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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]