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

Table 2 Haplotypes associated with DYD for SCS

Hap ID	Position (bp)			Length (Mb)	HapA	HF	β	P-value	Genetic variance %^#	Genes within HTB	Other nearby genes^‡
Hap ID	Chr	Start	End	Length (Mb)	HapA	HF	β	P-value	Genetic variance %^#	Genes within HTB	Other nearby genes^‡
BTA5_Hap5*	5	97862816	97948752	0.09	TCAG	0.35	-0.09	7.05E-07	0.37	LOH12CR1, MANSC1	CDKN1B
BTA6_Hap4*	6	85142067	85527109	0.39	CAGG	0.34	0.09	1.84E-07	0.44	GNRHR, TMPRSS11D	UBA6
BTA6_Hap8	6	86642355	86904512	0.26	AGGG	0.38	0.107	4.08E-08	0.54	LOC781988, UGT2A1	SULT1B1
BTA6_Hap12*	6	87929420	88174863	0.25	AAGGGC	0.32	0.103	3.37E-07	0.46	GRSF1, MOB1B, DCK	IGJ, DBP
BTA13_Hap10*	13	78383148	78858126	0.47	AAAGGAG	0.14	0.12	3.60E-08	0.33	SLC9A8, RNF114	UB2V1, PTGIS
BTA13_Hap17*	13	79730805	79775537	0.04	GA	0.34	0.08	9.79E-08	0.30		KCNG1, NFATC2
BTA13_Hap34	13	83917405	84002346	0.08	ACAA	0.12	0.12	3.94E-08	0.31		CBLN4
BTA18_Hap6a*†	18	43327273	43379174	0.05	CA	0.41	-0.07	4.61E-07	0.27	RGS9BP, TDRD12	CEBPG
BTA18_Hap6b*†	18	43327273	43379174	0.05	AG	0.58	0.07	7.38E-07	0.26	RGS9BP, TDRD12	CEBPG
BTA19_Hap7*	19	50547082	50647677	0.10	GAA	0.19	-0.11	2.64E-08	0.39	RAB40B, FN3KRP	FOXK2, CD7, NPB

Chr = chromosome; Hap ID = haplotype ID; Mb = megabase; HapA = haplotype alleles; HF = haplotype frequency; β = change per significant haplotype (regression coefficient); HTB = haplotype block; BTA = Bos taurus autosome;
^#genetic variance for significant haplotype is based on the formula 2β2f (1-f), where β denotes the change per significant haplotype and f denotes the frequency of the variant; ^‡other nearby genes = genes within an area of 1 Mb upstream or downstream of the haplotype block boundaries; genes of known immune functions are written in italic; ^*haplotype blocks contain SNPs which are significant in GWAS for single marker analyses; † two significant haplotypes were identified in this haplotype block, BTA18_Hap6 (a for the first haplotype and b for the second one); positions follow 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