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Table 5 Windows explaining the largest percentages of genetic variance for insect bite hypersensitivity in Icelandic horses

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

1

7

0.215

25

4.5

BIEC2 _2768

7,759,159

0.94

0.69

0.46

3

35

0.392

18

5.4

BIEC2 _776785

35,897,049

0.45

0.46

0.26

4

24

0.161

17

2.7

BIEC2 _855840

24,611,718

0.32

0.51

0.33

4

43

0.180

18

4.0

BIEC2 _861849

43,590,939

0.51

0.69

0.49

5

26

0.176

20

3.2

BIEC2 _898729

26,364,893

0.52

0.60

0.38

6

6

0.166

43

4.4

BIEC2 _937490

6,127,639

0.69

0.54

0.30

7

55

0.179

24

3.8

BIEC2 _1001715

55,888,542

0.36

0.35

0.18

9

78

0.182

30

3.9

BIEC2 _1106244

78,254,394

0.44

0.43

0.25

11

40

0.266

21

3.5

BIEC2 _152809

40,721,405

1.30

0.67

0.42

15

19

0.162

23

3.7

BIEC2 _293503

19,944,954

0.66

0.55

0.34

15

20

0.211

22

3.1

BIEC2 _293623

20,074,216

1.04

0.68

0.44

15

32

0.142

23

3.2

BIEC2 _301468

32,220,117

0.31

0.59

0.41

15

33

0.381

32

4.9

BIEC2-301721

33,565,370

2.23

0.70

0.42

18

32

0.179

27

3.9

BIEC2 _431445

32,561,292

0.69

0.54

0.34

19

15

0.186

24

3.5

BIEC2 _430270

15,644,656

0.45

0.54

0.35

19

21

0.151

26

3.3

BIEC2 _431289

21,754,514

0.33

0.75

0.57

20

30

0.162

17

2.2

BIEC2 _528135

30,619,697

0.87

0.78

0.53

23

4

0.159

27

3.4

BIEC2 _637804

4,466,955

0.49

0.74

0.55

X

59

0.658

29

7.9

BIEC2 _1126534

59,703,839

1.04

0.58

0.33

X

60

0.282

29

3.6

BIEC2 _1126713

60,238,370

1.32

0.59

0.33

  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 7 Mb includes SNP located on that particular chromosome between 7 to 8 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.