Table 1

Differential methylation analysis results showing the 10 most hypomethylated and hypermethylated CG sites (|Δβ|≥0.10) specific to (A) malar rash, (B) discoid rash or (C) neither cutaneous involvement in patients with systemic lupus erythematosus

CG site ID	Mean β case	Mean β control	Δβ	DiffScore	Location (HG19)	Gene name	Gene-relative location	CGI-relative location	Enhancer
(A) Malar rash
Hypomethylation
cg09885502	0.37	0.63	−0.27	−242.35	Chr20: 57463991	GNAS	TSS200, Body, 3′UTR	Island	FALSE
cg10090844	0.27	0.51	−0.24	−200.61	Chr12: 132167226			N_Shelf	TRUE
cg01821018	0.60	0.84	−0.24	−272.08	Chr1: 59043280	TACSTD2	TSS200	Island	TRUE
cg02891314	0.49	0.71	−0.22	−171.35	Chr5: 179741120	GFPT2	Body	Island	FALSE
cg23221052	0.45	0.67	−0.22	−158.78	Chr5: 179740743	GFPT2	Body	Island	FALSE
cg04863005	0.53	0.74	−0.21	−158.15	Chr1: 59043208	TACSTD2	TSS200	Island	TRUE
cg13944838	0.52	0.73	−0.20	−144.11	Chr5: 179740914	GFPT2	Body	Island	FALSE
cg26220594	0.28	0.48	−0.20	−129.25	Chr1: 19110978			S_Shore	TRUE
cg24853868	0.39	0.59	−0.19	−112.67	Chr1: 146555624			N_Shore	FALSE
cg01694488	0.78	0.96	−0.18	−328.93	Chr4: 1580172			Island	FALSE
Hypermethylation
cg19214707	0.65	0.32	0.33	341.10	Chr7: 3157722				TRUE
cg15591384	0.75	0.49	0.26	341.10	Chr6: 32525960	HLA-DRB6	Body		FALSE
cg17178900	0.54	0.28	0.26	341.10	Chr1: 205818956	PM20D1	Body	Island	TRUE
cg22355889	0.33	0.08	0.25	341.10	Chr11: 107461585	LOC643923, ELMOD1	TSS1500, TSS1500	N_Shore	FALSE
cg26354017	0.50	0.26	0.24	341.10	Chr1: 205819088	PM20D1	1stExon	Island	TRUE
cg14159672	0.50	0.26	0.24	341.10	Chr1: 205819179	PM20D1	1stExon	Island	TRUE
cg11224582	0.39	0.15	0.24	341.10	Chr12: 4919138	KCNA6	5′UTR, 1stExon	Island	FALSE
cg19870512	0.33	0.10	0.24	341.10	Chr12: 4919081	KCNA6	5′UTR, 1stExon	Island	FALSE
cg07167872	0.48	0.24	0.24	341.10	Chr1: 205819463	PM20D1	TSS200	S_Shore	FALSE
cg10671668	0.32	0.09	0.23	341.10	Chr12: 4919230	KCNA6	1stExon	Island	FALSE
(B) Discoid rash
Hypomethylation
cg24668570	0.09	0.30	−0.21	−254.37	Chr10: 134973778	KNDC1	TSS200	Island	FALSE
cg18480627	0.42	0.63	−0.21	−137.10	Chr2: 130795582	LOC440905	Body	Island	FALSE
cg24088508	0.26	0.47	−0.21	−146.58	Chr1: 38156462	C1orf109	TSS1500	N_Shore	FALSE
cg19214707	0.31	0.52	−0.21	−133.32	Chr7: 3157722				TRUE
cg26762873	0.68	0.88	−0.20	−228.93	Chr11: 5879799	OR52E8	TSS1500		FALSE
cg01797371	0.18	0.36	−0.19	−139.72	Chr3: 195578240				FALSE
cg20917491	0.15	0.34	−0.19	−149.47	Chr3: 195578259				FALSE
cg08103988	0.49	0.67	−0.19	−109.96	Chr17: 6558365			Island	FALSE
cg07157030	0.45	0.63	−0.18	−95.79	Chr14: 63671356	RHOJ	5′UTR, 1stExon		TRUE
cg05779406	0.37	0.54	−0.18	−90.21	Chr7: 1198841	ZFAND2A	5′UTR	N_Shore	FALSE
Hypermethylation
cg01079515	0.94	0.68	0.26	341.63	Chr3: 195576629				FALSE
cg00103771	0.67	0.41	0.26	341.63	Chr6: 32525805	HLA-DRB6	Body		FALSE
cg23350716	0.72	0.47	0.25	341.63	Chr1: 147956744	PPIAL4B, PPIAL4A	TSS1500, TSS1500		FALSE
cg05357209	0.42	0.17	0.25	341.63	Chr7: 872208	UNC84A	5′UTR, Body		TRUE
cg06550200	0.92	0.69	0.23	341.63	Chr5: 1325588	CLPTM1L	Body		FALSE
cg08477687	0.57	0.35	0.22	341.63	Chr1: 566570	MIR1977	TSS1500		FALSE
cg01694488	0.95	0.73	0.22	341.63	Chr4: 1580172			Island	FALSE
cg02239258	0.58	0.36	0.22	341.63	Chr8: 8241752			N_Shore	FALSE
cg12303247	0.88	0.67	0.21	341.63	Chr1: 155853542	SYT11	3′UTR		TRUE
cg03213289	0.52	0.32	0.19	114.27	Chr20: 61660250			Island	FALSE
(C) No cutaneous involvement
Hypomethylation
cg04346459	0.71	0.99	−0.28	−338.22	Chr6: 41068666	NFYA, LOC221442	3′UTR, TSS200	Island	TRUE
cg25110423	0.70	0.96	−0.26	−338.22	Chr6: 41068646	NFYA, LOC221442	3′UTR, TSS200	Island	TRUE
cg26893861	0.26	0.49	−0.22	−167.87	Chr17: 41843967	DUSP3	3′UTR		FALSE
cg19418458	0.42	0.64	−0.22	−154.86	Chr7: 158789849			Island	FALSE
cg10890302	0.28	0.49	−0.21	−142.85	Chr6: 32064246	TNXB	Body	Island	FALSE
cg14911689	0.33	0.54	−0.21	−135.21	Chr12: 739980	NINJ2	Body		FALSE
cg22531183	0.03	0.24	−0.20	−302.51	Chr19: 50554451	FLJ26850	Body	Island	FALSE
cg01079515	0.73	0.93	−0.20	−312.22	Chr3: 195576629				FALSE
cg01992382	0.24	0.44	−0.20	−140.47	Chr6: 32064212	TNXB	Body	Island	FALSE
cg05357209	0.15	0.34	−0.20	−175.62	Chr7: 872208	UNC84A	5′UTR, Body		TRUE
Hypermethylation
cg26287080	0.85	0.52	0.33	340.66	Chr17: 74086286	EXOC7	Body		FALSE
cg08479752	0.67	0.37	0.30	340.66	Chr19: 54567279	VSTM1	TSS200		FALSE
cg16066505	0.84	0.55	0.29	340.66	Chr2: 171316530	MYO3B	Body		FALSE
cg25225073	0.30	0.06	0.24	340.66	Chr14: 90528983	KCNK13	Body	S_Shore	FALSE
cg18025438	0.63	0.39	0.24	340.66	Chr1: 228756789			Island	FALSE
cg16154810	0.41	0.18	0.23	340.66	Chr22: 47135258	CERK	TSS1500		FALSE
cg13830619	0.93	0.71	0.22	340.66	Chr12: 9555480				FALSE
cg17783317	0.53	0.31	0.22	340.66	Chr19: 54567123	VSTM1	1stExon, 5′UTR		FALSE
cg24247231	0.52	0.31	0.21	340.66	Chr15: 67904302	MAP2K5	Body		TRUE
cg07784793	0.91	0.70	0.20	340.66	Chr5: 33794720	ADAMTS12	Body		TRUE