Table 2.

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

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
14	rs801151638	82,704,197	2.02 × 10−8	–	A (0.988)	0.42	Intergenic	80,104,349	83,212,505	RALYL, SNX16, CHMP4C
20	rs382942594	21,005,570	1.77 × 10−7	–	T (0.063)	0.19	Intergenic	20,574,362	22,008,166	RAB3C, ENSBTAG00000005229, GAPT, PLK2, ENSBTAG00000026505
6	rs439064316	44,643,846	1.96 × 10−7	–	C (0.008)	0.46	Intergenic	44,643,846	44,643,846	–
15	rs134727358	67,661,877	5.12 × 10−7	PRR5L	G (0.003)	0.66	Upstream	67,661,877	67,661,877	–
15	rs379765497	23,526,098	5.44 × 10−7	–	A (0.008)	0.44	Intergenic	23,515,275	2,3581,425	–
18	rs110443247	4,974,911	6.04 × 10−7	–	C (0.375)	0.08	Intergenic	4,974,911	5,158,840	NUDT7, VAT1L

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)