Table 4.

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

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]