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 |