A 2cM genome-wide scan of European Holstein cattle affected by classical BSE

BMC Genomic Data

Table 3 Comparison of SNPs observed in this study with locations indentified in other studies.

		Analysis		Location	Previously	Peak
CHR	SNP ID	Method	p-value	Mb	Observed	Location Mb
1	rs29009859	sib-TDT	2.0 × 10^-5	89.7	[14]	106.5
5	AAFC02012009	sib-TDT	**9.9 × 10^-3	30.6	No
5	E25B16-36408-3	sib-TDT	**8.8 × 10^-5	66.5	No
5	rs29012226	sib-TDT	**1.9 × 10^-3	67.7	No
5	rs29024670	sib-TDT	3.0 × 10^-5	112.8	[13]	107.0
6	SCAFFOLD106936_12205	sib-TDT	**1.8 × 10^-3	98.8	No
10	rs29024570	Case-control	*4.3 × 10^-4	4.4	No
10	rs29013631	sib-TDT	**6.5 × 10^-3	38.7	No
10	rs29015623	sib-TDT	9.0 × 10^-5	48.0	[13]	40.0
17	rs29021871	sib-TDT	**3.0 × 10^-3	44.2	No
19	rs29027102	sib-TDT	2.0 × 10^-5	62.5	[14]	53.5
20	rs29018531	sib-TDT	**3.7 × 10^-3	38.8	[13]	46.0
20	CART-SNP	sib-TDT	**1.0 × 10^-4	4.9^#	No
X	SCAFFOLD68962_9331	sib-TDT	**1.0 × 10^-5	7.6	No
X	SCAFFOLD285727_12117	sib-TDT	1.0 × 10^-5	85.5	[14]	112.5

Sib-TDT p values are reported as unadjusted unless denoted by ** which indicates Bonferroni corrected values that pass 10,000,000 permutations. All case control p-values are reported are as unadjusted and suggested significance is denoted as *. Only SNPs with appreciable or significant p-values located within the confidence intervals of ref# [14] or within 10 cM of ref# [13] are reported here. The location determined by older bovine sequence version 2.0 is denoted by ^#. All other locations were determined by blast to bovine sequence version 4.0 and are reported in mega bases. The previous studies reported location in cM however for the sake of uniformity the location is reported here, based on marker positions, in Mb.

ISSN: 2730-6844