Table 2

Unique differentially methylated regions (DMRs) in naïve CD4+ T cells from patients with systemic lupus erythematosus with a history of (A) malar rash, (B) discoid rash or (C) neither cutaneous involvement

DMR gene	DMR location	# DM sites in DMR	Mean β case	Mean β control	Mean Δβ
(A) Malar rash
Hypo-DMR
MIR886	Chr5: 135416331–135416412	6	0.33	0.44	−0.12
TACSTD2	Chr1: 59043199–59043280	4	0.51	0.70	−0.19
CTBP1, C4orf42	Chr4: 1243980–1244024	4	0.64	0.76	−0.12
GFPT2	Chr5: 179740743–179741120	3	0.49	0.70	−0.21
C1orf86, LOC100128003	Chr1: 2121039–2121349	2	0.38	0.51	−0.13
(Intergenic)	Chr5: 1857306–1857477	2	0.54	0.68	−0.14
HLAH, HLAG, HLAJ, HCG4B	Chr6: 29895175–29895187	2	0.25	0.35	−0.10
(Intergenic)	Chr6: 156983263–156983315	2	0.76	0.86	−0.11
SVOPL	Chr7: 138349158–138349443	2	0.44	0.55	−0.10
TRIM69	Chr15: 45028083–45028098	2	0.56	0.66	−0.10
JPH3	Chr16: 87682036–87682142	2	0.67	0.79	−0.12
LOC728392	Chr17: 5403337–5403516	2	0.53	0.63	−0.10
RUNX1	Chr21: 36258423–36258497	2	0.28	0.39	−0.11
RUNX1	Chr21: 36259067–36259383	2	0.29	0.41	−0.11
Hyper-DMR
LY6G5C	Chr6: 31650735–31651151	13	0.69	0.54	0.15
PM20D1	Chr1: 205818956–205819492	7	0.46	0.24	0.22
HTR2A	Chr13: 47472138–47472349	5	0.62	0.47	0.16
(Intergenic)	Chr3: 196705629–196705898	4	0.51	0.38	0.13
KCNA6	Chr12: 4918848–4919230	4	0.33	0.10	0.23
(Intergenic)	Chr5: 154026371–154026448	3	0.45	0.33	0.12
MUC5B	Chr11: 1283875–1283970	3	0.23	0.10	0.13
NINJ2	Chr12: 739980–740338	3	0.51	0.32	0.19
CRIP2	Chr14: 105945022–105945685	3	0.62	0.49	0.13
HOOK2	Chr19: 12876846–12877000	3	0.48	0.33	0.15
THADA	Chr2: 43398171–43398339	2	0.50	0.36	0.14
HDAC4	Chr2: 240142694–240142806	2	0.67	0.54	0.13
(Intergenic)	Chr8: 43132451–43132507	2	0.52	0.41	0.11
(Intergenic)	Chr11: 128694184–128694303	2	0.55	0.44	0.11
PLEKHG6	Chr12: 6419570–6419575	2	0.40	0.29	0.11
(Intergenic)	Chr12: 11700321–11700489	2	0.90	0.78	0.13
SLC38A4	Chr12: 47219737–47219793	2	0.46	0.34	0.12
(Intergenic)	Chr13: 23309892–23309930	2	0.66	0.53	0.13
LIG4	Chr13: 108867111–108867154	2	0.50	0.38	0.12
DEF8	Chr16: 90016020–90016061	2	0.73	0.57	0.16
DHX58	Chr17: 40259724–40259828	2	0.33	0.21	0.12
LASS4	Chr19: 8273505–8273693	2	0.57	0.46	0.11
(B) Discoid rash
Hypo-DMR
(Intergenic)	Chr3: 195578040–195578280	5	0.12	0.28	−0.16
TAP1	Chr6: 32819911–32820214	4	0.34	0.45	−0.11
RFPL2	Chr22: 32599511–32599648	4	0.40	0.52	−0.12
PRDM9	Chr5: 23507573–23507617	3	0.69	0.80	−0.11
RPH3AL	Chr17: 154420–154671	3	0.38	0.49	−0.11
C1orf109	Chr1: 38156462–38156652	2	0.28	0.45	−0.17
SPINK9	Chr5: 147699718–147699892	2	0.48	0.59	−0.11
LY6G5C	Chr6: 31651020–31651029	2	0.62	0.74	−0.12
PSMB8	Chr6: 32810706–32810833	2	0.50	0.63	−0.13
RHOJ	Chr14: 63671356–63671737	2	0.43	0.60	−0.17
BAIAP3	Chr16: 1393584–1393797	2	0.56	0.68	−0.12
(Intergenic)	Chr16: 53407722–53407808	2	0.50	0.64	−0.13
(Intergenic)	Chr17:6558365–6558440	2	0.50	0.67	−0.16
(Intergenic)	Chr17: 37024020–37024042	2	0.29	0.42	−0.13
TBC1D16	Chr17: 77997833–77997997	2	0.83	0.95	−0.11
SBNO2	Chr19: 1155030–1155184	2	0.81	0.94	−0.13
C21orf81	Chr21: 15352608–15352983	2	0.35	0.48	−0.13
Hyper-DMR
RNF39	Chr6: 30039142–30039524	11	0.47	0.30	0.16
(Intergenic)	Chr7: 158789849–158790115	3	0.55	0.42	0.14
(Intergenic)	Chr10: 43846281–43846539	3	0.35	0.22	0.13
MIPEPP3	Chr13: 21900426–21900810	3	0.60	0.48	0.12
ZNF714	Chr19: 21264896–21265421	3	0.39	0.26	0.14
C1orf65	Chr1: 223566761–223567173	2	0.39	0.29	0.10
MYT1L	Chr2: 1801628–1802045	2	0.70	0.59	0.11
TMEM175	Chr4: 940644–940893	2	0.63	0.52	0.11
(Intergenic)	Chr5: 74350132–74350214	2	0.38	0.27	0.11
GFPT2	Chr5: 179740743–179740914	2	0.60	0.47	0.13
TRIM31	Chr6: 30079265–30079280	2	0.63	0.51	0.12
(Intergenic)	Chr6: 167559851–167559913	2	0.59	0.45	0.14
RADIL	Chr7: 4848683–4848814	2	0.24	0.10	0.13
(Intergenic)	Chr8: 58055876–58056113	2	0.50	0.38	0.12
FGFR2	Chr10: 123355268–123355576	2	0.47	0.37	0.10
RAD51B	Chr14: 69095570–69095679	2	0.43	0.32	0.11
(Intergenic)	Chr15: 66947568–66947617	2	0.37	0.26	0.12
SMAD3	Chr15: 67356838–67356942	2	0.69	0.59	0.11
SPIB	Chr19: 50931432–50931515	2	0.32	0.20	0.12
(Intergenic)	Chr20: 61659980–61660250	2	0.58	0.41	0.17
(C) No cutaneous involvement
Hypo-DMR
TNXB	Chr6: 32063607–32064582	15	0.34	0.49	−0.15
NFYA, LOC221442	Chr6: 41068646–41068752	5	0.76	0.96	−0.21
MUC4	Chr3: 195489306–195489909	4	0.63	0.77	−0.13
(Intergenic)	Chr7: 158789723–158790115	4	0.43	0.59	−0.16
RAD51B	Chr14: 69095057–69095679	4	0.31	0.44	−0.12
(Intergenic)	Chr1: 75590912–75591353	3	0.34	0.46	−0.12
(Intergenic)	Chr6: 28447087–28447115	3	0.30	0.42	−0.12
NINJ2	Chr12: 739980–740338	3	0.38	0.57	−0.20
KCNA6	Chr12: 4919081–4919230	3	0.25	0.38	−0.13
LMTK3	Chr19: 49000743–49000998	3	0.65	0.76	−0.12
LMTK3	Chr19: 49001890–49002477	3	0.59	0.71	−0.12
MYT1L	Chr2: 1817263–1817409	2	0.58	0.70	−0.11
(Intergenic)	Chr4: 1550089–1550194	2	0.66	0.77	−0.12
(Intergenic)	Chr4: 6010075–6010164	2	0.46	0.56	−0.11
RGS14	Chr5: 176797920–176797999	2	0.46	0.57	−0.12
RNF39	Chr6: 30039202–30039442	2	0.32	0.45	−0.13
VARS2	Chr6: 30882641–30882708	2	0.44	0.57	−0.13
TAP2	Chr6: 32805548–32805570	2	0.55	0.67	−0.12
HOXA5	Chr7: 27183375–27183694	2	0.68	0.79	−0.11
PTPRN2	Chr7: 158046166–158046222	2	0.68	0.85	−0.17
(Intergenic)	Chr8: 1321333–1321375	2	0.40	0.53	−0.12
(Intergenic)	Chr10: 130726624–130726701	2	0.68	0.80	−0.12
TRIM5	Chr11: 5960015–5960081	2	0.69	0.80	−0.11
STAT3	Chr17: 40489584–40489785	2	0.27	0.40	−0.13
FLJ26850	Chr19: 50554451–50554510	2	0.06	0.22	−0.16
NLRP2	Chr19: 55477653–55477810	2	0.51	0.62	−0.11
HLCS	Chr21: 38362725–38362727	2	0.57	0.71	−0.14
C21orf56	Chr21: 47604166–47604291	2	0.24	0.38	−0.14
Hyper-DMR
NAPRT1	Chr8: 144659831–144660772	5	0.37	0.23	0.14
GSTM5	Chr1: 110254662–110254709	3	0.47	0.35	0.12
(Intergenic)	Chr10: 1939618–1939683	3	0.67	0.51	0.16
CD101	Chr1: 117544206–117544416	2	0.19	0.08	0.11
(Intergenic)	Chr2: 731298–731519	2	0.80	0.67	0.13
(Intergenic)	Chr2: 173539262–173539542	2	0.50	0.40	0.11
PRDM9	Chr5: 23507594–23507617	2	0.74	0.64	0.11
FLOT1	Chr6: 30706647–30706654	2	0.68	0.57	0.11
C11orf21, TSPAN32	Chr11: 2322507–2322517	2	0.21	0.10	0.12
(Intergenic)	Chr12: 19557334–19557343	2	0.25	0.13	0.11
RARG	Chr12: 53612551–53612734	2	0.53	0.41	0.12
VSTM1	Chr19: 54567123–54567279	2	0.60	0.34	0.26
SPATC1L	Chr21: 47581042–47581405	2	0.61	0.50	0.11
CERK	Chr22: 47135171–47135258	2	0.32	0.13	0.19
BCOR	ChrX: 39956534–39956558	2	0.31	0.19	0.12
BCOR	ChrX: 39958040–39958196	2	0.34	0.20	0.14