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Table 4 Windows explaining the largest percentages of insect bite hypersensitivity genetic variance in Shetland pony mares

From: Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands

Top 20 associated windowsa

SNP with highest model frequency within window

ECAb

Position (Mb)c

% of genetic variance explainedd

Number of SNP

% of iterations where variance explained > 0.04%e

SNP name

SNP position (bp)

Model frequencyf

Allele frequencyg

        

Cases

Controls

3

8

0.143

21

2.8

BIEC2 _810809

8,098,240

0.29

0.67

0.54

3

17

0.141

30

3.1

BIEC2 _773375

17,036,655

0.38

0.62

0.46

3

50

0.270

27

3.8

BIEC2 _779930

50,444,836

0.68

0.45

0.29

3

51

0.161

25

3.2

BIEC2 _780595

51,525,184

0.35

0.58

0.43

7

67

0.149

27

3.3

BIEC2 _1005528

67,597,722

0.36

0.67

0.54

7

85

0.171

24

2.9

BIEC2 _1010550

85,800,251

0.29

0.64

0.52

8

63

0.231

22

3.8

BIEC2 _1058160

63,839,900

0.47

0.59

0.44

11

22

0.201

21

3.6

BIEC2 _143974

22,769,190

0.32

0.50

0.35

11

23

0.149

24

3.1

BIEC2 _144465

23,873,176

0.31

0.59

0.45

11

26

0.178

26

3.3

BIEC2 _145801

26,946,633

0.20

0.51

0.39

11

32

0.193

31

4.1

BIEC2 _149137

32,010,755

0.37

0.27

0.13

17

1

0.141

24

2.7

BIEC2 _366411

1,024,001

0.27

0.45

0.31

17

6

0.147

28

2.6

BIEC2 _367597

6,640,619

0.29

0.65

0.51

17

75

0.303

23

4.4

BIEC2 _384363

75,401,514

0.67

0.67

0.52

17

76

0.159

18

2.3

BIEC2 _385267

76,776,877

0.81

0.70

0.55

20

35

0.624

23

5.3

UKUL3474

35,643,200

2.03

0.56

0.37

20

41

0.176

21

2.9

BIEC2 _532511

41,520,518

0.84

0.45

0.28

23

14

0.143

25

2.8

TBIEC2 _645769

14,286,784

0.16

0.36

0.27

27

13

0.214

18

3.2

BIEC2 _705454

13,198,799

0.78

0.71

0.54

28

41

0.154

24

3.2

BIEC2 _744415

41,130,845

0.24

0.73

0.61

  1. atop 20 1 Mb non-overlapping windows explaining the largest percentages of genetic variance; bEquus caballus autosome; cposition of the window in Mb pairs, where for instance window position 8 Mb includes SNP located on that particular chromosome between 8 to 9 Mb; dpercentage of total genetic variance explained by 1 Mb non-overlapping windows of consecutive SNP based on physical order (build EquCab2.0), averaged across post burn-in iterations, thereby including results from iterations that excluded the window from the model; epercentage of iterations (out of 1799 saved) during which the window captured over 0.04% of genomic variance (i.e. the expected percentage of variance explained by each window in an infinitesimal model); fpercentage of iterations where SNP was modelled to have an effect; gfrequency of the unfavourable allele.