The following loci have evidence of association with SLE, as evidenced by Published GWASs (genetic associations with a P value < 5e-8, tested in a total sample size of >=1000 individuals). 
Please cite [Lingyan Chen, David L Morris, and Timothy J Vyse. "Genetic advances in systemic lupus erythematosus: an update". Current opinion in rheumatology (2017)] when making use of these data.
No. Risk Region Lead SNP in Publication Position (Build 37) Risk allele dbSNP Function Locus Gene eGene Population References (PUBMEDID)
1 1p36.11 rs4649203 24519920 G intergenic  IL28RA   Chinese 24070858
2 1p13.2 rs2476601 114377568 A missense PTPN22 BCL2L15, DCLRE1B, MAGI3 American and European 19838195, 26502338
3 1q23.3 rs1801274 161479745 C missense FCGR2A FCGR2A, FCGR2B European 26502338
4 1q25.1 rs1234315 173178463 A intergenic  TNFSF4   Asian and European 19838193, 22820624
rs2205960 173191475 T intergenic  Asian, European-American, African-American and Hispanic 19838193, 19838195, 22820624, 23874208
rs704840 173226195 G intergenic  European 26502338
rs1418190 173361979 G intergenic  Chinese 25890262
rs4916219 173373183 A intergenic  Chinese 25890262
5 1q25.3 rs17849502 183532580 T missense NCF2   European-American, African-American, Hispanic and Korean 24163247
rs35937854 183536089 G missense European-American, African-American, Hispanic and Korean 24163247
rs10911363 183549757 T intron  UK, American and Swedish 22046141
rs10911628 184649503 NA intergenic  EDEM3   European 24871463
6 1q31.3 rs34889541 198594769 G intergenic  CD45   Chinese and European 27399966
7 1q32.1 rs2297550 206643772 G 5'-UTR IKBKE IKBKE Chinese and European 27399966
rs3024505 206939904 A intergenic  IL10 FCAMR, IL10, IL24 American and European 19838195, 26502338
8 1q42.3 rs9782955 236039877 C intron LYST LYST European 26502338
9 2p23.1 rs7579944 30445026 C intergenic  LBH LBH Chinese and European 27399966
rs17321999 30479857 C intron Chinese and European 27399966
10 2p22.3 rs13385731 33701890 G intron RASGRP3   Chinese 19838193
11 2p14 rs6740462 65667272 A intron SPRED2 SPRED2 European 26502338
12 2p13.1 rs4852324 74202578 T intron DGUOK-TET3   Asian  23273568
rs6705628 74208362 C non coding Asian  23273568
13 2q24.2 rs2111485 163110536 G intergenic  IFIH1 IFIH1 European 26502338
rs10930046 163137983 G  missense African and European 23441136
14 2q32.3 rs3821236 191902758 NA intron STAT4   Korean 23740238
rs7601754 191940451 NA intron Asian  19225526
rs11889341 191943742 T intron European 26502338
rs10931481 191954852 T intron European 23053960
rs6736175 191946322 C intron European 26502338
15 2q34 rs3768792 213871709 C 3'-UTR IKZF2 IKZF2 European 26502338
16 3p14.3 rs6445972 58321707 C intron ABHD6-PXK ABHD6, PXK, RPP14, PDHB European Americans, African Americans, Asian Americans and Hispanic Americans 25620976
rs6445975 58370177 C intron European 18204446
rs9311676 58470351 C intergenic  European 26502338
17 3q13.33 rs1132200 119150836 G missense TMEM39A   European, African American and Asian 22464253, 25890262
rs1131265 119222456 G synonymous European in press
rs6804441 119260944 A intron CD80   Asian  23273568
rs2222631 119272391 G intron Asian  25862617
18 3q25.33 rs564799 159728987 C intron IL12A IL12A, IFT80, SMC4, RP11-432B6.3 European 26502338
19 3q26.2 rs10936599 169492101 C synonymous MYNN   Asian and European 28108556
20 3q28 rs6762714 188470238 T intron LPP-TPRG1-AS1   Chinese and European 27399966
21 4p16 rs4690229 970724 T 3'-UTR DGKQ   European In press
22 4q21.3 rs340630 87958395 A intron AFF1   Japanese 22291604
23 4q24 rs10028805 102737250 G intron BANK1 BANK1 European 26502338
rs17266594 102750922 C intron Chinese 19357697
24 4q27 rs907715 123535053 G intron IL21   European and African American 21425124
25 5p15.33 rs7726159 1282319 A intron TERT   Asian  26808113
26 5q31.1 rs7726414 133431834 T intergenic  TCF7-SKP1 TCF7, SKP1 European and Asian 26502338, 26808113
27 5q33.1 rs7708392 150457485 C intron TNIP1   American and Swedish 19838195
28 5q33.3 rs2421184 159459931 A intron IL12B   Asian  26808113
rs2431697 159879978 A intergenic  PTTG1-MIR146A MIR146A Chinese and European 25890262, 26502338
rs2431697 159879978 A intergenic  African American In press
29 6p23 rs17603856 16630898 T intron ATXN1   Chinese and European 27399966
30 6p22 rs36014129 25884519 A intron SLC17A4   European In press
rs35789010 25514179 A intron LRRC16A   European In press
31 6p21.32-33 rs3906272 31262924 A intron HLA-C-HLA-B   UK, Spanish and Filipino 22233601
rs2246618 31478986 A upstream  MICB   European 23084292
rs1269852 32080191 A intron MSH5-SAPCD1-TNXB-ATF6B   European 18204446, 19838195
rs8192591 32185796 G missense NOTCH4   European 23084292
rs9270984 32573991 T intron HLA-DRB1   Asian and European 23273568, 20169177, 22233601
rs2187668 32605884 A intron HLA-DQA1   European 18204098
rs9275572 32678999 NA intergenic  HLAregion   European 18204446
rs2051549 32730086 A intron HLA-DQA2   European 23053960
32 6p21.31 rs3748079 33588147 C 5'-UTR ITPR3   Japanese 18219441
rs3734266 34823187 G intron UHRF1BP1   Asian and European 23273568, 26502338
rs11755393 34824636 G missense American and Swedish 19838195
rs2762340 35052635 G intron ANKS1A ANKS1A Asian and European 28108556
rs10807150 35304497 C intron DEF6   Asian  26808113
33 6q15 rs597325 91002494 G intron BACH2   Chinese and European 27399966
34 6q21 rs548234 106568034 G intergenic PRDM1-ATG5   Chinese 19838193
rs6568431 106588806 A intergenic American and European 19838195, 26502338
35 6q23 rs6932056 138242437 C intergenic TNFAIP3   European 26502338
rs2327832 137973068 C intron OLIG3-LOC100130476   European In press
36 7p15.1 rs849142 28185891 T intron JAZF1   American and European 19838195, 26502338
37 7p12.2 rs2366293 50227828 G intergenic IKZF1   UK, American and Swedish 22046141
rs4917014 50305863 A intergenic Chinese and European 19838193, 26502338
38 7q11.23 rs73135369 73940978 C intron GTF2IRD1-GTF2I   Chinese and European 27399966
rs73366469 74619286 C intergenic Asian and European 26808113
rs1167796 75173180 G intron HIP1   Chinese 19838193
rs6964720 75180344 NA intron Asian  26663301
39 7q32.1 rs729302 128568960 A intergenic TNPO3-IRF5 IRF5 Asian and European 23273568, 23053960
rs4728142 128573967 A intergenic Chinese and European 19838193, 24871463
rs2070197 128589000 C 3'-UTR American and Swedish 19838195
rs12537284 128717906 A intergenic European 18204446
40 8p11 rs1804182 42033519 A nonsense PLAT   African American In press
41 8p23.1 rs2980512 8140901 C intergenic FAM86B3P   European In press
rs6985109 10767748 A intron XKR6 XKR6 European 18204446
rs7836059 11272164 T intron C8orf12   European 18204446
rs12680762 11332026 A intron FAM167A FAM167A European 23053960
rs7812879 11340181 A intergenic BLK BLK, RP11-148O21.2, RP11-148O21.4 Chinese 19838193
rs2736340 11343973 T intergenic American and Swedish 19838195
rs2248932 11391650 A intron Chinese 19838193
42 8q12 rs7829816 56849386 C intron LYN   European 18204446
43 8q21 rs1966115 79556891 A intergenic PKIA-ZC2HC1A   European In press
44 9p24 rs1887428 4984530 G upstream JAK2   Chinese and European 27399966
45 10q11.23 rs7097397 50025396 G missense WDFY4 WDFY4 Asian  20169177
rs877819 50042951 A intron Asian and European 23273568, 26502338
rs1913517 50119054 A intron Chinese 19838193
46 10q21.2 rs4948496 63805617 C intron ARID5B   Asian and European 23273568, 26502338
47 10q24.33 rs4917385 103243964 NA intergenic USMG5-miR1307   American 26606652
48 11p15.5 rs12802200 566936 C intron IRF7-PHRF1 PHRF1, HRAS, TMEM80,RNH1, ANO9, RASSF7 European 26502338
rs4963128 589564 C intron American and European 19838195, 18204446
49 11p13 rs2732552 35084592 T intergenic CD44   European, African American and Asian 21194677, 26502338
50 11q13.1 rs1308020 65497558 T intergenic RNASEH2C CTSW, RNASEH2C, FIBP, MUS81 Asian and European 28108556
rs494003 65542298 A 3'-UTR Chinese and European 27399966
rs2009453 65632057 C intron PCNXL3   Asian  26808113
51 11q13.4 rs3794060 71187679 C intron DHCR7-NADSYN1 NADSYN1, RP11-660L16.2, DHCR7 European 26502338
rs11235604 72533536 T missense ATG16L2   Asian and European 28108556
rs11235667 72863697 NA intergenic FCHSD2-P2RY2   Asian  26663301
52 11q23.3 rs11603023 118486067 T intron PHLDB1   Asian  24001599
rs4639966 118573519 G downstream  Chinese 19838193
rs10892301 118735476 G intergenic CXCR5   Asian  24001599
53 11q24.3 rs6590330 128311059 A intergenic ETS1-FLI1   Asian  19838193, 23273568
rs7941765 128499000 C downstream  European 26502338
54 12p13 rs12822507 12773521 A intron CREBL2   Asian  23273568
rs10845606 12834894 C intron GPR19   Asian  23273568
rs34330 12870695 C 5'-UTR CDKN1B   Asian  23273568
55 12q12 rs10506216 43130885 T intergenic PRICKLE1   European 26316170
56 12q23.2 rs4622329 102321935 A intron DRAM1   Asian  23273568
57 12q24.12 rs10774625 111910219 A intron SH2B3-ATXN2 HECTD4 European 26502338
58 12q24.32 rs1059312 129278864 C synonymous SLC15A4 SLC15A4 European 26502338
rs10847697 129299385 A synonymous Chinese 19838193
59 13q14.11 rs7329174 41558110 G intron ELF1   Asian  21044949
60 14q13.2 rs8016947 35832666 A intron NFKBIA   Chinese 24070858
61 14q24.1 rs4902562 68731458 A intron RAD51B   European 26502338
62 14q31 rs11845506 88383035 C intron GALC   Hispanic In press
63 15q14 rs12900339 38635185 A intergenic RASGRP1   Asian  26808113
rs11073328 38764843 NA intron FAM98B   European 24871463
64 15q24 rs34933034 75079474 NA intron CSK FAM219B, CSK, MPI, C15ORF39, ULK3, UBE2Q2 European 23042117
rs2289583 75311036 A intron European 26502338
65 15q26.2 rs8023715 97607681 NA intergenic SPATA8   European 24871463
66 16p13 rs8054198 11038360 C 5'-UTR CLEC16A-CIITA-SOCS1 SOCS1 Hispanic In press
rs9652601 11174365 G intron European 26502338
rs12599402 11189888 A intron Chinese 20805369
67 16p11.2 rs16972959 23901376 A intron PRKCB PYCARD Chinese 21134959
rs7197475 30642867 A intergenic ITGAM-ITGAX ITGAM Chinese 19838193
rs34572943 31272353 A intron European 26502338, 18204446
rs11574637 31368874 C intron European 18204098
68 16q13 rs223881 57386566 C intergenic CCL22   Asian and European 28108556
69 16q22.1 rs1170426 68603798 C intron ZFP90 ZFP90 Chinese and European 27399966
70 16q24.1 rs2934498 85968282 G intergenic IRF8   Chinese 25890262
rs11644034 85972612 G intergenic European, African American and Asian 22464253, 26502338
rs2280381 86018633 A intergenic UK, American and Swedish 22046141
71 17p13.2 rs2286672 4712617 T missense PLD2 INCA1 European 26502338
72 17q12 rs2941509 37921194 A 3'-UTR IKZF3   European 26502338
73 17q25 rs930297 73404537 A intergenic GRB2   European In press
74 18q22.2 rs1610555 69875911 T intron CD226   Asian  26808113
75 19p13 rs3093030 10397403 A downstream ICAM1-ICAM4-ICAM5   European, African, Hispanic, and Korean 22523428
rs280519 10472933 A intron TYK2 TYK2 UK, American and Swedish 22046141
rs2304256 10475652 C missense European 26502338
76 19q13.41 rs2305772 51530488 G missense SIGLEC6   Asian  26808113
77 20q13.12 rs4810485 44747947 T intron CD40   Greek and Turkey 21914625
78 20q13.13 rs11697848 48575315 NA intergenic RNF114   European 24871463
79 22q11.21 rs463426 21809185 A intergenic UBE2L3-YDJC-HIC2 UBE2L3 Chinese 19838193
rs131654 21917190 A intron Chinese 19838193
rs7444 21976934 C  3'-UTR European 26502338
80 22q13.1 rs61616683 39359768 T intron SYNGR1   Asian  26808113
81 Xp22.2 rs7062536  12839152  A intron PRPS2   Asian  25149475
rs3853839 12907658 G 3'-UTR TLR7   Asian  20733074
82 Xp21.2 rs887369 30577846 C synonymous CXorf21   European 26502338
83 Xp11.21 rs5914778 56758231 NA intron LINC01420   Chinese 26635088
84 Xq28 rs17422 153227426 C intron NAA10-HCFC1-TMEM187   European Americans, African Americans, Asian Americans and Hispanic Americans 25149475, 19329491
rs1734787 153325446 C intron IRAK1-MECP2   European 26502338
* Locus gene, is the gene that located close to the GWAS SNP, or the gene that annotated in the corresponding publications.
** eGene, is a gene whose expression is affected by the GWAS SNP (eSNP), with a significant co-localisation of eQTL signal and GWAS signal.