Genetic Risk Score Modelling for Disease Progression in New-Onset Type 1 Diabetes Patients: Increased Genetic Load of Islet-Expressed and Cytokine-Regulated Candidate Genes Predicts Poorer Glycemic Control
Table 1
The 46 T1D candidate genes tested for expression and cytokine regulation in human islets.
Region
GWAS SNP
Locus
Gene tested
1p13.2
rs2476601
PTPN22
PTPN22
1p31.3
rs2269241
PGM1
PGM1
1q31.2
rs2816316
RGS1
RGS1
1q32.1
rs3024505
IL10
IL10
2p25.1
rs1534422
(Gene desert)
2q12.1
rs917997
IL18RAP
IL18RAP
2q24.2
rs1990760
IFIH1
IFIH1
2q33.2
rs3087243
CTLA4
CTLA4
3p21.31
rs11711054
CCR5
CCR5, CCR3
4p15.2
rs10517086
(Gene desert)
4q27
rs4505848
IL2
IL2, IL21, ADAD1
5q13.2
rs6897932
IL7R
IL7R
6p21.32
rs9268645
MHC
Not included
6q15
rs11755527
BACH2
BACH2
6q22.32
rs9388489
CENPW (C6orf173)
Not tested
6q23.3
rs2327832
TNFAIP3
TNFAIP3
6q25.3
rs1738074
TAGAP
TAGAP
7p15.2
rs7804356
SKAP2
SKAP2
7p12.1
rs4948088
COBL
COBL
9p24.2
rs7020673
GLIS3
GLIS3
10p15.1
rs12251307
IL2RA
IL2RA
10p15.1
rs11258747
PRKCQ
PRKCQ
10q23.31
rs10509540
RNLS
RNLS
11p15.5
rs7111341, rs689
INS
INS
12p13
rs4763879
CD69
CD69
12q13.2
rs2292239
ERBB3
ERBB3
12q24.12
rs3184504
SH2B3
SH2B3
14q24.1
rs1465788
C14orf181
C14orf181
14q32.2
rs4900384
(0; gene desert)
15q25.1
rs3825932
CTSH
CTSH
16p13.13
rs12708716
CLEC16A
CLEC16A, PRM3, TNP2
16p12.3
rs12444268
UMOD
UMOD
16p11.2
rs4788084
IL27 (NUPR1)
IL27, NUPR1
16q23.1
rs7202877
CTRB1
CTRB2; CTRB1
17p13.1
rs16956936
DNAH2
DNAH2
17q12
rs2290400
ORMDL3 (GSDMB)
ORMDL3, GSDMB
17q21.2
rs7221109
SMARCE1
SMARCE1
18p11.21
rs1893217
PTPN2
PTPN2
18q22.2
rs763361
CD226
CD226
19q13.32
rs425105
PRKD2
PRKD2
20p13
rs2281808
SIRPG
SIRPG
21q22.3
rs11203203
UBASH3A
Not tested
22q12.2
rs5753037
HORMAD2
HORMAD2
22q13.1
rs229541
C1QTNF6
C1QTNF6
Xq28
rs2664170
GAB3
GAB3
The genes that were transcriptionally regulated by cytokines in human islets are highlighted in bold, as are the corresponding risk SNPs included in the genetic risk score analysis.
