Table 3.
Top 5 SNPs explaining the largest phenotypic variance for immune relevant traits identified by GWAS in Landrace
| Trait | SNP | SSC | Pos. | Var. | MAF | p-value | rs code | SNP type | Gene | |
|---|---|---|---|---|---|---|---|---|---|---|
| WBC | H3GA0014703 | 4 | 124.4 | 4.5 | 0.317 | 2.53E-05 | B10 | rs80835478 | IV | EVI5 |
| WBC | H3GA0014699 | 4 | 124.5 | 4.3 | 0.320 | 3.44E-05 | B10 | rs80930480 | IV | EVI5 |
| WBC | MARC0027349 | 12 | 21.7 | 4.3 | 0.150 | 3.48E-05 | B5 | rs81222578 | IV | ENSSSCG00000043259 |
| WBC | ALGA0077342 | 14 | 45.0 | 4.0 | 0.195 | 6.79E-05 | rs80964268 | IGV | ||
| WBC | ISU10000541 | 14 | 47.2 | 4.1 | 0.282 | 5.64E-05 | rs80863047 | 3pUTR | LIF | |
| NEU | ALGA0121271 | 12 | 19.4 | 4.0 | 0.355 | 1.65E-04 | rs81328838 | UGV | MEOX1 | |
| NEU | ALGA0113322 | 12 | 27.6 | 3.8 | 0.421 | 2.16E-04 | rs81342064 | IGV | ||
| NEU | ALGA0066053 | 12 | 33.0 | 3.8 | 0.377 | 2.45E-04 | rs81433794 | IGV | ||
| NEU | DRGA0011723 | 12 | 33.1 | 3.8 | 0.377 | 2.45E-04 | rs81294298 | IV | C17orf67 | |
| NEU | ASGA0102924 | 12 | 60.3 | 4.0 | 0.386 | 1.41E-04 | rs81324324 | IV | FAM83G, SLC5A10 | |
| MON | H3GA0034268 | 12 | 36.0 | 4.1 | 0.159 | 4.18E-05 | B10 | rs81434487 | IV | VMP1 |
| MON | ALGA0066234 | 12 | 36.0 | 3.9 | 0.162 | 5.33E-05 | B10 | rs81434489 | IV | VMP1 |
| MON | ASGA0054380 | 12 | 36.1 | 3.9 | 0.162 | 5.33E-05 | B10 | rs81434493 | IV | TUBD1 |
| MON | ALGA0067033 | 12 | 54.0 | 3.7 | 0.077 | 7.93E-05 | rs81437196 | IV | PIK3R5 | |
| HAP | ALGA0013060 | 2 | 37.2 | 4.5 | 0.061 | 8.70E-06 | B5 | rs81357336 | IV | ANO5 |
| HAP | DRGA0002935 | 2 | 37.2 | 4.5 | 0.061 | 8.72E-06 | B5 | rs81296277 | IV | ANO5 |
| HAP | ALGA0013078 | 2 | 37.8 | 4.5 | 0.061 | 8.70E-06 | B5 | rs81357366 | IGV | |
| HAP | ALGA0053703 | 9 | 69.8 | 4.7 | 0.470 | 6.25E-06 | B5 | rs81413020 | IGV | |
| HAP | ALGA0053704 | 9 | 69.9 | 5.0 | 0.450 | 2.84E-06 | B5 | rs81413026 | IGV | |
| HCT | ASGA0002880 | 1 | 53.5 | 5.2 | 0.261 | 2.41E-05 | rs80853363 | IGV | ||
| HCT | M1GA0000961 | 1 | 53.9 | 4.5 | 0.227 | 8.90E-05 | rs80858850 | UGV | TBX18 | |
| HCT | INRA0002424 | 1 | 54.0 | 5.1 | 0.266 | 3.28E-05 | rs341132099 | IGV | ||
| HCT | INRA0002425 | 1 | 54.0 | 4.5 | 0.227 | 8.90E-05 | rs332231926 | IGV | ||
| HCT | ALGA0003516 | 1 | 54.1 | 5.1 | 0.266 | 3.28E-05 | rs80921572 | IGV | ||
| MCHC | H3GA0016097 | 5 | 23.4 | 3.1 | 0.449 | 6.16E-05 | rs80964787 | IGV | ||
| MCHC | ALGA0032074 | 5 | 58.6 | 3.0 | 0.015 | 9.13E-05 | rs80787531 | IV | GRIN2B | |
| MCHC | H3GA0016359 | 5 | 58.6 | 3.0 | 0.015 | 9.13E-05 | rs80942872 | IV | GRIN2B | |
| MCHC | H3GA0016379 | 5 | 58.8 | 3.0 | 0.015 | 9.13E-05 | rs80933182 | IV | GRIN2B | |
| MCHC | ALGA0032146 | 5 | 59.3 | 3.0 | 0.015 | 9.13E-05 | rs81384359 | IGV | ||
| IL-10 | ALGA0094933 | 17 | 39.0 | 3.7 | 0.122 | 1.95E-05 | B5 | rs80997686 | UGV | NFS1, ROMO1, RBM39 |
| IL-10 | ALGA0094942 | 17 | 39.2 | 3.7 | 0.122 | 1.95E-05 | B5 | rs81466504 | IGV | |
| IL-10 | ASGA0076872 | 17 | 39.2 | 3.7 | 0.122 | 1.95E-05 | B5 | rs81466495 | IGV | |
| IL-10 | ASGA0076896 | 17 | 39.4 | 3.7 | 0.122 | 1.95E-05 | B5 | rs80827927 | IV | EPB41L1 |
| IL-10 | ASGA0076900 | 17 | 39.5 | 3.7 | 0.122 | 1.95E-05 | B5 | rs80842622 | IV | EPB41L1 |
| IL-1 β | ALGA0094933 | 17 | 39.0 | 2.9 | 0.122 | 1.63E-04 | rs80997686 | UGV | NFS1, ROMO1, RBM39 | |
| IL-1 β | ALGA0094942 | 17 | 39.2 | 2.9 | 0.122 | 1.63E-04 | rs81466504 | IGV | ||
| IL-1 β | ASGA0076872 | 17 | 39.2 | 2.9 | 0.122 | 1.63E-04 | rs81466495 | IGV | ||
| IL-1 β | ASGA0076896 | 17 | 39.4 | 2.9 | 0.122 | 1.63E-04 | rs80827927 | IV | EPB41L1 | |
| IL-1 β | ASGA0076900 | 17 | 39.5 | 2.9 | 0.122 | 1.63E-04 | rs80842622 | IV | EPB41L1 | |
| IL-4 | ALGA0039474 | 7 | 22.1 | 4.0 | 0.303 | 6.04E-06 | B5 | rs81002011 | IV | ZSCAN26, PGBD1 |
| IL-4 | ALGA0094933 | 17 | 39.0 | 2.8 | 0.122 | 1.61E-04 | rs80997686 | UGV | NFS1, ROMO1, RBM39 | |
| IL-4 | ALGA0094942 | 17 | 39.2 | 2.8 | 0.122 | 1.61E-04 | rs81466504 | IGV | ||
| IL-4 | ASGA0076872 | 17 | 39.2 | 2.8 | 0.122 | 1.61E-04 | rs81466495 | IGV | ||
| IL-4 | ASGA0076896 | 17 | 39.4 | 2.8 | 0.122 | 1.61E-04 | rs80827927 | IV | EPB41L1 | |
| IL-8 | ALGA0086892 | 15 | 116.1 | 5.1 | 0.494 | 2.86E-07 * | B5* | rs81454413 | IV | SPAG16 |
| IL-8 | ASGA0070560 | 15 | 120.0 | 4.6 | 0.256 | 1.11E-06 * | B5* | rs81454672 | IV | TNS1 |
| IL-8 | ASGA0070582 | 15 | 120.1 | 4.7 | 0.257 | 8.45E-07 * | B5* | rs81454730 | IV | TNS1 |
| IL-8 | ASGA0070586 | 15 | 120.1 | 5.1 | 0.417 | 2.87E-07 * | B5* | rs80818610 | IV | TNS1 |
| IL-8 | ALGA0087116 | 15 | 120.3 | 5.0 | 0.428 | 4.19E-07 * | B5* | rs80913177 | IGV |
WBC White blood cells, NEU Neutrophils, MON Monocytes, HAP Haptoglobin, HCT Haematocrit, MCHC Mean corpuscular haemoglobin concentration, IL Interleukin, 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, IV Intron variant, IGV Intergenic variant, 3pUTR 3 prime UTR variant, UGV Upstream gene variant