Identification of single-nucleotide variants associated with susceptibility to Salmonella in pigs using a genome-wide association approach

Table 4 Top 15 SNVs ranked by significance for the GWAS analysis of Salmonella seropositivity from end of nursery to end of finisher

SNV ID	SSC^a	Location (bp)^b	Variant type	Gene^c	Gene location^b	p-value^d
rs81241392	17	28,616,449	intron	RALGAPA2	17: 28394827–28,679,538	7.6 × 10^− 5
rs323410857	1	201,886,813	intron	HACD4	1: 201886332–201,910,664	8.2 × 10^− 5
rs81459294	16	1,133,302	intron	CTNND2	16: 508245–1,521,550	1.0 × 10^− 4
rs80868434	7	30,048,501	intergenic	MLN	7: 30003291–30,013,128	1.2 × 10^− 4
rs80849858	1	77,472,299	intergenic	TRAF3IP2	1: 77484191–77,523,887	1.2 × 10^− 4
rs336677749	17	28,600,733	intron	RALGAPA2	17: 28394827–28,679,538	1.3 × 10^− 4
rs330020208	6	89,629,789	intron	PHC2	6: 89574035–89,685,278	1.3 × 10^− 4
rs81370878	3	56,211,114	intergenic	VWA3B	3: 55950591–56,171,826	1.4 × 10^− 4
rs323186575	6	91,486,462	intron	ZMYM4	6: 91455778–91,623,818	1.4 × 10⁻⁴
rs80970182	17	28,210,436	intron	CFAP61	17: 28111660–28,372,543	1.4 × 10⁻⁴
rs80930168	1	77,338,889	intron	REV3L	1: 77195253–77,401,051	1.9 × 10⁻⁴
rs80801203	17	28,465,351	intron	RALGAPA2	17: 28394827–28,679,538	2.1 × 10⁻⁴
rs338087144	14	77,361,157	intergenic	KAT6B	14: 77404443–77,597,673	2.4 × 10⁻⁴
rs81241392	17	28,616,449	intron	RALGAPA2	17: 28394827–28,679,538	2.6 × 10⁻⁴
rs81290595	15	6,253,250	intron	ENSSSCG00000036561	15: 6222423–6,266,771	2.8 × 10⁻⁴

^aSSC = Sus scrofa chromosome
^bLocation in Ensembl Sscrofa11.1
^cIf the variant was intergenic, the closest gene within a 1 Mbp window was indicated
^dSNVs under the suggestive significance threshold of 1.0 × 10⁻⁵ in bold [39]

ISSN: 1746-6148