Skip to main content

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

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

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

  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)