Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle

Table 3 Description and LD summary statistics for the candidate structural variants that are most highly correlated with tag SNPs rs451683615 (Chr6 g.64210286A>G) and rs463810013 (Chr6 g.71722665C>T)

Region spanning CNV	Type	rs451683615 correlation (R²)	rs46381013 correlation (R²)	Closest gene	Maximum R²	SNP ID	GWAS p-value
Chr6:64,092,201–64,092,752 bp	Deletion	0.172	0.099	KCTD8	0.544	rs110545184	3.24 × 10⁻²²
Chr6:65,557,508–65,559,004 bp	Deletion	0.102	0.066	GNPDA2	0.876	rs384078363	3.74 × 10⁻⁵
Chr6:65,657,051–65,657,595 bp	Deletion	0.128	0.089	GNPDA3	0.746	rs383024906	2.79 × 10⁻¹¹
Chr6:68,269,498–68,270,804 bp	Deletion	0.171	0.164	NFXL1	0.569	rs456305543	5.89 × 10⁻³⁴
Chr6:71,310,834–71,312,202 bp	Deletion	0.065	0.163	GSX2	0.695	rs466525306	4.78 × 10⁻¹²
Chr6:72,060,120–72,060,450 bp	Duplication	0.22	0.431	KIT	0.432	rs385773341	8.08 × 10⁻⁶¹

CNV copy number variant, R² linkage disequilibrium correlation coefficient, SNP ID single nucleotide polymorphism accession number

ISSN: 1297-9686