Genes Associated with SLE Are Targets of Recent Positive Selection

Table 1

Genetic regions with compelling evidence for association with SLE.

Gene(s) region	Chr	Pos (Mb)
C1q [21]	1	22.96
IL12RB2 [22]	1	67.55
PTPN22 [22–25]	1	114.16
FCGR2A, FCGR3A [26, 27]	1	159.74
TNFSF4 [22, 28–33]	1	171.42
NMNAT2 [22, 24, 32]	1	181.48
NCF2 [22]	1	181.79
APOBEC4 [28]	1	181.88
CFH [34]	1	194.89
CFHR1, CFHR4 [34]	1	196.79
CRP [35]	1	199.72
IL10 [22]	1	205.01
LYST [22]	1	233.89
RASGRP3 [28, 32]	2	33.51
TET3, DGUOK [28]	2	74.21
IFIH1 [22, 36]	2	162.83
STAT4 [22–24, 32, 37–41]	2	191.60
PDCD1 [42]	2	242.44
SCN10A [28]	3	38.71
TREX1 [43]	3	48.48
DNASE1L3 [44]	3	58.15
PXK [22–24]	3	58.29
TMEM39A [45]	3	120.63
CD80 [28]	3	120.73
AFF1 [46]	4	88.15
BANK1 [23, 28, 47]	4	102.93
LEF1 [46]	4	109.19
IL21 [48]	4	123.75
PPP2CA [49]	5	133.53
TNIP1 [22, 28, 32]	5	150.39
PTTG1 [22, 32]	5	159.78
C4 [50]	6	32.09
HLA-DRB1 [24, 39, 51–53]	6	32.59
ITPR3 [54]	6	33.70
UHRF1BP1 [22, 28]	6	34.87
BACH2 [28]	6	90.69
ATG5, PRDM1 [22–24, 28]	6	106.53
TNFAIP3 [22, 28, 32, 38, 55]	6	138.23
ICA1 [22, 24]	7	8.12
JAZF1 [22]	7	27.84
IKZF1 [28, 32]	7	50.31
IRF5, TNPO3 [22, 24, 28, 39, 40, 56, 57]	7	128.37
XKR6 [24]	8	10.79
BLK [22–24, 28, 39, 40]	8	11.39
LYN [24]	8	56.95
ARMC3 [22]	10	23.26
LRRC18, WDFY4 [28, 32, 33]	10	49.89
ARID5B, RTKN2 [28]	10	63.94
SLC29A3 [28]	10	72.75
PHRF1, IRF7 [22–24]	11	0.58
CD44, PDHX [28, 58]	11	34.94
DDX6 [22, 32]	11	118.13
ETS1 [28, 32, 33]	11	127.83
CREBL2, GPR19, CDKN1B [28]	12	12.66
DRAM1 [28]	12	102.27
SLC15A4 [28, 32]	12	127.84
ELF1 [28]	13	40.40
C2 [59]	14	20.75
CSK [60]	15	72.86
DNASE1 [61]	16	3.64
CLEC16A [28]	16	11.04
PRKCB [62]	16	23.75
SEZ6L2 [28]	16	29.79
ITGAM, ITGAX [23, 24, 28, 63]	16	31.18
IRF8 [22, 45]	16	84.49
IKZF3, ZPBP2 [45]	17	37.91
CD226 [22, 57, 64]	18	65.68
TYK2 [22, 57]	19	10.32
ICAM1, ICAM4, ICAM5 [65]	19	10.40
ACP5 [66]	19	11.55
DDA1 [28]	19	17.28
UBE2L3 [22–24, 28]	22	20.25
SCUBE1 [24]	22	41.93
IRAK1, MECP2 [22, 23, 67, 68]	X	152.93

The reference list for each gene region does not intent to be exhaustive; instead, only the first and/or strongest associations reported to date are mentioned. A comprehensive list of all the studies that report each region have been recently reviewed elsewhere [16–18]. Chr: chromosome; Pos: position (in Mega basepairs) according to Human Genome Build hg18.