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

Table 3 Top 15 SNVs ranked by significance for the GWAS analysis of isolation of Salmonella from tissues at slaughter

SNV ID	SSC^a	Location (bp)^b	Variant type	Gene^c	Gene location^b	p-value^d
rs322440805	3	130,637,256	intergenic	DCDC2C	3: 131097730–131,194,726	1.6 × 10⁻⁶
rs326411709	3	130,676,894	intergenic	DCDC2C	3: 131097730–131,194,726	3.7 × 10^− 6
rs319944764	3	130,689,632	intergenic	DCDC2C	3: 131097730–131,194,726	8.6 × 10⁻⁶
rs81348815	1	15,081,855	intergenic	AKAP12	1: 14906823–15,016,841	2.0 × 10⁻⁵
rs80951933	1	15,109,785	intergenic	AKAP12	1: 14906823–15,016,841	3.1 × 10⁻⁵
rs80903645	1	15,064,589	intergenic	AKAP12	1: 14906823–15,016,841	3.6 × 10⁻⁵
rs326617356	18	26,691,633	intergenic	KCND2	18: 26554190–26,623,034	1.3 × 10^− 4
rs323563819	19	109,560,455	intron	GPC3	X: 109536447–110,060,245	2.0 × 10⁻⁴
rs80820138	14	122,383,711	intergenic	GPAM	14: 122542205–122,577,239	2.0 × 10⁻⁴
rs80961723	7	120,400,325	intergenic	SETD3	7: 120412549–120,486,627	2.2 × 10⁻⁴
rs320610499	6	141,349,179	intron	NEGR1	6: 141115729–141,647,820	2.5 × 10⁻⁴
rs81296290	2	91,504,717	intron	VCAN	2: 91287931–91,811,674	2.8 × 10⁻⁴
rs324243793	18	38,747,572	intron	DPY19L2	18: 38693003–38,764,024	3.3 × 10⁻⁴
rs80840697	1	14,988,130	intron	AKAP12	1: 14906823–15,016,841	4.1 × 10⁻⁴
rs81361262	2	90,665,766	downstream	ATG10	2: 90437020–90,665,380	4.5 × 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