Table 3.

Summary of the SNPs identified from the RNA-seq datasets in genes mapping within the GWAS regions

SSC	Interval	Top SNP of the GWAS interval	# SNPs called	Highest LD	SNP with highest LD	Genotypic frequency (0/0; 0/1; 1/1)	# called samples	SNP effect	Gene	Trait
1	I3	rs327733412	3	0.07	rs710447566	0.34; 0.54; 0.11	35	Low	KATNAL2	HABN
7	I2	rs336588919	2	0.4	rs330912302	0.63; 0.12; 0.25	32	Low	CHD2	NABN
13	I1	rs690794887	21	0.4	rs331304027	0.06; 0.09; 0.85	33	Moderate	ULK4	HABN
13	I2	rs327865244	11	0.2	rs323872641	0.49; 0.37; 0.14	35	Low	ABHD14A	HABN

SSC, Sus scrofa chromosome; # SNPs called, number of SNPs identified in the SNP calling analysis; LD, linkage disequilibrium; Genotypic frequency: allelic frequency for each of the genotypes; # called samples, number of samples with reads in the given SNP position; HABN, head abnormalities; NABN, neck abnormalities

The columns SNP effect and gene refer to the SNP with the highest LD in the region