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Table 2 SNPs within candidate genes used for association analysis

From: Genome-wide association study reveals a QTL and strong candidate genes for umbilical hernia in pigs on SSC14

Gene Name SNP name Location Allelesa MAFb Pc %vard
Versican VCAN_1 Exon 8 A/G 0.45 n.s. 0.2
Versican VCAN_2 Exon 8 G/A 0.45 n.s. 0.4
Versican VCAN_3 Exon 8 T/G 0.45 n.s. 0.4
Versican VCAN_4 Exon 8 C/T 0.45 n.s. 0.2
Versican VCAN_5 Exon 8 C/A 0.38 n.s. 0.4
Versican VCAN_6 Exon 8 C/T 0.38 n.s. 0.4
Leukemia inhibitory factor LIF_1 Intron 1 A/G 0.47 0.001 8.6
Matrix metallopeptidase 13 MMP13_1 Intron 7 G/A 0.33 n.s. 0.08
Matrix metallopeptidase 13 MMP13_2 Intron 7 T/G 0.33 n.s. 0.05
Matrix metallopeptidase 13 MMP13_3 Exon 8 A/G 0.33 n.s. 0.1
Matrix metallopeptidase 13 MMP13_4 Intron 8 C/T 0.33 n.s. 0.03
Matrix metallopeptidase 13 MMP13_5 Intron 8 T/C 0.32 n.s. 0.01
Matrix metallopeptidase 13 MMP13_6 Intron 8 G/T 0.33 n.s. 0.3
Oncostatin M OSM_1 Exon 3 C/T 0.47 0.001 7.7
Oncostatin M OSM_2 Exon 3 T/C 0.47 0.001 8.6
Oncostatin M OSM_3 Exon 3 T/C 0.47 0.001 8.6
Oncostatin M OSM_4 Exon 3 G/T 0.47 0.0008 8.6
Oncostatin M OSM_5 Exon 3 A/G 0.47 0.001 8.6
Oncostatin M OSM_6 Intron 3 C/T 0.47 0.001 7.7
Oncostatin M OSM_7 Intron 3 T/C 0.47 0.001 7.7
Oncostatin M OSM_8 Intron 3 A/G 0.47 0.001 7.7
Pyrroline-5-carboxylate reductase 1 PYCR1_1 5’ UTR A/T 0.11 n.s. 2.5
Pyrroline-5-carboxylate reductase 1 PYCR1_2 5’ UTR C/T 0.13 n.s. 1.0
Pyrroline-5-carboxylate reductase 1 PYCR1_3 Intron 1 C/T 0.03 n.s. 1.0
Vimentin VIM_1 Intron 5 C/T 0.21 n.s. 0.2
Vimentin VIM_2 Intron 5 A/G 0.36 n.s. 0.3
Vimentin VIM_3 Intron 5 C/T 0.17 n.s. 0.01
Vimentin VIM_4 Intron 5 A/G 0.19 n.s. 0.6
Vimentin VIM_5 Intron 5 C/T 0.15 n.s. 0.00
Vimentin VIM_6 Intron 5 C/A 0.34 n.s. 0.3
Vimentin VIM_7 Intron 5 C/A 0.11 n.s. 0.7
  1. amajor/minor allele, where risk allele is indicated in bold
  2. bminor allele frequency (MAF)
  3. cp-value (p > 0.001 is n.s)
  4. dthe percentage of explained phenotypic variance (%var)