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Table 3 Haplotype association analysis for markers flanking BTB-00352779

From: A genome-wide association study reveals a locus for bilateral iridal hypopigmentation in Holstein Friesian cattle

First Marker a Position b Haplotype -log10(p) (p)B c OR d 0.95 CI e
ARS-BFGL-NGS-40630 60800770 AGAGC 0.57 1 0.65 0.30–1.40
GAGGC 0.02 1 1.02 0.46–2.27
GGAGC 1.16 1 0.28 0.07–1.20
AAAGA 7.63 0.0085 7.90 3.46–18.04
AGAAC 0.15 1 0.67 0.09–5.24
AAAGC 0.54 1   
AAGGC 0.45 1 0.04  
ARS-BFGL-NGS-115798 60823250 GAGCA 0.52 1 0.67 0.31–1.44
AGGCA 0.10 1 0.90 0.40–2.00
GAGCC 1.21 1 0.27 0.06–1.17
AAGAA 7.62 0.0087 7.90 3.46–18.04
GAACA 0.19 1 0.61 0.08–4.78
AAGCC 0.54 1   
ARS-BFGL-NGS-12436 60872538 AGCAA 0.51 1 0.67 0.31–1.45
GGCAA 0.10 1 0.90 0.40–1.99
AGCCG 1.57 1 0.22 0.05–0.95
AGAAA 7.62 0.0087 7.90 3.46–18.04
AACAG 0.19 1 0.61 0.08–4.78
ARS-BFGL-NGS-102 60952836 GCAAA 0.68 1 0.64 0.31–1.30
GCCGA 0.71 1 0.39 0.09–1.70
GAAAA 7.72 0.0069 7.99 3.50–18.23
GCCGG 1.14 1   
ACAGA 0.19 1 0.62 0.08–4.83
BTB-00352779 60990733 CAAAG 0.76 1 0.61 0.30–1.25
CCGAG 0.68 1 0.40 0.09–1.75
AAAAA 7.97 0.0038 8.31 3.62–19.08
CCGGG 1.12 1   
CAGAG 0.18 1 0.64 0.08–4.96
  1. a A moving window of 5 SNPs was used to determine haplotype associations. Each haplotype begins with the listed first SNP followed by four of the following consecutive SNPs: ARS-BFGL-NGS-40630, ARS-BFGL-NGS-115798, ARS-BFGL-NGS-12436, ARS-BFGL-NGS-102, BTB-00352779, Hapmap39688-BTA-81545, Hapmap49326-BTA-81546, ARS-BFGL-NGS-55438, Hapmap36177-SCAFFOLD210634_2319
  2. b Positions according to NCBI UMD3.1.1
  3. c Bonferroni corrected p-value
  4. d OR: Odds ratio
  5. e 95% confidence interval upper and lower limit