Single nucleotide polymorphisms in the bovine MHC region of Japanese Black cattle are associated with bovine leukemia virus proviral load

Table 1 SNPs showing a significant association with BLV proviral load

Chromosome	Ilumina_ID^a	Reference cluster ID^b	Position^c	p	Minor allele^d	Minor allele^d (case)	Minor allele^d (control)	Major allele^e	Odds ratio^f
23	Hapmap57616-rs29026690	rs29026690	27421348	1.91 × 10⁻⁷	A	0.2903	0.1297	G	2.745
23	ARS-BFGL-NGS-113235	rs17872126	28223274	1.91 × 10⁻⁷	G	0.2849	0.4906	A	0.414
22	Hapmap33580-BTA-136506	rs110616206	27280154	5.37 × 10⁻⁷	A	0.0914	0.01504	G	6.589

^aSNP ID assigned by Illumina, Inc
^bReference SNP (refSNP) ID assigned in the single nucleotide polymorphism database (dbSNP)
^cPositions are based on the bovine genome, assembled in UMD3.1
^dMinor allele is minor frequency allele determined in this study
^eMajor allele is major frequency allele determined in this study
^fOdds ratio is the effective value for estimating how strongly the SNPs associated to the proviral load, using following formula
\( {\text{Odds}}\;{\text{ratio}} = \frac{{\frac{{Minor\,allele\;frequency\,\left( {case} \right)}}{{Minor\;allele\;frequency\;\left( {control} \right)}}}}{{\frac{{Major\;allele\;frequency\;\left( {case} \right)}}{{Major\;allele\;frequency\;\left( {control} \right)}}}} \)

ISSN: 1742-4690