International Journal of Endocrinology / 2014 / Article / Tab 2 / Review Article
The Architecture of Risk for Type 2 Diabetes: Understanding Asia in the Context of Global Findings Table 2 Published SNPs associated with Type 2 diabetes mellitus at suggestive significance (
).
Number SNP (allele)1,2 Mapped Gene(s) Region3 Disc4 Pop Rep5 Pop RAF6
OR (95% CI)
value1 rs7542900 (C) [148 ] F3-PGBD4P7 1p21.3 AA 0.56 0.80 0.72 0.79 0.56 1.16 (1.09–1.25)
2 rs11165354 (A) [151 ] TGFBR3 1p22.1 SA All SA 0.78 0.62 0.52 0.85 0.28 1.17 (1.10–1.25)
3 rs17045328 (G) [124 ] CR2 1q32.2 SEA (M) 0.30 0.03 0.35 0.07 0.02 1.38 (1.20–1.59)
4 rs6426514 (A) [152 ] RHOU 1q42.13 PS 0.06 0.09 0.03 0.02 0.12 1.51 (1.27–1.78)
5 rs12027542 (A) [124 ] PCNXL2 1q42.2 SEA (M) 0.61 0.93 0.69 0.95 0.95 1.41 (1.23–1.61)
6 rs11677370 (T)[124 ] DCDC2C 2p25.3 SEA (I) 0.4 0.68 0.71 — 0.78 1.35 (1.19–1.53)
7 rs6712932 (C) [174 ]* MRPS9-GPR45 2q12.1 EUR NR 0.34 0.22 0.32 0.28 1.52 (1.27–1.82)
8 rs6723108 (T) [151 ] TMEM163-MIR5590 2q21.3 SA All SA 0.86 0.50 1 0.93 1 1.27 (1.17–1.39)
9 rs358806 (C) [104 ] LRTM1-WNT5A 3p14.3 EUR 0.80 0.77 0.84 0.90 0.92 1.16 (1.03–1.33)
10 rs13081389 (A) [116 ] SYN2-GSTM5P1 3p25.2 EUR NR 0.95 0.98 — 1.00 1.24 (1.15–1.35)
11 rs17036101 (G) [109 ] SYN2-GSTM5P1 3p25.2 EUR 0.93 0.95 0.98 — 0.98 1.15 (1.10–1.21)
12 rs1801282 (C) [103 ] PPARG 3p25.2 EUR 0.86 0.90 0.94 0.91 1.00 1.14 (1.08–1.20)
13 rs2063640 (A) [124 ] ZPLD1-NDUFA4P2 3q12.3 SEA (M, C, I) 0.17 0.08 0.27 0.11 0.04 1.23 (1.13–1.34)
14 rs3773506 (C) [124 ] PLS1 3q23 SEA (I) 0.06 0.04 0.11 0.04 0.14 1.81 (1.39–2.35)
15 rs7630877 (A) [124 ] PEX5L 3q26.33 SEA (C) 0.17 0.35 0.18 0.36 0.31 1.32 (1.17–1.49)
16 rs1374910 (T) [149 ] IGF2BP2 3q27.2 HIS NR 0.02 0.08 — 0.15 1.24 (1.15–1.34)
17 rs7659604 (T) [104 ] ANXA5-TMEM155 4q27 EUR 0.38 0.44 0.36 0.45 0.71 1.35 (1.19–1.54)
18 rs3792615 (T) [124 ] 36951 4q32.3 SEA (I) 0.95 0.97 0.84 0.96 0.85 1.93 (1.45–2.59)
19 rs10461617 (A) [151 ] RPL26P19-MAP3K1 5q11.2 SA All SA 0.21 0.18 0.39 0.26 0.44 1.17 (1.09–1.25)
20 rs12518099 (C) [115 ] MIR3660-CETN3 5q14.3 EUR 0.23 0.23 0.39 0.31 0.23 1.16 (1.10–1.22)
21 rs17053082 (T) [152 ] PPIGP1-SGCD 5q33.2 PS 0.1 0.06 0.06 0.06 0.08 1.49 (1.28–1.73)
22 rs9472138 (T) [109 ] VEGFA-C6orf223 6p21.1 EUR 0.28 0.24 0.11 0.23 0.14 1.06 (1.04–1.09)
23 rs3916765 (A) [171 ] MTCO3P1-HLA-DQA2 6p21.32 EUR 0.12 0.17 0.08 0.08 0 1.21 (1.12–1.31)
24 rs9295474 (G) [124 ] CDKAL1 6p22.3 SEA (M, C, I) 0.36 0.30 0.41 — 0.36 1.16 (1.09–1.24)
25 rs9465871 (C) [104 ] CDKAL1 6p22.3 EUR 0.18 0.16 0.52 0.21 0.58 1.18 (1.04–1.34)
26 rs7769051 (A) [121 ] SNORA33-HMGB1P13 6q23.2 AA 0.29 0.10 0.04 0.16 0.38 1.28 (1.16–1.42)
27 rs642858 (A) [124 ] ATP5F1P6-MIR3668 6q24.1 SEA (I) 0.40 0.25 0.40 0.36 0.13 1.35 (1.19–1.53)
28 rs6930576 (A) [121 ] SASH1 6q24.3 AA 0.28 0.34 0.18 0.44 0.24 1.31 (1.18–1.45)
29 rs741301 (C) [175 ]* ELMO1 7p14.2 EA NR 0.32 0.32 0.43 0.67 2.67 (1.71–4.16)
30 rs1525739 (C) [176 ]* LOC100287613 7p21 EUR NR 0.49 0.16 0.27 0.33 NR
31 rs7636 (A) [124 ] ACHE 7q22.1 EA 0.06 0.04 0 0.05 0.33 1.85 (1.42–2.41)
32 rs4527850 (T) [152 ] SLA-WISP1 8q24.22 PS 0.75 0.72 0.42 0.69 0.89 1.23 (1.13–1.34)
33 rs564398 (T) [74 ] CDKN2B-AS1 9p21.3 EUR 0.56 0.57 0.92 0.67 1.00 1.13 (1.08–1.19)
34 rs7020996 (C) [109 ] CDKN2B-AS1-DMRTA1 9p21.3 EUR NR 0.81 0.57 — 0.74 1.26 (1.15–1.38)
35 rs649891 (C) [150 ] PTPRD 9p23 MA 0.35 0.20 0.73 0.43 0.79 NR
36 rs10993738 (C) [138 ] SYK 9q22.2 EA 0.15 0.02 0.26 — 0 1.16 (1.09–1.23)
37 rs773506 (G) [121 ] SYK-AUH 9q22.31 AA 0.77 0.63 0.25 0.50 0.13 1.32 (1.18–1.49)
38 rs10980508 (A) [176 ]* SVEP1-RPS21P5 9q31 EUR NR 0.86 0.97 0.97 0.94 NR
39 rs1327796 (G) [138 ] PALM2 9q31.3 EA 0.24 0.22 0.27 — 0.21 1.13 (1.08–1.20)
40 rs6583826 (G) [124 ] IDE-RPL11P4 10q23.33 SEA (M, C, I) 0.26 0.53 0.27 0.33 0.50 1.18 (1.10–1.27)
41 rs10741243 (G) [124 ] TCERG1L 10q26.3 SEA (I) 0.93 0.95 0.89 — 0.49 1.75 (1.38–2.23)
42 rs9300039 (C) [98 ] RPL9P23-HNRNPKP3 11p12 EUR 0.89 0.87 0.70 0.82 0.85 1.48 (1.28–1.71)
43 rs2722769 (C) [148 ] HMGN1P22-MTND5P21 11p15.3 AA 0.53 0.56 0.56 0.76 0.99 1.35 (1.19–1.54)
44 rs7107217 (C) [148 ] RPS27P20-TMEM45B 11q24.3 AA 0.91 0.50 0.34 0.65 0.54 1.18 (1.10–1.27)
45 rs12304921 (G) [104 ] HIGD1C 12q13.12 EUR 0.15 0.16 0.50 0.36 0.15 2.5 (1.53–4.09)
46 rs1153188 (A) [109 ] DCD-VDAC1P5 12q13.2 EUR 0.73 0.74 0.99 0.83 0.79 1.08 (1.05–1.11)
47 rs2358944 (G) [121 ] PCNPP3-RPSAP52 12q14.3 AA 0.77 0.14 0.67 0.38 0.89 1.33 (1.18–1.49)
48 rs1495377 (G) [104 ] TSPAN8-LGR5 12q21.1 EUR 0.50 0.48 0.24 0.41 0.15 1.28 (1.11–1.49)
49 rs4760790 (A) [116 ] TSPAN8-LGR5 12q21.1 EUR NR 0.22 0.24 — 0.14 1.11 (1.06–1.16)
50 rs730570 (G) [149 ] BEGAIN-DLK1 14q32.2 HIS NR 0.16 0.80 0.45 0.80 1.14 (1.08–1.21)
51 rs1436953 (G) [145 ] C2CD4A-C2CD4B 15q22.2 EA 0.64 0.43 0.57 0.57 0.24 1.14 (NR)
52 rs1436955 (C) [120 ] C2CD4A-C2CD4B 15q22.2 EA 0.73 0.74 0.74 0.75 0.65 1.13 (1.08–1.19)
53 rs7119 (T) [124 ] HMG20A 15q24.3 SEA (M, C, I) 0.19 0.40 0.17 0.24 0.38 1.24 (1.14–1.34)
54 rs17177078 (C) [176 ]* TNRC6A 16p12 EUR NR 0.93 1.00 0.97 1.00 NR
55 rs16955379 (C) [127 ] CMIP 16q23.2 EA 0.80 0.98 0.77 — 0.96 1.08 (1.05–1.12)
56 rs17797882 (T) [127 ] RPS3P7-MAF 16q23.2 EA 0.32 0.01 0.18 0.04 0.05 1.08 (1.05–1.12)
57 rs623323 (T) [152 ] RNMTL1-NXN 17p13.3 PS 0.15 0.20 0.11 0.13 0.50 1.28 (1.15–1.42)
58 rs10460009 (C) [124 ] LPIN2; LOC727896 18p11.31 SEA (M) 0.60 0.92 0.53 0.73 0.95 1.35 (1.18–1.54)
59 rs472265 (G) [124 ] PAPL 19q13.2 SEA (I) 0.22 0.16 0.26 0.27 0.26 1.39 (1.20–1.61)
60 rs328506 (C) [152 ] RBM38-HMGB1P1 20q13.31 PS SA 0.80 0.72 1.00 0.90 0.72 1.11 (1.06–1.15)
61 rs2833610 (A) [124 ] HUNK-MIS18A 21q22.11 SEA (M, C, I) 0.57 0.30 0.57 0.51 0.32 1.17 (1.09–1.24)
62 rs2106294 (T) [121 ] LIMK2 22q12.2 AA 0.94 0.70 0.86 0.75 1.00 1.75 (1.39–2.22)
63 rs470089 (G) [176 ]* SULT4A1 22q13.3 EUR NR 0.8 0.93 0.76 0.60 NR
SNP-risk allele: SNP(s) most strongly associated with trait (risk allele).
Reference for the largest study reporting association of the SNP with T2D or fasting plasma glucose at genome-wide significance (
).
Cytogenetic region associated with the SNP (NCBI).
Discovery population; EUR: European; SA: South Asian; EA: East Asian; SEA: Southeast Asian; AA: African-American, MA: Mexican-American; HIS: Hispanic; PS: Punjabi Sikh; M: Malay; C: Chinese; I: Indian.
Replication population: it has been confirmed in other populations; EUR: European; SA: South Asian; EA: East Asian; SEA: Southeast Asian; AA: African- American, MA: Mexican American; HIS: Hispanic; PS: Punjabi Sikh; M: Malay; C: Chinese; I: Indian.
Reported risk allele frequency (RAF) for the SNP; NR if not reported.
RAF in HapMap population for Utah residents with Northern and Western European-ancestry from the CEPH collection; “—” denotes data not listed in HapMap.
RAF in HapMap population for Han Chinese in Beijing, China; “—” denotes data not listed in HapMap.
RAF in HapMap population for Gujarati Indians in Houston, Texas; “—” denotes data not listed in HapMap.
RAF in HapMap population for Yoruban in Ibadan, Nigeria; “—” denotes data not listed in HapMap.
Risk Allele and RAF not reported, but chosen based on minor allele frequency (MAF) in the population mentioned in the original publication.