Table 4.

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

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

^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.