Download List of genes previously associated with T2D – compiled by Cristen

Supplemental Table S1: 147 SNPs reported to be associated with T2D as of May 2005
Gene Name
Full gene name
Reference
Common name dbSNP ID
(if
available)
ABCA1
ATP-binding cassette, subfamily A member 1
ATP-binding cassette, subfamily C (CFTR/MRP,
member 8
1; 2
IMS-JST105322
rs2020927
3-5
4; 6-9
7; 10
11
11
11
11
11
11
1
11
Syn T759T
Intron 24 T/C
Syn R1273R
IV38+54
IV18-36
IVS11-74
K649
S1369A
IVS19+123
IMS-JST032704
IVS13-76
rs1801261
rs1799854
rs4148643
rs4148646
rs4148628*
rs2074308
rs1799858
rs757110‡†
rs8192692
rs2283257
rs1283802
C/T
T/C
C/A
2-sided A/G
T/C
G/T
12; 13
12; 13
14-16
14; 17
18
15; 16
19
45G/T
276T/G
-11377 G/C
-11426 A/G
I164T
– 11391G/A
G54D
rs2241766
rs1501299
rs266729
rs16861194
G/T
G/T
C/G
G/A
rs17300539
rs2856966‡
2-sided A/G
G/A
20
21; 22
23
1
24
25
26
5’UTR -47 T/C
Q27E
W64R
IMS-JST005886
-106 C/T
TaqI
Ala567Gly
rs1042711
rs1042714†
rs4994‡
rs506571
rs759853
rs2280520
rs1803274
C/T
G/C
C/T
A/G
C/T
G/A
T/C
27; 28
SNP 19
SNP 43 Intron 3
SNP 63
§
ABCC8
ABCC9
ACDC/APM1
ADCYAP1
ADRB2
ADRB3
ALDOB
AKR1B1
ApoD
BCHE
/CHLE
CAPN10
ATP-binding cassette, subfamily C, member 9
Adiponectin
adenylate cyclase activating
polypeptide 1 (pituitary
adrenergic, beta-2-, receptor,
surface
adrenergic, beta-3-, receptor
Aldolase B
aldose reductase
Apolipoprotein D
butyrylcholinesterase
calpain – 10
*‡
rs3842570
rs3792267
rs5030952
Risk/nonrisk allele
from
previous
report1
flanking sequence on
strand assayed
A/G
A/G
A/G
T/C
2-sided G/C
2-sided G/A
T/C
gcaaaataca[A/G]gccacttctt
tatccaagtc[A/G]gtcgctgtct
cagctggcct[A/G]cagggaggga
cagagagctc[T/C]ctgtgcaggg
acggccacaa[G/C]aggccagtcc
gggtgcggaa[G/A]gcattctcag
acgctcagca[C/T]tggaagggaa
gggctggacg[T/C]ttgcggttca
tgtccagggg[C/A]gatgagggca
tggagtgcag[A/G]taagcacctg
aatccatcca[T/C]gggtgataac
cttactcaca[G/T]tgctacctaa
ctctgcccgg[G/T]catgaccagg
ctatatgaag[G/T]cattcattat
cagatcctgc[C/G]cttcaaaaac
tggggtcgta[G/A]tttaattcat
gcctaccaca[T/C]cacagtctat
tgcaagaacc[A/G]gctcagatcc
ccagacttcg[G/A]tggctcggag
tgggtccgcc[C/T]gctgaggcgc
cgtcacgcag[G/C]aaagggacga
ggccatcgcc[C/T]ggactccgag
caatgaacct[A/G]ccagaaaagt
gcggcacccc[C/T]agcgcaacca
gggacaatcg[G/A]aggggcatgc
tcccattctg[T/C]ttcatcaata
not successfully genotyped
gaagtaaggc[G/A]tttgaaggtg
gggggtggag[T/C]gaggggtggg
29; 30
CASQ1
calsequestrin 1
CD38
COG2/LDLC
GYS1
HFE
CD38 antigen
Low density lipoprotein
receptor defect Ccomplementing protein
C-reactive protein, pentraxinrelated
proprotein convertase
subtilisin/kexin type 1
intestinal fatty acid binding
protein 2
Friedreich ataxia
Glucagon receptor
glutamine-fructose-6phosphate transaminase 2
guanine nucleotide binding
protein (G protein, beta
polypeptide 3
glycogen synthase 1
hemochromatosis
HNF1A/TCF1
hepatic nuclear factor 1
CRP
ENPP1/PCSK1/P
C1
FABP2
FRDA
GCGR
GFPT2
GNB3
HSD11B1
HSP70-2/HSPA2
HTR2C
IDE
IL-6
hydroxysteroid (11-beta
dehydrogenase 1
heat shock 70kDa protein 1B
5-hydroxytryptamine
(serotonin receptor 2C
insulin-degrading enzyme
interleukin 6 (interferon, beta
SNP 44 C/T and
T504A
CASQ2312
CASQ2399
rs2275703
R140W
2312A/G
IMS-JST051114
rs2975760
rs617698
rs617599†
rs2275703
rs1800561*‡
rs1051038
34
SNP 133552
rs2794521
35; 36
K121Q
rs1044498
C/A
1
IMS-JST031915
rs1397613
T/G
37
38; 39
40
rs2498429
G40S
I471V
rs2498429
rs1801483*‡
rs2303007‡
A/T
41
825T
rs5443
T/C
42
43
44
45
46
46
46
47
46
46
46
46
48
XbaI A2
H63D
C282Y
G391S
GE117881_360
GE117884_349
rs8103451
rs1799945‡
rs1800562‡
rs1169305§
A/G
G/C
A/G
31; 32
31
32
33
1
C/T
2-sided G/A
G/A
C/A
acgcttgctg[C/T]gaagtaaggc
tctattcctt[G/A]tgaagttcca
tggagggaag[G/A]ggagtcgggg
ccagacaagc[C/A]cctccagtat
acaggtccag[C/T]gggacatgtt
G/A
agcagcctta[G/A]gcatcttgga
‡
C/T
agtgagaaca[C/T]gcggtgtttg
ctgcaaggac[C/A]agggcgactg
agttaaagag[T/G]gaaggaaaca
ctaagtaaaa[A/T]gtatatacat
gaagctctac[G/A]gtgaccagtg
C/T
gccacgccga[C/T]ctccggccct
49
50
51; 52
53; 54
Ala98Val
SNP1
SNP5
P2
-995 G/A
-759 C/T
-179 T/C
-174 G/C
rs1169289†
rs1800574‡
rs1920792
rs2178463†
rs2393792†
rs2701175
rs846910§
rs12086634
rs1061581§
rs3813928§
rs3813929
rs4646953
rs1800795
G/A
G/A
2-sided C/G
T/C
T/C
A/G
G/A
C/A
T/G
C/G
T/C
A/G
C/G
gcatcacgtc[T/C]gtggccttct
gttactctag[A/G]atggagtgca
gttctatgat[G/C]atgagagtcg
agatatacgt[A/G]ccaggtggag
not successfully genotyped
aaaattagcc[G/A]ggtgtagtgg
catagaatta[G/A]cgtgtccttt
cggccctgct[C/G]gagtcagggc
gaggaggcgg[T/C]ccaccagaaa
agatcctacc[T/C]cattgggttg
ccactgcgcc[A/G]tgcctgtcct
caagtgatcc[G/A]cctgcctcag
ttttttgtag[C/A]gatgaggtct
not successfully genotyped
caaccccaga[T/G]gatttcttaa
not successfully genotyped
not successfully genotyped
cccctcatcc[T/C]gcttttggcc
aggacggtga[A/G]gaccgcggac
tgtgtcttgc[C/G]atgctaaagg
IL-6R
2
interleukin 6 receptor
INS
INSR
proinsulin precursor
insulin receptor
IPF1
insulin promoter factor 1,
homeodomain
insulin receptor substrate 1
IRS1
IRS2
ITGB3/PIA1/GPII
Ia
KCNJ9
KCNJ11
Insulin receptor substrate-2
integrin, beta 3 (platelet
glycoprotein IIIa, antigen
CD61
potassium inwardlyrectifying channel, subfamily
J, member 9
potassium inwardlyrectifying channel, subfamily
J, member 11
Lep
LIPC
Leptin
lipase, hepatic
LPL
LTA
lipoprotein lipase
lymphotoxin alpha (TNF
superfamily
chemokine (C-C motif ligand
2
Hepatocyte growth factor
receptor
MCP1/CCL2
MET
MGEA5
NEUROD1
NOS3
/eNOS
PAX4
Meningioma-expressed
antigen 5
neurogenic differentiation 1
Endothelial nitric oxide
synthase
paired box gene 4
54
55
56
11
57
11
11
11
58
-598A/G
Asp358Ala
V385I (SNP12
3p+9
V985M
IVS6+43 (SNP131
IVS6+31 (SNP132
IVS7+28 (SNP130
Asp76Asn
rs1800797†
rs8192284‡
rs2228146‡§
rs3842752
rs1799816*‡
rs2860177
rs2860178
rs7252268
A/G
T/C
2-sided T/G
2-sided A/G
A/C
41; 59; 60
61
61
61
62
63; 64
G972R
-7120 G/A
-446 G/A
Ala 804
G1057D
A2
rs1801278‡
rs12053536
rs13306465
rs1801123
rs1805097‡
rs5918
A/G
T/C
T/C
C/T
2-sided T/C
T/C
65
11; 66-70
11
11
1
11
71
72
73
SNP3 A/G
SNP11 T/C
SNP13 A/G
E23K (I337V
A190
3p+215
IMS-JST026278
IVS1+49
-250 G/A
Intron 6 PvuII
T60N
rs2180752
rs2737705
rs2753268
rs5219‡
rs5218†
rs5210
rs2278815
rs8192701
rs2070895§
rs285
rs1041981‡
A/G
C/T
G/A
A/G
G/A
G/A
G/A
C/T
74
-2518 G/A
rs3760399
A/G
1
IMS-JST054758
T3912C, IMSJST000713
LLY-MGEA5-14
rs38848
rs41736
T/C
T/C
Ala45Thr
E298D
IVS18 + 27A/C
R121W
rs1801262‡
rs1799983
rs1799984§
rs2233578*‡
*‡
G/A
A/C
T/C
A/C
aaatttgagg[G/A]tggccaggca
ctagtgcaag[A/C]ttcttcttca
not successfully genotyped
ggctgcctgc[A/G]ggctgcgtct
tcgtccggca[T/C]gtacacagag
cctcgcctcc[T/G]cagcgtctct
ccggtccctc[A/G]tgccaaaaag
tcttccacta[A/C]accggtccct
cctcgccgac[A/G]accccgcggt
tgcacctccc[A/G]gggctgctag
attgctaggt[T/C]accatgtccc
cctctggaag[T/C]agcgattccc
aagaatcatc[C/T]gctgttgcag
tgaggcggcg[T/C]ccgggccctg
gccctgcctc[T/C]gggctcacct
aaactagacc[A/G]tgatggtcag
cagtagacaa[C/T]tggtccactc
ggatgaaggc[G/A]tgcaaggggc
ggaccctgcc[A/G]agcccaggta
cgtggcgcag[G/A]gcgatcaccg
agccagtcct[G/A]aattgggttg
aatgagaggg[G/A]ctgtgtaagg
ctttttaaaa[C/T]gtgtgtcaca
not successfully genotyped
catcttttag[T/C]agctgtgggg
gcccacagca[A/C]cctcaaacct
75
76; 77
78
79-81
tgaaatggcc[A/G]ctccatagag
tagatatgtt[T/C]tcaaatgcaa
cttatcctga[T/C]gtaaacacct
§
T/C
T/G
not successfully genotyped
gcgttcatgg[T/C]ttcgaggtcg
ccccagatga[T/G]cccccagaac
not successfully genotyped
gacctgagcc[G/A]tgtgcacggt
PCK1
PIK3R1
PKLR
PPARG
PPARGC1A/PGC
1
PPP1R3
PRKCZ
PTGS2
PTPN1/PTP1B
PYY
RETN
SLC2A1/GLUT1
SLC2A2
phosphoenolpyruvate
carboxykinase 1
phosphoinositide-3-kinase,
regulatory subunit
pyruvate kinase, liver and
RBC
82
-232 C/G
rs2071023
11
IVS4+82
rs8192680§
83
PKLR1
PKLR2
PKLR4 R569R
PKLR5
rs3020781
rs2071053†
rs1052176†
rs1052177†
G/A
G/A
T/G
G/A
peroxisome proliferative
activated receptor, gamma
peroxisome proliferative
activated receptor, gamma,
coactivator 1
84-91
92
11; 93; 94
see
95
11
96; 97
P12A
1431 C/T
G482S
rs1801282‡
rs3856806
rs8192678‡
C/G
T/C
G/A
T528T
D905Y
rs3755863†
rs1799999‡
C/T
C/A
98
99
rs436045
rs20417
rs436045
rs20417
G/A
C/G
rs2066826
rs16995309*‡
rs2282146
rs718630
rs2206656
rs3787345†
rs4811078
rs718049†
rs941798
rs3787348†
rs718050†
rs754118†
rs2282147†
rs162430
rs1862513
rs841853
C/T
T/C
C/T
G/T
G/C
C/T
C/T
G/A
A/G
11
103; 104
105-108
rs2066826
Nons P387L
Syn exon8 C/T
rs718630
rs2206656
rs3787345
rs4811078
rs718049
rs941798
rs3787348
rs718050
rs754118
rs2282147
IVS3+68
-420
XbaI
109
11
11
TaqI
IVS5-15
T198
rs6785803†
rs5406†
rs5404
Protein phosphatase type-1
glycogen targeting subunit
protein kinase C, zeta
prostaglandin-endoperoxide
synthase 2 precursor
protein tyrosine phosphatase,
non-receptor type 1
peptide YY
resistin
solute carrier family 2
(facilitated glucose
transporter, member 1
solute carrier family 2
(facilitated glucose
transporter, member 2
C/G
tgtgtcaaaa[C/G]tcactatggt
100-102
A/G
A/G
C/G
A/C
2-sided C/G
2-sided A/G
2-sided T/C
not successfully genotyped
aatttttgtt[G/A]aatgaatgac
ccaaccctac[G/A]ggcgccgcct
cttagcaccc[T/G]catgatgttg
gggccagagg[G/A]gggaggggc
g
tcctattgac[C/G]cagaaagcga
tcacggaaca[T/C]gtgcagctac
agacaagacc[G/A]gtgaactgag
aataggattg[C/T]gtgccatccc
ctattagtgt[C/A]tgagttaaaa
tgcctgtcag[G/A]tttggtccaa
gaaagagagg[C/G]gggaaaggt
a
tgggtataag[C/T]ggtaataact
gctgcctccc[T/C]agccaaaggg
agcccccacc[C/T]gagcatatcc
ctgttgcaca[G/T]gtaaagtgcc
tgcaataata[G/C]cttgtgacat
gctacctctg[C/T]ggagctgtgg
gaaactccgt[C/T]taaaaaaaaa
tggtccacgc[G/A]ccctgttccc
gcaccaaagt[A/G]tcatcctagt
not genotyped
ttgagtacct[A/G]ttgatatgtg
not genotyped
not genotyped
acgtcgttaa[A/G]tgatgttgcc
gacatgaaga[C/G]ggaggccctg
gaagagcttt[A/C]tagacttcag
gtataggctc[C/G]attattgtcg
ccaagaaaat[A/G]atcaggttga
taagaatgcc[T/C]gtgacgatgg
SORBS1
11
110
111
T110I
Phe497
T228A
rs5400‡
rs5398
rs2281939‡
2-sided A/G
2-sided A/G
T/C
11
112
IVS17+53
N34S
rs7577088
rs17107315‡
A/G
C/T
113
rs2297508
G/C
117; 118
119
120
121
SNP17, +54G/C,
exon 18c
IMS-JST005889
-308 G/A
-857 C/T
5’ UTR A/C
M229L
-866G/A
Ala55Val
5’ -55 C/T
S89N
rs1800610
rs1800629
rs1799724†
rs10011540
rs2270565†
rs659366
rs660339‡
rs1800849
rs2890565‡
A/G
A/G
T/C
G/T
A/T
2-sided C/T
T/C
G/A
T/C
rs2242103
A/T
TNF
sorbin and SH3 domain
containing 1
son of sevenless homolog 1
serine protease inhibitor,
Kazal type 1
Sterol regulatory elementbinding protein -1
Tumor necrosis factor alpha
UCP1
uncoupling protein 1
UCP2
uncoupling protein 2
UCP3
UTS2
uncoupling protein 3
urotensin 2
VLDLR
very low density lipoprotein
receptor
Wolfram syndrome 1
1
IMS-JST014197
122; 123
wingless-type MMTV
integration site family,
member 5B
124
R456H
H611R
Intron 4+438
IMS-JST024404
Intron 4 + 6763
IMS-JST024409
SOS1
SPINK1
SREBF1
gaatgatgca[A/G]tcattccacc
taaaaaatgt[A/G]aacagggtaa
gatggtggcg[T/C]ctggctaatg
ttaatgaaat[A/G]agtgttttgt
attaagttca[C/T]tgtaacattt
1
49; 114
115
116
ggaagccttt[G/C]cctaggtgct
agaaaaaaac[A/G]tggagaaaga
gaggggcatg[A/G]ggacggggtt
ccccccttaa[T/C]gaagacaggg
ccgatttctg[G/T]tttttgaacc
ggggaggaca[A/T]agctgttgcg
gggtaactga[C/T]gcgtgaacag
cgcgctacag[T/C]cagcgcccag
ttatacacac[G/A]ggctgacctg
aatgttggta[T/C]ttgagtctga
WFS1
WNT5b
1
‡
rs1801208
rs734312‡
rs2270031
G/A
A/G
C/G
rs2270036
C/T
agacttaatc[A/T]ggttagtttg
ccctacacgc[G/A]cagggccctg
ctgctgttgc[A/G]ctggtggacc
tcttccactt[C/G]aacctttgac
cttaccgccc[C/T]ggcctcattc
Alleles are designated according to the strand typed in our study
2-sided indicates SNPs tested with a 2-sided test because the previous risk allele was difficult to determine for ambiguous SNPs (such as C/G) or
the SNP shows evidence for association with both alleles in different studies
* SNPs that were monomorphic or MAF < .005 in our sample
‡
nonsynonymous SNPs
†
SNPs in r2 > .8 with another genotyped SNP (r2 values are given in Table S3)
§
SNP could not be successfully genotyped in our sample
References for Table S1
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Muramatsu M, Kato T: Large-scale search of SNPs for type 2 DM susceptibility genes in a Japanese population. In Biochem Biophys Res
Commun, 2003, p. 751-758
2. Daimon M, Kido T, Baba M, Oizumi T, Jimbu Y, Kameda W, Yamaguchi H, Ohnuma H, Tominaga M, Muramatsu M, Kato T: Association of
the ABCA1 gene polymorphisms with type 2 DM in a Japanese population. In Biochem Biophys Res Commun, 2005, p. 205-210
3. Hani EH, Clement K, Velho G, Vionnet N, Hager J, Philippi A, Dina C, Inoue H, Permutt MA, Basdevant A, North M, Demenais F, GuyGrand B, Froguel P: Genetic studies of the sulfonylurea receptor gene locus in NIDDM and in morbid obesity among French Caucasians. In
Diabetes, 1997, p. 688-694
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Diabetes, 1996, p. 825-831
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receptor gene. In Diabetes, 1998, p. 598-605
6. Hart LM, de Knijff P, Dekker JM, Stolk RP, Nijpels G, van der Does FE, Ruige JB, Grobbee DE, Heine RJ, Maassen JA: Variants in the
sulphonylurea receptor gene: association of the exon 16-3t variant with Type II diabetes mellitus in Dutch Caucasians. In Diabetologia, 1999, p.
617-620
7. Rissanen J, Markkanen A, Karkkainen P, Pihlajamaki J, Kekalainen P, Mykkanen L, Kuusisto J, Karhapaa P, Niskanen L, Laakso M:
Sulfonylurea receptor 1 gene variants are associated with gestational diabetes and type 2 diabetes but not with altered secretion of insulin. In
Diabetes Care, 2000, p. 70-73
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sulfonylurea receptor 1 genetic variability on non-insulin-dependent diabetes mellitus prevalence and treatment: a population study. In Am J Med
Genet, 2001, p. 4-8
9. Ji L, Han X, Wang H: [Sulfonylurea receptor gene polymorphism is associated with non-insulin dependent diabetes mellitus in Chinese
population]. In Zhonghua Yi Xue Za Zhi, 1998, p. 774-775
10. Reis AF, Ye WZ, Dubois-Laforgue D, Bellanne-Chantelot C, Timsit J, Velho G: Association of a variant in exon 31 of the sulfonylurea
receptor 1 (SUR1) gene with type 2 diabetes mellitus in French Caucasians. In Hum Genet, 2000, p. 138-144
11. Barroso I, Luan J, Middelberg RP, Harding AH, Franks PW, Jakes RW, Clayton D, Schafer AJ, O'Rahilly S, Wareham NJ: Candidate Gene
Association Study in Type 2 Diabetes Indicates a Role for Genes Involved in beta-Cell Function as Well as Insulin Action. In PLoS Biol, 2003, p.
E20
12. Hara K, Boutin P, Mori Y, Tobe K, Dina C, Yasuda K, Yamauchi T, Otabe S, Okada T, Eto K, Kadowaki H, Hagura R, Akanuma Y, Yazaki
Y, Nagai R, Taniyama M, Matsubara K, Yoda M, Nakano Y, Tomita M, Kimura S, Ito C, Froguel P, Kadowaki T: Genetic variation in the gene
encoding adiponectin is associated with an increased risk of type 2 diabetes in the Japanese population. In Diabetes, 2002, p. 536-540
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