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 IDMean β caseMean β controlΔβDiffScoreLocation (HG19)Gene nameGene-relative locationCGI-relative locationEnhancer
(A) Malar rash
Hypomethylation
 cg098855020.370.63−0.27−242.35Chr20: 57463991GNASTSS200, Body, 3′UTRIslandFALSE
 cg100908440.270.51−0.24−200.61Chr12: 132167226N_ShelfTRUE
 cg018210180.600.84−0.24−272.08Chr1: 59043280TACSTD2TSS200IslandTRUE
 cg028913140.490.71−0.22−171.35Chr5: 179741120GFPT2BodyIslandFALSE
 cg232210520.450.67−0.22−158.78Chr5: 179740743GFPT2BodyIslandFALSE
 cg048630050.530.74−0.21−158.15Chr1: 59043208TACSTD2TSS200IslandTRUE
 cg139448380.520.73−0.20−144.11Chr5: 179740914GFPT2BodyIslandFALSE
 cg262205940.280.48−0.20−129.25Chr1: 19110978S_ShoreTRUE
 cg248538680.390.59−0.19−112.67Chr1: 146555624N_ShoreFALSE
 cg016944880.780.96−0.18−328.93Chr4: 1580172IslandFALSE
Hypermethylation
 cg192147070.650.320.33341.10Chr7: 3157722TRUE
 cg155913840.750.490.26341.10Chr6: 32525960HLA-DRB6BodyFALSE
 cg171789000.540.280.26341.10Chr1: 205818956PM20D1BodyIslandTRUE
 cg223558890.330.080.25341.10Chr11: 107461585LOC643923, ELMOD1TSS1500, TSS1500N_ShoreFALSE
 cg263540170.500.260.24341.10Chr1: 205819088PM20D11stExonIslandTRUE
 cg141596720.500.260.24341.10Chr1: 205819179PM20D11stExonIslandTRUE
 cg112245820.390.150.24341.10Chr12: 4919138KCNA65′UTR, 1stExonIslandFALSE
 cg198705120.330.100.24341.10Chr12: 4919081KCNA65′UTR, 1stExonIslandFALSE
 cg071678720.480.240.24341.10Chr1: 205819463PM20D1TSS200S_ShoreFALSE
 cg106716680.320.090.23341.10Chr12: 4919230KCNA61stExonIslandFALSE
(B) Discoid rash
Hypomethylation
 cg246685700.090.30−0.21−254.37Chr10: 134973778KNDC1TSS200IslandFALSE
 cg184806270.420.63−0.21−137.10Chr2: 130795582LOC440905BodyIslandFALSE
 cg240885080.260.47−0.21−146.58Chr1: 38156462C1orf109TSS1500N_ShoreFALSE
 cg192147070.310.52−0.21−133.32Chr7: 3157722TRUE
 cg267628730.680.88−0.20−228.93Chr11: 5879799OR52E8TSS1500FALSE
 cg017973710.180.36−0.19−139.72Chr3: 195578240FALSE
 cg209174910.150.34−0.19−149.47Chr3: 195578259FALSE
 cg081039880.490.67−0.19−109.96Chr17: 6558365IslandFALSE
 cg071570300.450.63−0.18−95.79Chr14: 63671356RHOJ5′UTR, 1stExonTRUE
 cg057794060.370.54−0.18−90.21Chr7: 1198841ZFAND2A5′UTRN_ShoreFALSE
Hypermethylation
 cg010795150.940.680.26341.63Chr3: 195576629FALSE
 cg001037710.670.410.26341.63Chr6: 32525805HLA-DRB6BodyFALSE
 cg233507160.720.470.25341.63Chr1: 147956744PPIAL4B, PPIAL4ATSS1500, TSS1500FALSE
 cg053572090.420.170.25341.63Chr7: 872208UNC84A5′UTR, BodyTRUE
 cg065502000.920.690.23341.63Chr5: 1325588CLPTM1LBodyFALSE
 cg084776870.570.350.22341.63Chr1: 566570MIR1977TSS1500FALSE
 cg016944880.950.730.22341.63Chr4: 1580172IslandFALSE
 cg022392580.580.360.22341.63Chr8: 8241752N_ShoreFALSE
 cg123032470.880.670.21341.63Chr1: 155853542SYT113′UTRTRUE
 cg032132890.520.320.19114.27Chr20: 61660250IslandFALSE
(C) No cutaneous involvement
Hypomethylation
 cg043464590.710.99−0.28−338.22Chr6: 41068666NFYA, LOC2214423′UTR, TSS200IslandTRUE
 cg251104230.700.96−0.26−338.22Chr6: 41068646NFYA, LOC2214423′UTR, TSS200IslandTRUE
 cg268938610.260.49−0.22−167.87Chr17: 41843967DUSP33′UTRFALSE
 cg194184580.420.64−0.22−154.86Chr7: 158789849IslandFALSE
 cg108903020.280.49−0.21−142.85Chr6: 32064246TNXBBodyIslandFALSE
 cg149116890.330.54−0.21−135.21Chr12: 739980NINJ2BodyFALSE
 cg225311830.030.24−0.20−302.51Chr19: 50554451FLJ26850BodyIslandFALSE
 cg010795150.730.93−0.20−312.22Chr3: 195576629FALSE
 cg019923820.240.44−0.20−140.47Chr6: 32064212TNXBBodyIslandFALSE
 cg053572090.150.34−0.20−175.62Chr7: 872208UNC84A5′UTR, BodyTRUE
Hypermethylation
 cg262870800.850.520.33340.66Chr17: 74086286EXOC7BodyFALSE
 cg084797520.670.370.30340.66Chr19: 54567279VSTM1TSS200FALSE
 cg160665050.840.550.29340.66Chr2: 171316530MYO3BBodyFALSE
 cg252250730.300.060.24340.66Chr14: 90528983KCNK13BodyS_ShoreFALSE
 cg180254380.630.390.24340.66Chr1: 228756789IslandFALSE
 cg161548100.410.180.23340.66Chr22: 47135258CERKTSS1500FALSE
 cg138306190.930.710.22340.66Chr12: 9555480FALSE
 cg177833170.530.310.22340.66Chr19: 54567123VSTM11stExon, 5′UTRFALSE
 cg242472310.520.310.21340.66Chr15: 67904302MAP2K5BodyTRUE
 cg077847930.910.700.20340.66Chr5: 33794720ADAMTS12BodyTRUE