Table 4 Top 5 SNPs explaining the largest phenotypic variance for immune relevant traits identified by GWAS in Large White
From: Genome-wide associations for immune traits in two maternal pig lines
Trait | SNP | SSC | Pos. | Var. | MAF | p-value | Â | rs code | SNP type | Gene |
|---|---|---|---|---|---|---|---|---|---|---|
MON | H3GA0050761 | 18 | 37.3 | 4.3 | 0.458 | 1.41E-04 | Â | rs81469020 | IGV | Â |
MON | H3GA0050788 | 18 | 38.3 | 4.1 | 0.466 | 2.05E-04 | Â | rs81469187 | IGV | Â |
MON | ALGA0098112 | 18 | 39.3 | 4.0 | 0.462 | 2.51E-04 | Â | rs81469256 | IGV | Â |
MON | MARC0069672 | 18 | 39.3 | 4.0 | 0.463 | 2.38E-04 | Â | rs81255938 | IGV | Â |
MON | MARC0089391 | 18 | 39.3 | 4.0 | 0.462 | 2.51E-04 | Â | rs81270496 | IGV | Â |
PLT | ASGA0029231 | 6 | 113.4 | 4.1 | 0.026 | 1.70E-05 | B5 | rs81390902 | IGV | Â |
PLT | ASGA0029288 | 6 | 120.2 | 4.1 | 0.027 | 1.71E-05 | B5 | rs81391141 | IV | FHOD3 |
PLT | ALGA0057477 | 10 | 17.2 | 3.6 | 0.383 | 5.42E-05 | B10 | rs81421220 | IGV | Â |
PLT | H3GA0053711 | 10 | 17.4 | 4.0 | 0.377 | 2.19E-05 | B5 | rs81345552 | IGV | Â |
PLT | ALGA0116316 | 10 | 17.5 | 3.4 | 0.331 | 9.22E-05 | Â | rs81345791 | IV | HNRNPU |
HAP | ALGA0022724 | 4 | 7.5 | 4.1 | 0.300 | 1.27E-05 | B5 | rs80997926 | IGV | Â |
HAP | ALGA0096031 | 17 | 54.9 | 3.7 | 0.298 | 3.18E-05 | B5 | rs80828451 | IV | BCAS1 |
RBC | ALGA0066876 | 12 | 50.1 | 5.0 | 0.318 | 2.70E-05 | B5 | rs81436461 | IV | ZZEF1 |
RBC | ALGA0066881 | 12 | 50.1 | 5.0 | 0.318 | 2.70E-05 | B5 | rs81436486 | IV | ZZEF1 |
RBC | ALGA0079331 | 14 | 83.0 | 4.8 | 0.065 | 4.43E-05 | Â | rs80806469 | IGV | Â |
RBC | SIRI0000773 | 14 | 136.4 | 5.3 | 0.084 | 1.69E-05 | Â | rs325538072 | IV | INSYN2A, DOCK1 |
RBC | ASGA0074790 | 16 | 78.0 | 5.5 | 0.011 | 1.21E-05 | B5 | rs81463953 | IGV | Â |
HGB | ASGA0025952 | 5 | 65.8 | 5.4 | 0.203 | 6.80E-06 | B5 | rs81384737 | MV | AKAP3 |
HGB | H3GA0016570 | 5 | 66.0 | 5.3 | 0.202 | 9.73E-06 | B5 | rs80994174 | IV | FGF6 |
HGB | ALGA0085557 | 15 | 56.0 | 5.4 | 0.014 | 7.79E-06 | B5 | rs81453155 | IGV | Â |
HGB | ASGA0074790 | 16 | 78.0 | 4.7 | 0.011 | 2.96E-05 | B5 | rs81463953 | IGV | Â |
HCT | ALGA0085557 | 15 | 56.0 | 5.0 | 0.014 | 5.43E-06 | B5 | rs81453155 | IGV | Â |
HCT | ASGA0074790 | 16 | 78.0 | 4.9 | 0.011 | 5.90E-06 | B5 | rs81463953 | IGV | Â |
MCHC | ASGA0005789 | 1 | 221.2 | 4.9 | 0.126 | 6.61E-05 | Â | rs80903521 | IV | KANK1 |
MCHC | MARC0079029 | 1 | 254.2 | 4.8 | 0.181 | 7.18E-05 | Â | rs81263277 | IV | RGS3 |
MCHC | ASGA0102333 | 1 | 254.2 | 4.9 | 0.182 | 6.95E-05 | Â | rs81323628 | IGV | Â |
MCHC | H3GA0053907 | 1 | 254.2 | 4.8 | 0.181 | 7.18E-05 | Â | rs81347166 | IGV | Â |
MCHC | MARC0026691 | 1 | 255.2 | 4.9 | 0.148 | 6.05E-05 | Â | rs80929320 | IV | ATP6V1G1 |
IFN- γ | H3GA0011038 | 3 | 128.4 | 4.3 | 0.318 | 1.49E-05 | B5 | rs81378478 | IGV |  |
IL-10 | MARC0016481 | 13 | 17.5 | 4.8 | 0.221 | 8.34E-06 | B5 | rs81285895 | IGV | Â |
IL-12 | INRA0000110 | 1 | 3.1 | 3.8 | 0.312 | 6.29E-05 | Â | rs80934703 | IV | PDE10A |
IL-12 | MARC0102958 | 1 | 3.2 | 3.8 | 0.312 | 6.29E-05 | Â | rs80961411 | IV | PDE10A |
IL-12 | ALGA0000305 | 1 | 3.3 | 3.8 | 0.312 | 6.29E-05 | Â | rs80793535 | IV | PDE10A |
IL-12 | DRGA0012960 | 13 | 152.9 | 3.8 | 0.499 | 5.77E-05 | Â | rs81298281 | IV | ENSSSCG00000042450 |
IL-12 | ASGA0092143 | 13 | 153.6 | 4.0 | 0.500 | 3.33E-05 | Â | rs81478305 | IV | CBLB |
IL-6 | ASGA0051648 | 11 | 68.5 | 4.3 | 0.055 | 2.39E-05 | B5 | rs81431737 | IV | CLYBL |
IL-6 | H3GA0032382 | 11 | 68.6 | 3.9 | 0.042 | 5.45E-05 | B10 | rs80961677 | IV | CLYBL |
TNF- α | ASGA0001772 | 1 | 26.5 | 3.8 | 0.446 | 1.78E-05 | B10 | rs81351651 | IGV |  |
TNF- α | ASGA0001781 | 1 | 26.7 | 4.9 | 0.498 | 8.52E-07 * | B5* | rs80894799 | IV | ENSSSCG00000043500 |
TNF- α | ASGA0105343 | 9 | 138.4 | 3.9 | 0.159 | 1.26E-05 | B5 | rs81305425 | IGV |  |
TNF- α | ASGA0097568 | 9 | 138.5 | 4.9 | 0.064 | 7.99E-07 * | B5* | rs81317558 | IGV |  |
TNF- α | ALGA0056053 | 9 | 138.8 | 4.2 | 0.062 | 5.21E-06 | B5 | rs81419664 | IGV |  |