBS2 | Intron | DEL | 879 | 1.49335E-06 | |
7 | 35,332,237 | LncRNA | Gene upstream | DEL | 306 | 1.59814E-06 | |
Total weight of front lean meat | 7 | 41,494,812 | PLA2G7 | Intron | MEI | 294 | 6.03091E-07 |
Total weight of hind bone | 7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 7.95851E-13 |
7 | 38,794,225 | - | Intergenic | DEL | 357 | 3.41618E-11 | |
7 | 36,897,444 | TFEB | Intron | DEL | 136 | 3.51948E-11 | |
7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 9.62978E-11 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 9.81726E-11 | |
7 | 37,641,459 | LncRNA | Intron | DEL | 127 | 2.8606E-10 | |
7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 9.30272E-10 | |
7 | 19,232,872 | ENSSSCG00000057632 | Gene upstream | MEI | 292 | 3.80882E-09 | |
7 | 37,055,115 | USP49 | Gene upstream | DEL | 304 | 4.22536E-09 | |
7 | 34,419,953 | DNAH8 | Intron | DEL | 302 | 4.37384E-09 | |
7 | 30,962,999 | ANKS1A | Intron | DEL | 92 | 1.12907E-08 | |
7 | 37,488,354 | TRERF1 | Intron | DEL | 300 | 2.10081E-08 | |
7 | 19,322,838 | GPLD1 | Intron | DEL | 101 | 2.53408E-08 | |
7 | 31,757,248 | SLC26A8 | Intron | DEL | 2,450 | 2.65487E-08 | |
7 | 36,074,049 | - | Intergenic | DEL | 268 | 6.61502E-08 | |
7 | 34,536,073 | GLP1R | Gene downstream | DEL | 221 | 8.30738E-08 | |
7 | 31,311,879 | FANCE | Gene upstream | DEL | 288 | 9.31817E-08 | |
7 | 37,261,717 | C6orf132 | Gene upstream | DEL | 297 | 2.37267E-07 | |
7 | 39,605,564 | - | Intergenic | DEL | 694 | 2.55411E-07 | |
7 | 30,002,117 | MLN | Gene downstream | DEL | 396 | 4.61386E-07 | |
7 | 24,311,068 | ENSSSCG00000030901 | Coverage | DUP | 31,737 | 4.69345E-07 | |
7 | 33,093,365 | - | Intergenic | DEL | 1547 | 5.24922E-07 | |
7 | 19,463,307 | KIAA0319 | Intron | DEL | 309 | 6.42425E-07 | |
7 | 38,094,955 | RRP36 | Gene downstream | DEL | 309 | 7.07833E-07 | |
7 | 36,811,392 | - | Intergenic | DEL | 53 | 1.32686E-06 | |
7 | 28,324,725 | PRIM2 | Intron | INV | 388 | 1.32768E-06 | |
7 | 27,338,884 | - | Intergenic | DEL | 2,446 | 1.46419E-06 | |
Total weight of middle bone | 7 | 33,224,291 | MDGA1 | Intron | DEL | 75 | 6.19796E-09 |
7 | 30,669,698 | ILRUN | Gene upstream | MEI | 294 | 1.16594E-07 | |
7 | 37,650,773 | LncRNA | Intron | DEL | 311 | 1.39685E-07 | |
7 | 34,419,953 | DNAH8 | Intron | DEL | 302 | 1.59434E-07 | |
7 | 31,540,442 | FKBP5 | Intron | DEL | 441 | 1.89109E-07 | |
6 | 158,747,897 | GLIS1 | Intron | DEL | 85 | 1.49265E-06 | |
Vertebral number | 7 | 97,615,896 | VRTN | Intron | MEI | 294 | 5.41E-11 |
1 | 266,822,698 | - | Intergenic | MEI | 294 | 2.51235E-09 | |
1 | 268,351,956 | AK1 | Gene downstream | DEL | 258 | 2.35774E-07 | |
1 | 268,687,871 | DNM1 | Intron | DEL | 60 | 3.94325E-07 | |
1 | 267,960,645 | ZNF79 | Exon | MEI | 294 | 7.2393E-07 | |
7 | 97,653,457 | SYNDIG1L | Gene downstream | DEL | 765 | 8.30871E-07 | |
1 | 261,580,807 | ENSSSCG00000005518 | Intron | DEL | 291 | 1.05102E-06 | |
1 | 262,031,225 | TTLL11 | Intron | DEL | 955 | 1.51808E-06 |