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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.