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

Table 1 Details of the most strongly associated SNPs (with a p value < 10⁻⁶) in each QTL region with deregressed EBV for F. hepatica-damaged liver

BTA	SNP name	Pos (bp)	p value	Gene	Favourable allele (freq)	Effect^a	Annotation	Start of QTL	End of QTL	Other genes in the QTL region
18	rs384464701	22,279,521	1.92 × 10⁻⁸	FTO	A (0.988)	0.09	Intron	22,279,521	22,279,521
1	–	146,726,679	3.76 × 10⁻⁸	AGPAT3	G (0.998)	0.18	Intron	146,465,269	14,6811,109	PDXK, CSTB, RRP1, TRAPPC10
17	rs110361447	71,554,867	1.26 × 10⁻⁷	SEC14L2	A (0.470)	0.02	Intron	71,554,867	71,554,867
16	rs800135980	14,007,063	5.27 × 10⁻⁷	–	A (0.002)	0.19	Intergenic	14,007,063	14,007,063
11	rs384697649	87,844,503	7.79 × 10⁻⁷	YWHAQ	T (0.996)	0.13	Intron	87,844,503	87,844,503
8	rs109859381	24,008,154	8.79 × 10⁻⁷	MLLT3	T (0.888)	0.02	Intron	24,008,154	24,008,154

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