Skip to main content

Table 4 A summary of all coding SNVs in EAE and arthritis regulating QTLs

From: Identification of candidate risk gene variations by whole-genome sequence analysis of four rat strains commonly used in inflammation research

Chr.

Phenotype/QTL

Start

End

QTL length (Mb)

Ensmbl genes in QTL

All genes with cSNVs

NS SNVs

STOP c. SNVs

Splice site SNVs

Indels

New candidate genes

Evidence

Strains

Reference

1

PIA8

11

19

8

43

3

2

0

0

1

NS SNVs in Ect2l, and ATG4B, indel in ALDH8A1

F2

DA.PVG,

[42]

1

Eae29

15

17

3

18

2

1

0

0

1

conserved SNVs in IL22RA2, short indel in ALDH8A1, NS SNV in ATG4B

G10, congene

DA/PVG

[29, 31]

1

Eae30

129

130

1

7

1

1

0

0

0

RGMA, NS SNV in Top1

G10, congene

DA/PVG

[29, 33]

1

CIAA6/EAE6/7

156

247

91

1343

225

136

2

93

12

stopcodon in Ltbp3 and in Ms4a5

F2 BC

DA/E3

[16]

1

Eae6

176

218

42

764

147

84

1

62

6

stopcodon in Ms4a5

F2

DA/E3

[18]

1

Eae31

185

185

1

6

3

2

0

1

0

IL21R 1 cons SNV, splice site in IL4R, NS SNVs in Gtf3c and LOC361646

G10, congene

DA/PVG

[15, 29, 33]

1

Eae7

240

247

7

64

25

16

0

12

1

indel in Myof, splice site SNV in Znf518a

F2

DA/E3

[18]

4

PIA2/AIA2

32

42

10

28

7

6

0

3

2

indel in Dpp6, and frameshift SNV in Tmem106b

F2 BC

DA/BN, E3

[8, 16]

4

Eae24

60

75

15

146

28

21

1

9

0

stop in an orf in a intron of Dgki

G10, congene

DA/PVG

[21, 43, 44]

4

Eae25

75

83

8

88

22

19

0

6

1

indel in Znf282 (HUB1)

G10, congene

DA/PVG

[21, 43, 44]

4

PIA5/CIA3

78

104

26

248

56

45

2

9

2

2 Stop in Igk genes

F2 BC congene

DA/BN,E3

[15, 16]

4

Eae26

83

104

21

206

28

24

0

5

2

indel in Herc6, and RPS7

G10, congene

DA/PVG

[21, 43, 44]

4

Eae27

104

114

10

61

7

6

0

1

0

NS SNVs in both CD8a and Cd8b

G10,congene

DA/PVG

[21, 43, 44]

4

Eae20

156

161

5

88

24

18

2

8

1

indel in Rad52, stop in Clec4b2, stop in Q6QI20

G10, congene

DA/PVG

[24, 44]

4

PIA7/OIA2/CIA13

159

160

1

23

8

6

2

2

0

stop in Clec4b2

F2 congene

DA/E3,PVG

[45, 46]

4

Eae21

161

162

1

23

4

2

0

3

0

splice SNV in Pianp, Zfp384, NS SNV Vwf

G10,congene

DA/PVG

[24, 44]

4

Eae22

162

172

10

137

34

27

1

14

1

Essential splice site SNV in Klrc2, stop Clec2

G10, BC

DA/PVG

[24, 44]

5

CIAA5

138

172

34

554

113

92

1

27

4

Stop in orf, indel in Nmnat1, Myom3, SZT2

F2 BC

DA/E3

[15, 16, 18]

6

PIA3/eae9

117

144

31

249

70

55

1

16

6

stop in F1M0Z7_RAT

F2 congene

DA/E3

[15, 16, 18]

7

PIA13

62

78

16

116

15

12

0

2

1

indel in Ptdss1

F2

DA/E3

[15, 16, 18]

8

PIA14

79

87

8

53

11

8

0

3

0

splice site in Lrrc1, Ick, Eef1a1

F2

DA/E3

[15, 16, 18]

10

Vra4/Eae

0

11

11

94

13

11

0

2

0

no coding SNVs in Ciita

congene

DA/PVG

[47, 48]

10

Eae18a

55

67

12

303

67

47

1

20

2

stop in krt18-b, 2 NSC and splice site SNV in Nos2

G7,G10,congene

DA/PVG

[20, 22, 25]

10

Eae18b

67

72

5

68

22

12

0

10

2

CCL11 conserved SNVs

G7,G10,cong.

DA/PVG

[20, 25, 30, 49]

10

CIA5A OIA3 PIA10 EAN5

95

110

15

214

36

29

0

8

3

Cd300 hyper polymorphic regions, indel in Fdxr, Acox1, Tnrc6c

G10 F2 congene

DA/PVG

[14, 50]

11

Pia27, RF

84

86

2

53

6

4

0

2

1

Essential splice site in Lac2

F2 congene

DA/E3

[51]

12

Eae5

20

24

4

70

16

11

0

5

0

NCF1, CLN4, splice site SNV i Gtfi1

G7, congene

DA/PVG

[28, 49]

12

PIA4/NCF1

  

*

  

1

   

NCF1 NS SNV aa153

congene

DA/E3

[16, 52]

14

PIA6/EAE10/CIAA7

32

103

71

408

39

25

0

12

3

NS SNV Tlr10, Igfbp3, indel Aebp1, Apex2

F2

DA/E3

[53, 54]

15

Eae19

83

97

14

33

7

7

0

1

0

Lmo7, Tbc1d4, Mycbp2, Uchl3, Slitrk6

G7,congene

DA/PVG

[20, 26]

17

Eae23a

36

57

21

180

13

12

0

1

0

NS SNVs in Ripk1, Serpinb1a, Gpx6, splice-SNV in Agtr1a

G10, cong.

DA/PVG

[29, 32, 55]

17

Eae23b

57

66

9

49

11

8

1

3

1

stop in Prelid1

G10, cong.

DA/PVG

[29, 32, 55]

20

Pia1

3

5

2

114

50

40

1

16

0

NS SNVs in Ncr3, Lst1, RT1-Ba, Tap2, Psmb8, Tap1, Psmb9, Stop in RT1-CE4

F2

DA/E3, PVG DA/LEW,BN

[8, 15]

20

Eae1

5

7

2

55

14

8

0

4

3

NS SNVs in Tapbp, RT1-A2, RT1-A2 frameshift mutation in Grm3

F2

DA/E3, PVG DA/LEW,BN

[18]