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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