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

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

BTA	SNP name	Pos (bp)	p value	Gene	Favourable allele (freq)	Effect^a	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	–

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
^aBinary trait (0/1)

ISSN: 1297-9686