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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
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