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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.