Table 4.
Top 5 SNPs explaining the largest phenotypic variance for immune relevant traits identified by GWAS in Large White
| Trait | SNP | SSC | Pos. | Var. | MAF | p-value | rs code | SNP type | Gene | |
|---|---|---|---|---|---|---|---|---|---|---|
| MON | H3GA0050761 | 18 | 37.3 | 4.3 | 0.458 | 1.41E-04 | rs81469020 | IGV | ||
| MON | H3GA0050788 | 18 | 38.3 | 4.1 | 0.466 | 2.05E-04 | rs81469187 | IGV | ||
| MON | ALGA0098112 | 18 | 39.3 | 4.0 | 0.462 | 2.51E-04 | rs81469256 | IGV | ||
| MON | MARC0069672 | 18 | 39.3 | 4.0 | 0.463 | 2.38E-04 | rs81255938 | IGV | ||
| MON | MARC0089391 | 18 | 39.3 | 4.0 | 0.462 | 2.51E-04 | rs81270496 | IGV | ||
| PLT | ASGA0029231 | 6 | 113.4 | 4.1 | 0.026 | 1.70E-05 | B5 | rs81390902 | IGV | |
| 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 | |
| PLT | H3GA0053711 | 10 | 17.4 | 4.0 | 0.377 | 2.19E-05 | B5 | rs81345552 | IGV | |
| PLT | ALGA0116316 | 10 | 17.5 | 3.4 | 0.331 | 9.22E-05 | rs81345791 | IV | HNRNPU | |
| HAP | ALGA0022724 | 4 | 7.5 | 4.1 | 0.300 | 1.27E-05 | B5 | rs80997926 | IGV | |
| 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 | rs80806469 | IGV | ||
| RBC | SIRI0000773 | 14 | 136.4 | 5.3 | 0.084 | 1.69E-05 | rs325538072 | IV | INSYN2A, DOCK1 | |
| RBC | ASGA0074790 | 16 | 78.0 | 5.5 | 0.011 | 1.21E-05 | B5 | rs81463953 | IGV | |
| 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 | |
| HGB | ASGA0074790 | 16 | 78.0 | 4.7 | 0.011 | 2.96E-05 | B5 | rs81463953 | IGV | |
| HCT | ALGA0085557 | 15 | 56.0 | 5.0 | 0.014 | 5.43E-06 | B5 | rs81453155 | IGV | |
| HCT | ASGA0074790 | 16 | 78.0 | 4.9 | 0.011 | 5.90E-06 | B5 | rs81463953 | IGV | |
| MCHC | ASGA0005789 | 1 | 221.2 | 4.9 | 0.126 | 6.61E-05 | rs80903521 | IV | KANK1 | |
| MCHC | MARC0079029 | 1 | 254.2 | 4.8 | 0.181 | 7.18E-05 | rs81263277 | IV | RGS3 | |
| MCHC | ASGA0102333 | 1 | 254.2 | 4.9 | 0.182 | 6.95E-05 | rs81323628 | IGV | ||
| MCHC | H3GA0053907 | 1 | 254.2 | 4.8 | 0.181 | 7.18E-05 | rs81347166 | IGV | ||
| MCHC | MARC0026691 | 1 | 255.2 | 4.9 | 0.148 | 6.05E-05 | 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 | |
| IL-12 | INRA0000110 | 1 | 3.1 | 3.8 | 0.312 | 6.29E-05 | rs80934703 | IV | PDE10A | |
| IL-12 | MARC0102958 | 1 | 3.2 | 3.8 | 0.312 | 6.29E-05 | rs80961411 | IV | PDE10A | |
| IL-12 | ALGA0000305 | 1 | 3.3 | 3.8 | 0.312 | 6.29E-05 | rs80793535 | IV | PDE10A | |
| IL-12 | DRGA0012960 | 13 | 152.9 | 3.8 | 0.499 | 5.77E-05 | rs81298281 | IV | ENSSSCG00000042450 | |
| IL-12 | ASGA0092143 | 13 | 153.6 | 4.0 | 0.500 | 3.33E-05 | 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 |
MON Monocytes, PLT Platelets, HAP Haptoglobin, RBC Red blood cells, HGB Haemoglobin, HCT Haematocrit, MCHC Mean corpuscular haemoglobin concentration, IFN Interferon, IL Interleukin, TNF Tumor necrosis factor, SSC Sus Scrofa Chromosome, Pos. Position [Mb], Var. phenotypic variance explained [%], MAF Minor allele frequency, * genome-wide significance, B5 Additionally significant after Bonferroni correction with adjusted p-value <0.05, B10 Additionally significant after Bonferroni correction with adjusted p-value <0.1, Gene SNP within gene, IGV Intergenic variant, IV Intron variant, MV Missense variant