Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus

Lee, Michael A; Keane, Orla M; Glass, Belinda C; Manley, Tim R; Cullen, Neil G; Dodds, Ken G; McCulloch, Alan F; Morris, Chris A; Schreiber, Mark; Warren, Jonathan; Zadissa, Amonida; Wilson, Theresa; McEwan, John C

doi:10.1186/1471-2164-7-298

BMC Genomics

Table 2 SNP allele frequencies and associations with measured traits.

From: Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus

SNP_ID	Gene	Breed	A	C	G	T	P value
*Puberty*
CS2000955300001_532	ANAPC5	Angus		0.16		0.84	N.S.
CS2000053300001_175	HMOX2	Angus			0.58	0.42	N.S.
CS2000507200001_1768	ITIH2	Angus	0.41	0.59			N.S.
CS2000742700001_590	TNFAIP6	Angus		0.86		0.14	N.S.
CS2001189600001_489	ITHI5	Angus	0.84	0.16			N.S.
CS2000742700001_881	TNFAIP6	Angus			1		N.S.
*FE resistance*
CS2000348000001_262	ABCB8	Friesian		0.62	0.38		N.S.
		Jersey		0.63	0.37		N.S.
CS2001041800001_1020	SELP	Friesian	0.40	0.60			N.S.
		Jersey	0.44	0.56			N.S.
CS2001337000001_147	CAMP	Friesian		0.50		0.50	N.S.
		Jersey		0.51		0.49	N.S.
CS2000058700002_510	CD1D	Friesian	0.48		0.52		N.S.
		Jersey	0.49		0.51		N.S.
CS2001176100001_1124	LTB4R	Friesian			0.16	0.84	N.S.
		Jersey			0.24	0.76	N.S.
CS2000288200001_809	BCL10	Friesian		0.93		0.07	N.S.
		Jersey		0.93		0.07	0.004
CS2000088400007_1168	GBP1	Friesian		0.50		0.50	N.S.
		Jersey		0.52		0.48	N.S.
CS2001051700001_529	C8A	Friesian		0.88		0.12	N.S.
		Jersey		0.75		0.25	0.03
CS2000129600001_1471	HRG	Friesian		0.93		0.07	0.05
		Jersey		0.96		0.04	N.S.
CS2001364900001_48	LTB	Friesian		0.74	0.26		N.S.
		Jersey		0.65	0.35		N.S.
CS2000088400007_1687	GBP1	Friesian	0.49			0.51	N.S.
		Jersey	0.49			0.51	N.S.
CS2000088400007_313	GBP1	Friesian		0.35		0.65	N.S.
		Jersey		0.29		0.71	0.006
CS2000088400007_996	GBP1	Friesian	0.50		0.50		N.S.
		Jersey	0.50		0.50		N.S.
CS2000257600002_413	ABCC3	Friesian		0.76	0.24		0.008
		Jersey		0.77	0.23		N.S.
CS2000313400001_398	OAS1	Friesian	0.23		0.77		N.S.
		Jersey	0.22		0.78		N.S.
CS2000348000001_980	ABCB8	Friesian			1		N.S.
		Jersey			1		N.S.
CS2001315600002_1764	SERPING1	Friesian			0.54	0.46	N.S.
		Jersey			0.56	0.44	N.S.
CS2000173400002_1082	IGSF8	Friesian			0.50	0.50	N.S.
		Jersey			0.73	0.27	N.S.
CS2000058700002_496	CD1D	Friesian			0.50	0.50	N.S.
		Jersey			0.50	0.50	N.S.
CS2000058700002_976	CD1D	Friesian	0.50		0.50		N.S.
		Jersey	0.48		0.52		N.S.
CS2001406800001_259	TAP2	Friesian		0.70		0.30	N.S.
		Jersey		0.73		0.27	N.S.
CS2000313400001_155	OAS1	Friesian		0.14	0.86		0.04
		Jersey		0.13	0.87		N.S.
CS2000176900001_1229	HP	Friesian	0.17		0.83		N.S.
		Jersey	0.35		0.65		N.S.
CS2000045400004_497	CYP4A11	Friesian		1			N.S.
		Jersey		1			N.S.
CS2000218500001_1206	CD44	Friesian	0.60	0.40			N.S.
		Jersey	0.43	0.57			N.S.
CS2000068700001_485	GIMAP5	Friesian	0.38		0.62		N.S.
		Jersey	0.38		0.62		N.S.
*Meat yield*
CS2000104200001_1729	PLG	Angus		0.48		0.52	N.S.
		Hereford		0.53		0.47	N.S.
		Simmental		0.68		0.32	N.S.
CS2000443600001_487	EPHX2	Angus	0.98		0.02		N.S.
		Hereford	0.63		0.37		N.S.
		Simmental	0.86		0.14		N.S.
CS2001349700001_285	ALDOB	Angus	0.72		0.28		N.S.
		Hereford	0.58		0.42		N.S.
		Simmental	0.43		0.57		N.S.
CS2000071200002_488	ACADS	Angus	0.13		0.87		N.S.
		Hereford	0.22		0.78		N.S.
		Simmental	0.14		0.86		N.S.
CS2000660700001_630	PHYH	Angus	0.24		0.76		N.S.
		Hereford	0.02		0.98		N.S.
		Simmental			1		N.S.
CS2000613600001_354	WARS2	Angus	0.36		0.64		N.S.
		Hereford	0.55		0.45		N.S.
		Simmental	0.18		0.82		N.S.
CS2003511700001_128	LEP	Angus		0.40		0.6	N.S.
		Hereford		0.31		0.69	N.S.
		Simmental		0.58		0.42	N.S.
CS2000005800001_509	ACP1	Angus		0.51		0.49	N.S.
		Hereford		0.53		0.47	N.S.
		Simmental		0.50		0.50	N.S.
CS2001330700002_10011	TNXB	Angus	0.55		0.45		N.S.
		Hereford	0.49		0.51		N.S.
		Simmental	0.61		0.39		N.S.

N.S. = not significant (P > 0.05).
Allele frequencies in bold are not in Hardy-Weinberg equilibrium.

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