Table 2.

Genomic regions that potentially display pairwise epistatic interaction based on the high frequency of it being descendent pair for milk and fertility traits across countries

Countrya	Trait	SNP 1		SNP 2		Average depth	P-value*	Individual rank based on importance score
		BTAb	Locationb	BTAb	Locationb			SNP 1	SNP 2
US	Milk Yield	23	32,682,177	5	95,459,836	1.18	0.0003	1	5
		30	140,296,904	20	69,528,142	1.24	0.0009	14	30
		19	14,409,010	11	10,271,653	1.24	0.0009	3	46
	Fat Yield	19	41,615,615	19	14,409,010	1.42	0.0002	2	1
		19	41,615,615	2	83,919,557	1.36	0.0006	2	7
		11	56,825,445	5	62,248,841	1.29	0.0006	6	10
		12	12,685,397	7	96,192,503	1.16	<0.001	31	15
	Protein Yield	23	32,682,177	1	24,549,757	1.41	0.0005	1	19
		9	7,645,969	1	24,549,757	1.05	0.0009	65	19
		25	29,428,407	2	113,716,333	1.30	0.0009	2	4
	Calving Interval	7	82,173,456	2	83,616,368	1.53	0.0002	1	3
		25	17,166,118	9	44,951,803	1.18	0.0006	7	2
		26	30,607,485	7	82,173,456	1.15	0.0006	12	1
		7	82,173,456	7	41,207,144	1.43	0.0007	1	5
		8	34,242,903	7	82,173,456	1.43	0.0009	32	1
AU	Milk Yield	22	39,545,402	1	112,497,788	1.03	0.0002	25	14
		21	62,115,138	11	38,445,947	1.04	0.0003	35	47
		14	16,526,322	1	13,304,658	1.27	0.0004	68	17
		20	35,012,179	20	29,322,034	1.46	0.0006	51	3
		22	31,649,896	16	42,262,470	1.32	0.0008	4	41
	Fat Yield	6	56,522,979	2	13,411,225	1.08	0.0002	10	18
		9	59,036,606	8	51,460,409	1.73	0.0005	5	3
		8	51,460,409	7	8,860921	1.26	0.0009	3	4
	Protein Yield	14	38,155,245	7	107,837,688	1.27	0.00007	2	18
		17	38,275,065	17	5,445,294	1.38	0.0005	17	20
		14	38,155,245	8	51,695,384	1.40	0.0006	2	22
		16	64,623,464	11	109,818	1.00	0.0008	42	11
	Calving Interval	24	37,002,274	24	7,380,047	1.04	0.0003	16	44
		5	33,334,061	3	9,686,101	1.38	0.0004	1	3
		15	16,416,329	10	53,560,658	1.25	0.0004	14	6
		17	9,753,430	3	80,517,326	1.40	0.0009	8	27

^aAU refers to Australia and US refers to United States

^bBTA refers to chromosome and the region and location are in Mb build UMD 3.1 (http://bovinegenome.org/cgi-bin/gbrowse/bovine_UMD31/)

*P-values were generated based on a permutation test (Doerge and Churchill [23]) for each analysis