Table 1. Most significant SNPs identified through case-control (bilaterally deaf vs. controls) genome-wide association studies in Dalmatians, Australian cattle dogs, and English setters.

Breed	N	CFA	bp	SNP ID	af all (deaf/controls)	pvea	beta	P-value
Dalmatians North America	20 deaf, 91 controls	30	37,235,914	BICF2P1106247	0.104 (0.300/0.060)	0.167	-0.353	7.25×10−6*
		30	33,816,254	BICF2P113616	0.333 (0.625/0.269)	0.155	-0.222	1.60×10−5*
		23	48,506,877	BICF2G630365393	0.441 (0.725/0.379)	0.150	-0.220	2.28×10−5*
		30	22,647,163	BICF2G630405064	0.068 (0.200/0.038)	0.130	-0.408	8.93×10−5*
		37	27,255,309	BICF2G630132623	0.243 (0.450/0.198)	0.122	-0.245	1.54×10−4*
Dalmatians UK	72 deaf, 43 controls	38	21,626,523	BICF2G63068103	0.152 (0.083/0.267)	0.127	0.350	8.22×10−5*
Australian cattle dogs	16 deaf, 61 controls	3	37,793,043	BICF2G630338450	0.299 (0.656/0.205)	0.277	-0.313	6.46×10−7**
		3	17,067,881	BICF2G630703558	0.117 (0.344/0.057)	0.229	-0.408	8.45×10−6*
		16	36,220,138	BICF2P1229299	0.091 (0.281/0.041)	0.213	-0.453	1.91×10−5*
		6	10,527,823	BICF2S23125774	0.240 (0.500/0.172)	0.212	-0.330	2.05×10−5*
		17	18,275,241	chr17_18275241	0.110 (0.313/0.057)	0.187	-0.377	6.96×10−5*
		6	75,622,113	BICF2P481353	0.071 (0.219/0.033)	0.184	-0.505	8.37×10−5*
		22	48,747,165	BICF2G630335709	0.494 (0.188/0.574)	0.181	0.239	9.66×10−5*
		9	8,460,580	BICF2S23511312	0.130 (0.313/0.082)	0.178	-0.395	1.09×10−4*
		24	47,255,337	TIGRP2P322787_rs9139922	0.136 (0.344/0.082)	0.176	-0.344	1.19×10−4*
English setters	11 deaf, 39 controls	39	111,315,267	BICF2G6304357	0.220 (0.421/0.154)	0.192	-0.276	1.20×10−3

af = allele frequency, beta = effect size, pve = proportion of variance explained

All bp positions are listed in canFam3.1 assembly

^aCalculated using output of GEMMA with equation pve = 1/(1+(N*(se(beta)^2)/beta^2) where N = sample size, se(beta) = standard error of beta. This equation is simplified from Shim et al. (2015) [38]

**Significant association using genome-wide threshold determined from unlinked SNPs

*Suggestive association using threshold determined from unlinked SNPs at the chromosome level