|
Region
|
Position (bp)
|
SNP
|
Gene
|
A1
|
P2sided
|
Best subset
|
|---|
|
1p36.32
|
2,534,978
|
rs6664969
|
MMEL1
|
A
|
2.86E−10
|
CeD RA
|
|
1p36.13
|
17,655,407
|
rs1748041
|
PADI4
|
C
|
3.63E−08
|
RA SSc
|
|
1p13.2
|
114,377,568
|
rs2476601
|
PTPN22
|
A
|
6.36E−119
|
RA T1D
|
|
1p13.2
|
114,388,804
|
rs1217403
|
PTPN22
|
C
|
4.66E−11
|
RA* T1D*
|
|
1q24.3
|
172,674,776
|
rs10912267
|
FASLG
|
A
|
3.90E−09
|
CeD T1D
|
|
2q11.2
|
100,764,004
|
rs13415465
|
AFF3
|
G
|
3.72E−12
|
CeD RA T1D
|
|
2q31.3
|
182,057,640
|
rs12619531
|
ITGA4
|
G
|
1.18E−18
|
CeD SSc
|
|
2q32.3
|
191,538,562
|
rs10931468
|
NAB1
|
A
|
1.56E−08
|
RA SSc
|
|
2q32.3
|
191,902,184
|
rs6749371
|
STAT4
|
T
|
3.84E−08
|
CeD SSc*
|
|
2q32.3
|
191,964,633
|
rs7574865
|
STAT4
|
T
|
3.16E−09
|
CeD* RA SSc T1D*
|
|
2q33.2
|
204,612,058
|
rs7426056
|
CD28
|
A
|
6.68E−12
|
CeD RA
|
|
2q33.2
|
204,738,919
|
rs3087243
|
CTLA4
|
A
|
5.08E−16
|
RA T1D
|
|
3p14.3
|
58,183,636
|
rs35677470
|
DNASE1L3
|
A
|
1.04E−11
|
RA SSc
|
|
3q25.33
|
159,647,674
|
rs17753641
|
IL12A
|
G
|
1.64E−29
|
CeD SSc*
|
|
4p15.2
|
26,088,128
|
rs16878091
|
RBPJ
|
A
|
2.53E−12
|
RA T1D
|
|
5q33.1
|
150,438,988
|
rs1422673
|
TNIP1
|
T
|
1.87E−09
|
CeD RA SSc
|
|
6q15
|
90,976,768
|
rs72928038
|
BACH2
|
A
|
9.34E−12
|
CeD RA T1D
|
|
6q23.3
|
138,003,822
|
rs11757201
|
TNFAIP3
|
C
|
1.27E−11
|
CeD RA T1D
|
|
6q23.3
|
138,243,739
|
rs58721818
|
TNFAIP3
|
T
|
5.26E−10
|
RA SSc
|
|
6q25.3
|
159,470,417
|
rs212407
|
TAGAP
|
G
|
6.74E−14
|
CeD RA T1D
|
|
7p14.1
|
37,382,465
|
rs60600003
|
ELMO1
|
G
|
4.25E−13
|
CeD SSc
|
|
7p12.1
|
51,015,193
|
rs7780389
|
COBL
|
T
|
2.25E−08
|
RA T1D
|
|
7q32.1
|
128,572,766
|
rs4731532
|
IRF5
|
A
|
1.25E−10
|
RA SSc
|
|
9p13.3
|
34,710,260
|
rs2812378
|
CCL21
|
G
|
1.04E−09
|
CeD RA
|
|
10p15.1
|
6,101,713
|
rs3118470
|
IL2RA
|
C
|
5.92E−09
|
RA T1D
|
|
10p15.1
|
6,116,254
|
rs72776098
|
IL2RA
|
A
|
7.10E−10
|
SSc T1D
|
|
10p15.1
|
6,390,450
|
rs947474
|
PRKCQ
|
G
|
1.28E−08
|
CeD RA T1D
|
|
10p14
|
8,102,272
|
rs3802604
|
GATA3
|
G
|
4.67E−08
|
RA T1D
|
|
10q22.3
|
81,045,280
|
rs1250568
|
ZMIZ1
|
C
|
3.87E−15
|
CeD SSc T1D
|
|
11q23.3
|
118,726,843
|
rs10892299
|
DDX6
|
T
|
2.25E−13
|
CeD SSc T1D
|
|
12q13.2
|
56,470,625
|
rs11171739
|
IKZF4
|
C
|
1.87E−20
|
RA T1D
|
|
15q14
|
38,828,140
|
rs8043085
|
RASGRP1
|
T
|
1.53E−08
|
RA T1D
|
|
15q25.1
|
79,234,957
|
rs34593439
|
CTSH
|
A
|
1.47E−14
|
CeD T1D
|
|
17q12
|
38,033,277
|
rs1054609
|
ORMDL3
|
C
|
3.70E−08
|
RA SSc T1D
|
|
18p11.21
|
12,777,573
|
rs2542148
|
PTPN2
|
C
|
5.11E−16
|
CeD T1D
|
|
19p13.2
|
10,427,721
|
rs74956615
|
TYK2
|
A
|
1.62E−17
|
RA SSc T1D
|
|
21q22.3
|
43,855,067
|
rs1893592
|
UBASH3A
|
C
|
4.86E−12
|
CeD T1D
|
|
22q11.1
|
21,936,152
|
rs66534072
|
YDJC
|
G
|
2.05E−08
|
CeD SSc
|
- The selected lead SNP in each region is shown, together with the best subset obtained from the subset-based meta-analysis. Position (bp), base pair position in hg19; SNP, single nucleotide polymorphism; Gene, annotated gene as described in methods; A1, alternative allele used in the logistic regression; P2sided, p value from the two-sided subset-based meta-analysis; Best subset, phenotypes contributing to the association signal. Diseases included in the best subset and for which identified associations have not been previously reported are shown in bold; novel signals within known risk loci are indicated by “*”
