Table 2.

Loci associated with IIM, PM, DM and JDM cases

Subgroup	Gene Region	Chr	Position	Most Significant SNP	Minor Allele	MAF cases	MAF controls	P-value	OR (95% CI)	Localisation of LD to nearest genes (r2 ≥ 0.9)	Overlap with other autoimmune diseases
IIM	HLA	6	32395726	rs3129843	G	0.24	0.11	9.14×10−133	2.74 (2.53–2.97)	MHC	Multiple
IIM	PTPN22	1	114377568	rs2476601	A	0.12	0.09	7.22×10−9	1.32 (1.20–1.45)	Exon 12 of PTPN22	ATD,[17] IBD,[16] JIA,[18] RA,[19] SLE,[20] SSC,[21] T1D,[22] VIT,[23]
IIM	YDJC	22	21985094	rs5754467	G	0.23	0.20	4.67×10−7	1.21 (1.12–1.30)	Intron 1 of UBE2L3 | complete YDJC	CEL,[6] IBD,[16] JIA,[18] PSO,[24] RA,[19] SLE,[20]
IIM	DGKQ	4	956047	rs6599390	A	0.30	0.34	6.48×10−7	0.85 (0.79–0.90)	Intron 21 of DGKQ to intron 2 of SLC26A1 and intron 2 of IDUA
IIM	STAT4	2	191917317	rs4853540	T	0.19	0.22	1.57×10−6	0.83 (0.77–0.89)	Intron 3 to intron 14 of STAT4	JIA,[18] PBC,[25] RA,[19] SLE,[20]
IIM	MGAT4A	2	99389870	rs10189330	T	0.50	0.46	2.68×10−6	1.16 (1.09–1.23)	Intergenic of C2orf55 (KIAA1211L) and MGAT4A incorporating uncharacterized LOC101927070
IIM	PRR5L | TRAF6	11	36492191	rs570676	A	0.37	0.40	9.42×10−6	0.87 (0.82–0.92)	Intergenic PRR5L (also known as FLJ14213) | complete TRAF6
IIM	CCL17	16	57445376	rs223900	T	0.28	0.25	9.97×10−6	1.17 (1.09–1.25)	Intron 1 of CCL17
IIM	EOMES	3	28076283	rs376072	T	0.26	0.29	1.45×10−5	0.86 (0.80–0.92)	310.68kb upstream of EOMES
IIM	CD28	2	204592021	rs3116494	G	0.28	0.26	1.54×10−5	1.16 (1.09–1.24)	Intron 1 to 8.5kb downstream of CD28	PSC,[26] RA,[19]
IIM	RPL31P10	12	6523249	rs11064180	T	0.38	0.41	1.61×10−5	0.87 (0.82–0.93)	Intergenic of LTBR and CD27
PM	HLA	6	31434366	rs3094013	T	0.25	0.12	6.36×10−76	2.97 (2.64–3.33)	MHC	Multiple
PM	PTPN22	1	114377568	rs2476601	A	0.12	0.09	7.90×10−11	1.58 (1.38–1.81)	Exon 12 of PTPN22	ATD,[17] IBD,[16] JIA[18], RA,[19] SLE,[20] SSC,[21] T1D,[22] VIT,[23]
PM	LOC728073 | RPL38	17	71527243	rs9905921	C	0.48	0.43	2.01×10−6	1.26 (1.14–1.39)	Intronic (provisional in refseq) of SDK2
PM	UBE3B | MMAB	12	109980516	rs7956536	C	0.44	0.46	3.66×10−6	0.80 (0.72–0.88)	Intron 19 of MYO1H, complete KCTD10; UBE3B; MMAB; MVK
PM	NAB1	2	191535576	rs2286896	G	0.15	0.13	3.76×10−6	1.35 (1.19–1.53)	Complete NAB1
PM	FAM167A | BLK	8	11333521	rs17799348	T	0.36	0.39	4.13×10−6	0.80 (0.71–0.87)	Intergenic FAM167A | BLK
PM	IL18R1	2	103012902	rs1420095	G	0.07	0.09	6.16×10−6	0.63 (0.52–0.78)	Intron 3 of IL18R1 : 1L18RAP
PM	SLC26A1 | IDUA	4	980464	rs4690220	G	0.49	0.45	7.47×10−6	1.25 (1.13–1.37)	2.14 Kb 3’ to intron 2 of SLC26A1	SJO,[27]
PM	RGS1	1	192545099	rs7535818	G	0.17	0.18	1.37×10−5	0.74 (0.65–0.85)	25kb upstream to intron 1 of RGS1	CEL,[6] MS,[28] T1D,[22]
DM+JDM	HLA	6	32395726	rs3129843	G	0.21	0.11	1.72×10−48	2.18 (1.97–2.42)	MHC	Multiple
DM+JDM	ROPN1L | ANKRD33B	5	10517908	rs4702698	G	0.34	0.30	4.77×10−6	1.22 (1.12–1.33)	Intergenic of ROPN1L and ANKRD33B
DM+JDM	PTTG1 | ATP10B	5	159928876	rs4921293	G	0.39	0.35	8.27×10−6	1.21 (1.11–1.31)	Intergenic of PTTG1 and ATP10B
DM+JDM	GSDMB	17	38066267	rs1008723	T	0.47	0.49	9.05×10−6	1.20 (1.11–1.30)	Complete IKZF3, ZPBP2 GSDMB	IBD,[16] MS,[28] PBC,[25] RA,[29] T1D,[30]

Analysis of 2,566 IIM cases, 931 PM cases, and 1,360 DM and JDM cases, compared to 15,651 controls. Loci reported at genome wide significance p <5×10⁻⁸ (bold) or at suggestive significance p <2.25×10⁻⁵. Coordinates based on GRCh37 assembly. Overlap defined as high LD (r² >0.7) between the associations in IIM (including independent effects) and the lead association in another autoimmune disease (as reported on www.immunobase.org). ATD – Autoimmune Thyroid Disease, CEL – Celiac Disease, Chr – chromosome, IBD – Inflammatory Bowel Disease, JIA – Juvenile Idiopathic Arthritis, MAF – minor allele frequency, MS – Multiple Sclerosis, OR – Odds ratio, PBC – Primary Biliary Cirrhosis, PSC - Primary Sclerosing Cholangitis, PSO – Psoriasis, RA – Rheumatoid Arthritis, SJO - Sjogren Syndrome, SLE – Systemic Lupus Erythematosus, SSC - Systemic Scleroderma, T1D – Type 1 Diabetes, VIT – Vitiligo, 95% CI – 95% confidence interval