Table 1.

Summary of established genes implicated in SLE

Gene	Location	Known function	ORa	Variation	Discoveryb
HLA-DR2, -DR3	6p21.32	Antigen presentation	2.4	haplotypes	1971 12,13
C2	6p21.32	Immune complex clearance	5.0	deletion	1972 23
C4	6p21.32	Immune complex clearance	4.3	CNV	1974 24
C1q	1p36.12	Immune complex clearance	10	deletion	1981 25
FCGR2A	1q23.3	Immune complex clearance	1.6	H131R	1996 31
FCGR3A	1q23.3	Immune complex clearance	1.4	F176V	1997 30
FCGR2B	1q23.3	Immune complex clearance	1.7	I232T	2002 32
PDCD1	2q37.3	T cell signaling	1.2	PD1.3G/A	2002 36
PTPN22	1p13.2	TCR and BCR signaling	1.4	R620W	2004 48
IRF5	7q32.1	Regulator of type I IFN production	1.6	SNPs	2005 53
TYK2	19p13.2	Regulator of type I IFN production	1.2	SNPs	2005 53
FCGR3B	1q23.3	Immune complex clearance	2.2	CNV	2006 93
STAT4	2q32.2	Transcriptional regulator of IFNγ signaling; apoptosis	1.5	SNPs	2007 60
IRAK1*	Xq28	Toll, IL1R and NFkB signaling	1.4	SNPs	2007 66
TREX1	3p21.31	Regulator of IFNα production	25	SNPs	2007 78
MECP2*	Xq28	Regulation of gene expression through DNA methylation	1.3	SNPs	2008 69
TNFSF4	1q25.1	T cell signaling	1.4	SNPs	2008 73
CRP	1q32.2	Immune complex clearance	1.3	-707 SNP	2008 75
ATG5	6q21	Unknown	1.2	SNP	2008 81
PTTG1	5q33.3	Unknown	1.2	SNP	2008 81
UBE2L3	22q11.21	Ubiquitination	1.2	SNP	2008 81
PXK	3q14.3	Unknown	1.2	SNP	2008 81
PHRF1	11p15.5	Unknown	1.2	SNP	2008 81
ICA1	7p21.3	Unknown	1.2	SNP	2008 81
NMNAT2	1q25.3	Unknown	1.1	SNP	2008 81
ITGAM	16p11.2	Immune complex clearance; leukocyte adhesion	1.6	R77H	2008 81,82,83
TNFAIP3	6q23.3	TNFR and NFkB signaling; ubiquitination	2.0	SNPs	2008 86,108
BLK	8p23.1	B cell activation	1.3	SNP	2008 86,81,82
BANK1	4q24	B cell activation; BCR signaling	1.2	R61H	2008 88
TNIP1	2q35	NFkB signaling	1.3	SNP	2009 58,89

^aOR: Approximate Odds Ratio

^bYear first reported

^*These genes lie in the same haplotype block