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Table 4 Details of the most strongly associated SNPs (with a p value < 10−6) in each QTL with antibody response to N. caninum

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 Number of genes in the QTL region
25 rs133449464 13,507,716 2.56 × 10−10 PARN T (0.005) 0.09 Intron 13,037,560 14,102,058 9
21 – 55,835,765 2.26 × 10−9 PPIP5K1 A (0.003) 0.11 Intron 55,069,089 56,273,280 29
1 rs466868917 46,464,860 4.08 × 10−8 NXPE3 C (0.007) 0.08 Intron 45,131,004 49,146,658 18
1 rs381312356 111,186,754 1.24 × 10−7 VEPH1 C (0.039) 0.03 Intron 106,928,970 113,261,468 32
9 rs714447117 15,859,873 3.19 × 10−7 ENSBTAG00000021175 C (0.004) 0.07 Downstream 15,859,873 15,859,873 –
3 – 10,934,190 3.89 × 10−7 – C (0.037) 0.03 Intergenic 9,428,852 15,031,457 126
5 rs208471794 70,717,913 7.34 × 10−7 – G (0.929) 0.02 Intergenic 70,717,913 70,717,913 –
21 rs478339448 9,874,248 7.83 × 10−7 – C (0.006) 0.07 Intergenic 9,874,248 10,045,196 –
  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