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Table 1 The allele genotypes, frequencies and significance of SNPs discovered

From: Polymorphisms of HOMER1 gene are associated with piglet splay leg syndrome and one significant SNP can affect its intronic promoter activity in vitro

ID Name Region Position on genomic SNP Site (Reverse stand) Allele Allele Freq. (Normal pigs/Affect pigs) HW-test Chi-square test (P-Value)
SNP1 rs339135425 Intron4 Chr2:88207019 G > A G 0.72/0.52 0.4566 0.001223**
      A 0.28/0.48   
SNP2 rs344370846 Intron4 Chr2:88206832 G > A G 0.87/0.77 0.4212 0.02992*
      A 0.13/0.23   
SNP3 rs335396960 Intron4 Chr2:88206806 C > T C 0.88/0.76 0.4212 0.006143**
      T 0.12/0.24   
SNP4 rs325197091 Intron4 Chr2:88206745 A > G A 0.51/0.29 0.05079 3.032E-05***
      G 0.49/0.71   
SNP5 rs342088137 Intron4 Chr2:88206700 C > T C 0.88/0.76 0.4212 0.006143**
      T 0.12/0.24   
SNP6 rs333077091 Intron4 Chr2:88206655 T > C T 0.81/0.67 0.0002 0.004711**
      C 0.19/0.33   
SNP7 rs323497886 Intron4 Chr2:88206523 G > A G 0.71/0.60 0.749 0.4179ns
      A 0.29/0.40   
SNP8 rs332280474 Intron4 Chr2:88206451 C > T C 0.50/0.75 0.05749 3.83E-03**
      T 0.50/0.25   
SNP9 rs322755731 Intron4 Chr2:88206438 T > G T 0.47/0.27 0.2829 0.00013***
      G 0.53/0.73   
SNP10 rs343753765 Intron4/exon5 Chr2:88206361 C > T C 0.63/0.54 0.7639 0.1004ns
      T 0.37/0.46   
SNP11 rs331422651 Intron4/exon5 Chr2:88206349 C > T C 0.88/0.76 0.7409 0.005049**
      T 0.12/0.24   
SNP12 rs318637436 exon5 Chr2:88206180 C > T C 0.87/0.77 0.5831 0.08725
      T 0.13/0.23   
SNP13 rs344145865 Intron11 Chr2:88144031 G > T G 0.48/0.30 0.2249 0.000729**
      T 0.51/0.70   
SNP14 rs793766633 exon12/3’UTR Chr2:88125722 - > A/AA/AAA 0.64/0.56 2.00E-04 0.1589ns
      A 0.36/0.44   
SNP15 rs792865901 exon12/3’UTR Chr2:88125522 - > TT/TTT/TTTT/TTTTT/TTTTTTT 0.58/0.57 1.00E-04 0.8211ns
      T 0.42/0.43   
SNP16 rs711466420 exon12/3’UTR Chr2:88124963 - > T 0.19/0.06 1 0.001152***
      T 0.81/0.94   
SNP17 rs701289492 exon12/3’UTR Chr2:88124822 A > G A 0.93/0.95 0.501 0.6271ns
      G 0.07/0.05   
SNP18 rs698648923 exon12/3’UTR Chr2:88124516 T > C T 0.93/0.95 0.5341 0.6069ns
       0.07/0.05   
SNP19 rs709236548 exon12/3’UTR Chr2:88123927 - > AG 0.63/0.42 1.60E-07 0.0001241***
      AG 0.37/0.58   
SNP20 rs336678612 exon12/3’UTR Chr2:88123776 G > A / / / /
SNP21 rs326987887 exon12/3’UTR Chr2:88123705 C > T / / / /
  1. The ID and position of all the SNPs were referred to Sscrofa11.1. HW-test was the Hardy-Weinberg test. ns P > 0.05;*P < 0.05;**P < 0.01;***P < 0.001. Reverse strand sequence was used