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Table 1 Estimated lead variants (2) associated with cattle flight time in the meta-analysis

From: Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament

Chr

bp

A1/A2

Freq (A1)

b (A1)

P

%Vga

Dirb

Variant type

Candidate genesc

3

52,892,109

A/C

0.56

− 0.089

2 × 10−9

1.50

–

Intergenic

BARHL2 (196 kb)

21

1,058,688

A/C

0.48

− 0.107

3 × 10−10

2.19

–

Intergenic

MAGEL2 (274 kb), NDN (321 kb) SNRPN (1033 kb)

  1. Lead variants are obtained using clumping for all variants with P < 5 × 10−8, clumping windows of 5 Mb and r2 = 0.1
  2. a%Vg = 2*FreqA1*FreqA2*b2/Vg*100, Vg = 0.259 (TropComp2)
  3. bDirection of SNP effect in each cohort of the meta-analysis (TropComp1, Brahman, TropComp2)
  4. cProtein-coding genes within 200 kb of the clumping window. Distance from top variant in parenthesis
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Genetics Selection Evolution

ISSN: 1297-9686