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. Author manuscript; available in PMC: 2017 Apr 1.
Published in final edited form as: J Immunol. 2016 Feb 24;196(7):3043–3053. doi: 10.4049/jimmunol.1502056

Table I.

List of reported T1D SNPs located in 59 non HLA T1D loci.

ID Locus T1D SNP CHR BP Gene P-value Ref. Tables
1 1p31.3 rs2269241 chr1 63881359 PGM1 4.00×10−7 2 II, S
2 1p13.2 rs2476601 chr1 114179091 PTPN22 8.50×10−85 2 II
3 1q31.2 rs2816316 chr1 190803436 RGS1 3.10×10−5* 2
4 1q32.1 rs3024493 chr1 205010591 IL10 1.90×10−9 2
5 2p24.3 rs1534422 chr2 12558192 Intergenic 2.00×10−6 2 IV
6 2p23.3 rs2165738 chr2 24546313 Intergenic 4.00×10−6 14 III, S
7 2p13.1 rs363609^ chr2 74756380 DQX1 8.53×10−6^ 15 II, III, S
8 2q11.2 rs9653442 chr2 100191799 AFF3 5.00×10−6 15 S
9 2q12.1 rs6543134 chr2 102416890 IL18RAP 8.03×10−5* 16 III, S
10 2q24.2
2q24.2		 rs1990760
rs3747517		 chr2
chr2		 162832297
162837070		 IFIH1
IFIH1 		6.60×10−9
4.70×10−7 		2
2		 II, IV
11 2q33.2
2q33.2
2q33.2		 rs11571291
rs3087243
rs231727		 chr2
chr2
chr2		 204429377
204447164
204449795		 CTLA4
CTLA4
CTLA4 		1.19×10−12
1.20×10−15
2.13×10−18 		17
2
13		 IV

II, S
12 2q35 rs3731865 chr2 218958247 SLC11A1 1.55×10−6 18 III
13 3p21.31 rs11711054 chr3 46320615 CCR5 1.70×10−5* 2 IV
14 4p15.2 rs10517086 chr4 25694609 Intergenic 4.60×10−10 2
15 4q27
4q27
4q27		 rs4505848
rs17388568
rs2069763		 chr4
chr4
chr4		 123351942
123548812
123596932		 IL2
IL2
IL2 		4.70×10−13
3.00×10−6
1.91×10−10 		2
19
13
16 5p13.2 rs6897932 chr5 35910332 IL7R 8.00×10−6 15 II
17 6q15
6q15		 rs597325
rs56297233		 chr6
chr6		 91059215
91070750		 BACH2
BACH2 		3.38×10−10
5.40×10−8 		17
2		 S
III
18 6q22.32 rs9388489 chr6 126740412 C6orf173 4.20×10−13 2 III
19 6q23.3
6q23.3		 rs2327832
rs10499194		 chr6
chr6		 138014761
138044330		 TNFAIP3
TNFAIP3 		1.60×10−4*
3.00×10−4* 		2
2		 S
III, IV
20 6q25.3 rs1738074 chr6 159385965 TAGAP 7.59×10−9 16 S
21 7p15.2 rs7804356 chr7 26858190 Intergenic 5.30×10−9 2 III, IV
22 7p12.2 rs10272724 chr7 50444707 IKZF1 4.80×10−9 20 III
23 9p24.2
9p24.2		 rs7020673
rs10758593		 chr9
chr9		 4281747
4282083		 GLIS3
GLIS3 		5.40×10−12
1.18×10−8 		2
17		 IV, S
S
24 10p15.1 rs12251307 chr10 6163501 IL2RA 1.30×10−13 2 IV
25 10p15.1
10p15.1		 rs947474
rs11258747		 chr10
chr10		 6430456
6512897		 PRKCQ
PRKCQ 		4.00×10−9
1.20×10−7 		14
2		 IV, S
26 10p11.22 rs722988 chr10 33466153 NRP1 4.88×10−8 21 S
27 10q23.31 rs10509540 chr10 90013013 C10orf59 1.30×10−28 2 III, S
28 11p15.5
11p15.5
11p15.5		 rs7928968
rs3842727
rs7111341		 chr11
chr11
chr11		 2006875
2141424
2169742		 INS
TH
INS 		2.78×10−14
4.89×10−196
4.40×10−48 		17
13
2		 IV
29 12p13.31
12p13.31
12p13.31		 rs3764021
rs10466829
rs4763879		 chr12
chr12
chr12		 9724895
9767358
9801431		 NR
CLECL1
CD69 		5.00×10−8
9.19×10−9
1.90×10−11 		19
17
2		 III, S
III, S
30 12q13.2
12q13.2
12q13.2		 rs705704
rs11171739
rs2292239		 chr12
chr12
chr12		 54721679
54756892
54768447		 ERBB3
ERBB3
ERBB3 		4.31×10−31
1.00×10−11
2.20×10−25 		17
19
2		 III, IV, S

III, S
31 12q13.3 rs3809114 chr12 56134906 NR 6.90×10−4* 2
32 12q14.1 rs10877012 chr12 56448352 CYP27B1 3.80×10−6 22 II, III, S
33 12q24.12
12q24.12		 rs1265565
rs3184504		 chr12
chr12		 110199580
110368991		 CUX2
SH2B3 		1.00×10−16
2.80×10−27 		23
2		 IV, S
II
34 12q24.13 rs17696736 chr12 110971201 C12orf30 1.73×10−13 15 IV, S
35 13q32.3 rs9585056 chr13 98879767 GPR183 5.20×10−9 24 IV
36 14q24.1 rs1465788 chr14 68333352 Intergenic 1.80×10−12 2
37 14q32.2 rs4900384 chr14 97568704 Intergenic 3.70×10−9 2
38 14q32.2 rs56994090 chr14 100376200 DLK1 1.62×10−10 25
39 15q14
15q14		 rs17574546
rs12908309		 chr15
chr15		 36689768
36715969		 RASGRP1
RASGRP1 		3.35×10−8
4.31×10−8 		13
17		 III
IV
40 15q25.1 rs3825932 chr15 77022501 CTSH 7.70×10−8 2 II, III, IV
41 16p13.13
16p13.13
16p13.13		 rs12708716
rs12927355
rs416603		 chr16
chr16
chr16		 11087374
11102272
11271580		 CLEC16A
DEXI
C16orf75 		2.20×10−16
1.91×10−16
3.00×10−6 		2
17
14		 II, III, IV
42 16p11.2
16p11.2		 rs4788084
rs9924471		 chr16
chr16		 28447349
28499031		 IL27
IL27 		2.60×10−13
1.21×10−11 		2
17		 II, III, S
II
43 16q23.1
16q23.1		 rs7202877
rs8056814		 chr16
chr16		 73804746
73809828		 Intergenic
NR		 3.10×10−15
1.13×10−7 		2
17
44 17p13.1 rs16956936 chr17 7574417 Intergenic 5.00×10−7 2
45 17q12 rs2290400 chr17 35319766 ORMDL3 5.50×10−13 2 II, III, IV, S
46 17q21.2 rs7221109 chr17 36023812 Intergenic 1.30×10−9 2 III, IV, S
47 18p11.21 rs1893217 chr18 12799340 PTPN2 3.60×10−15 2 IV, S
48 18q22.2 rs763361 chr18 65682622 CD226 1.56×10−8 16 II, III, IV
49 19p13.2 rs2304256 chr19 10336652 TYK2 4.13×10−9 25 II, IV, S
50 19q13.32 rs425105 chr19 51900321 Intergenic 2.70×10−11 2 IV
51 19q13.33 rs679574 chr19 53897920 FUT2 4.30×10−18 16 IV, S
52 20p13 rs2281808 chr20 1558551 Intergenic 1.20×10−11 2 II
53 21q22.3
21q22.3		 rs11203203
rs876498		 chr21
chr21		 42709255
42714896		 UBASH3A
UBASH3A 		1.70×10−9
7.06×10−9 		2
13		 III, S
IV
54 22q12.2 rs5753037 chr22 28911722 Intergenic 2.60×10−16 2 III, S
55 22q12.3 rs229541 chr22 35921264 C1QTNF6 2.10×10−7 2 II, S
Four newly discovered loci
56 1q32.1 rs6691977 chr1 200814959 NR 4.30×10−8 13
57 2q13 rs4849135 chr2 111615079 NR 4.40×10−8 13
58 4q32.3 rs2611215 chr4 166574267 NR 1.80×10−11 13 S
59 5p13.2 rs11954020 chr5 35883251 IL7R 4.40×10−8 13

Ref.: Publication reference. ID: unique T1D loci identifiers. BP: NCBI36 chromosome positions.

^

rs363609 is in LD with reported SNP rs6546909 (r2 = 0.84) whose p-value is stated.

*

P-values are derived from Barrett et al. (from Table 2 in (2)). ‘NR’ denotes no gene of interest was reported at the locus.

II, III, IV, S corresponds to Tables where SNPs are featured; II – Non-synonymous LD SNPs, III – cis- interacting genes, or IV – trans- interacting genes, S – Supplementary cis- interacting genes (see Suppl. Table II(i)).