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Table 1 A summary of loci associated with systemic lupus erythematosus in one or more genome-wide association studies, a meta-analysis, and replication studies (P <1

From: The genetics of lupus: a functional perspective

Locus Gene Position Variant Pvalue (significance) OR (CI) effect(size) Autoimmune disease association Function
ITGAM a Intergrin alpha M 16p11.2 (intronic) rs9888739 (T) 1.61×10-23 1.62 (1.47-1.78)   Phagocytosis
FcγR Fcγ receptors Multiple(see text) Multiple (see text) Multiple (see text) Multiple (see text) UC Phagocytosis
PRDM1-ATG5 b PR domain zinc finger protein 1-autophagy-related 5 homolog 6q21-q22.1 (intergenic) rs548234 (G) 5.18×10-12 1.25 (1.17-1.33)   Autophagy and B-cell differentiation
TNFAIP3 b Tumor necrosis factor-alpha-induced protein 6q23 (exonic) rs2230926 (C) 1.37×10-17 1.72 (1.52-1.94) RA, CeID, UC, and PS Ubiquitination
TNIP1 e TNFAIP3-interacting protein 1 5q32-q33.1 (intronic) rs7708392 (C) 3.8×10-13 1.27 (1.10-1.35) PS  
UBE2L3 b Ubiquitin-conjugating enzyme E2L 3 22q11.2- q13.1 (upstream) rs463426 (G) 1.48×10-16 0.78 (0.74-0.83) CD, RA, and CeID  
ETS1 b V-ETS avian erythroblastosis virus E26 oncogene homolog 1 11q23.3 (downstream) rs6590330 (A) 1.77×10-25 1.37 (1.29-1.45) RA Lymphocyte development and activation
IKZF1 b IKAROS family zinc finger 1 7p12 (upstream) rs4917014 (C) 2.75×10-23 1.23 (1.03-1.42)   
CD44 d CD44 11p13 (upstream) rs507230 3.98×10-12 0.71 (0.63-0.79)   
BANK1 c B-cell sca3 old protein with ankyrin repeats 1 4q22-q24 (exonic) rs10516487 (G) 3.7×10-10 1.38 (1.25-1.53) RA B-cell activation and signaling
BLK b B lymphoid tyrosine kinase 8p23-p22 (upstream) rs7812879 (A) 2.09×10-24 0.69 (0.64-0.74) RA  
LYN a V-yes-1 Yamaguchi sarcoma viral-related oncogene homolog 8q13 (intronic) rs7829816 (C) 5.40×10-9 0.77 (0.70-0.84)   
RasGRP3 b RAS guanyl releasing protein 3 (calcium and DAG-regulated) 2p25.1-p24.1 (intronic) rs13385731 (G) 1.25×10-15 0.70 (0.64-0.76)   
NCF2 f Neutrophil cytosolic factor 2 1q25(intronic) rs10911363 (T) 2.87×10-11 1.18 (1.10-1.30)   
STAT4 b Signal transducer and activator of transcription 4 2q32.2-q 32.3 (intronic) rs7574865 (A) 5.17×10-42 1.51 (1.43-1.61) RA, IBD, T1D, and Sjögren's syndrome T-cell development and signaling
PTPN22 e Protein tyrosine phosphatase non-receptor type 22 1p13 (exonic) rs2476601 (A) 3.4×10-12 1.35 (1.24-1.47) T1D and Graves' disease  
TNFSF4 b Tumor necrosis factor (ligand) superfamily member 4 1q25 (upstream) rs2205960 (A) 2.5×10-32 1.46 (1.37-1.56)   
HLA-DRB1 e HLA class II histocompatibility antigen 6p21.3(downstream) rs3135394 (G) 2.0×10-60 1.98 (1.84-2.14) T1D, RA, CeID, IBD, and CD Antigen presentation
SLC15A4 b Solute carrier family 15, member 4 12q24.32 (exonic) rs10847697 (A) 3.54×10-11 1.26 (1.17-1.34)   
IRF5 e Interferon regulatory factor 5 7q32(3' untranslated region) rs2070197 (C) 5.8×10-24 1.88 (1.78-1.95) Rheumatic disease and RA Interferon regulation and production
IRF7 a Interferon regulatory factor 7 11p15.5(downstream) rs4963128 (T) 3.0×10-10 0.78 (0.73-0.85) T1D  
IRF8 f Interferon regulatory factor 8 16q24.1 (downstream) rs2280381 (A) 1.24×10-8 1.17 (1.10-1.24) UC and MS  
IFIH1 f Interferon-induced helicase C domain- containing protein 1 2q24 (exonic) rs1990760 (T) 1.63×10-8 1.23 (1.09-1.39)   
TYK2 f Tyrosine kinase 2 19p13.2(intronic) rs280519 (A) 3.88×10-8 1.29 (1.15-1.47) MS  
LRRC18- Leucine-rich repeat 10q11.22-q11.23 rs1913517 (A) 7.22×10-12 1.24 (1.17-1.32)   Unknown function
WDFY4 b containing 18-WD repeat and FYVE domain-containing protein 4 (intergenic)      
PXK a PX domain containing serine/threonine kinase 3p14.3(intronic) rs6445975 (C) 7.10×10-9 1.25 (1.16-1.35) RA  
JAZF1 e Juxtaposed withanother zinc finger gene 1 7p15 (intronic) rs849142 (T) 1.5×10-9 1.19 (1.13-1.26)   
UHRF1BP1 e UHRF-binding protein 1 6q23(exonic) rs11755393 (G) 2.2×10-8 1.17 (1.10-1.24)   
XKR6 a XK, Kell blood group complex subunit- related family, member36 8p23.1(intronic) rs6985109 (G) 2.51×10-11 1.23 (1.16-1.30)   
  1. Odds ratios (ORs) and confidence intervals (CIs) are noted with the primary function of each locus. The genome-wide association studies from which this table was generated were conducted by aHarley and colleagues [95] (1,846 systemic lupus erythematosus (SLE) women cases and 1,825 controls), bHan and colleagues [53] (1,047 Han Chinese cases and 1,205 controls), and cKozyrev and colleagues [59] (279 Swedish SLE cases and 515 controls). The meta-analysis study was conducted by dRamos and colleagues [58] (939 Caucasian cases and 3,398 controls). The replication studies were conducted by Han and colleagues [53] (3,152 Han Chinese cases and 7,050 controls), eGateva and colleagues [6] (1,963 cases and 4,329 controls), and fCunninghame Graham and colleagues [69] (870 UK SLE cases and 5,551 controls). All loci that have been reported to be associated with other autoimmune diseases - Crohn's disease (CD), celiac disease (CeID), irritable bowel syndrome (IBD), multiple sclerosis (MS), psoriasis (PS), rheumatoid arthritis (RA), type 1 diabetes (T1D), and ulcerative colitis (UC) - are also stated [58].