Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle

Table 1 SNPs associated with DYD for SCS

SNP ID	Chr	Pos (bp)	FA	FAF	β	P-value	Genetic variance %^#	Nearest gene*	Nearby immune genes^§
ARS-BFGL-NGS-44153	5	97430973	G	0.61	-0.08	5.87E-07	0.30	GPRC5A	CDKN1B
Hapmap53773-ss46526912	5	97948752	G	0.35	-0.09	8.00E-07	0.37	MANSC1	CDKN1B
Hapmap47511-BTA-114200	5	98579869	A	0.64	-0.09	1.47E-08	0.37	ETV6
BTA-77077-no-rs	6	85527109	A	0.60	-0.09	1.39E-06	0.39	TMPRSS11F	TMPRSS11D
ARS-BFGL-NGS-112872	6	88069548	A	0.68	-0.10	9.68E-07	0.44	DCK	DCK, IGJ, DBP
ARS-BFGL-NGS-95538	13	78644697	G	0.86	-0.12	3.55E-08	0.35	SLC9A8	UB2V1
Hapmap47255-BTA-34035	13	79730805	A	0.67	-0.08	8.73E-08	0.28	KCNG1	NFATC2
BTA-33950-no-rs	13	80094921	A	0.42	-0.08	3.67E-07	0.31	NFATC2	NFATC2
Hapmap32551-BTA-128831	13	81743652	A	0.74	-0.08	1.68E-07	0.25	snoU2_19
ARS-BFGL-NGS-14974	13	83242122	A	0.90	-0.12	1.50E-06	0.26	DOK5
Hapmap52325-rs29020544	18	43327273	C	0.43	-0.07	4.86E-07	0.24	RGS9BP	CEBPG
ARS-BFGL-NGS-57076	18	43379174	A	0.42	-0.07	5.85E-07	0.24	TDRD12	CEBPG
Hapmap57515-ss46526957	19	50647677	A	0.19	-0.12	2.19E-08	0.44	FOXK2	FOXK2, CD7, NPB
ARS-BFGL-NGS-117290	19	51680150	A	0.37	-0.08	2.15E-07	0.30	GCGR	NPB, HGS
UA-IFASA-5300	19	52436005	A	0.30	-0.10	9.04E-09	0.42	RPTOR	CARD14
Hapmap47243-BTA-31267	X	30639394	A	0.79	-0.11	1.04E-07	0.40	U6

Chr = chromosome; FA = favorable allele; FAF = favorable allele frequency; β = change per favorable allele (regression coefficient); ^#genetic variance for favorable alleles is based on the formula 2β2f (1-f), where β denotes the change per favorable allele and f denotes the frequency of the variant; *nearest gene = genes within an area of 1 Mb centered at the SNP; ^§nearby immune genes = genes of known immune functions within a window of 1 Mb around SNP; positions are according to the University of Maryland bovine genome assembly (UMD3.1); candidate genes are extracted from the Ensembl data base (UMD3.1 Ensembl data base build 73).

ISSN: 1297-9686