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Table 3 Details of the most strongly associated SNPs (with a p value < 10−6) in each QTL region with antibody response to O. osteratgi

From: Genome-wide association study of endo-parasite phenotypes using imputed whole-genome sequence data in dairy and beef cattle

BTA SNP name Pos (bp) p value Gene Favourable allele (freq) Effecta Annotation Start of QTL End of QTL Other genes in the QTL region
23 rs455561091 33,302,807 3.61 × 10−7 – A (0.004) 0.13 Intergenic 33,029,305 34,481,525 GPLD1, MRS2, DCDC2, NRSN1, PRP4, PRP8, PRP6
21 rs475710014 65,072,681 4.26 × 10−7 – A (0.054) 0.03 Intergenic 65,072,681 65,072,681 –
14 rs523857350 35,375,134 4.62 × 10−7 – A (0.005) 0.11 Intergenic 35,375,134 35,740,556 SULF1, ENSBTAG00000037399, SLCO5A1
4 rs29026148 62,981,078 4.85 × 10−7 – A (0.650) 0.02 Intergenic 62,981,078 62,993,200 –
19 – 7,584,712 5.43 × 10−7 – A (0.198) 0.02 Intergenic 7,584,712 7,584,712 –
14 rs439873982 7,893,299 7.67 × 10−7 – T (0.008) 0.08 Intergenic 7,866,148 7,899,389 –
3 – 1,746,600 7.74 × 10−7 GPA33 T (0.004) 0.12 Intron 945,572 6,388,604 MPZL1, RCSD1, CREG1, CD247, POU2F1, DUSP27, MAEL, ILDR2, TADA1, POGK, ENSBTAG00000022504, ENSBTAG00000022954, FAM78B, UCK2, TMCO1, ALDH9A1, MGST3, LRRC52, RXRG, LMX1A, PBX1, ENSBTAG00000045987, ENSBTAG00000034449, NUF2, RGS5, RGS4
12 rs379990763 9,621,581 8.25 × 10−7 – A (0.010) 0.08 Intergenic 9,402,063 9,801,565 –
13 rs209722101 70,057,265 9.50 × 10−7 – G (0.002) 0.15 Intergenic 70,057,265 70,057,265 –
  1. BTA: Bos taurus chromosome number, SNP: name of the single nucleotide polymorphism, pos: position of base pair on the chromosome, p value: p value of the SNP, gene: gene name in which the SNP is located, favourable allele (freq): allele with favourable effect (frequency of the favourable allele), effect: effect of the favourable allele, annotation: annotation of the SNP, start of QTL: base pair on the chromosome at the start of the QTL, end of QTL: base pair on the chromosome at the end of the QTL, other genes in the QTL region: protein-coding genes located in the QTL region that the SNP is not located in
  2. aBinary trait (0/1)
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Genetics Selection Evolution

ISSN: 1297-9686