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 (𝑃<1×10⁻⁵).

Number	SNP (allele)^1,2	Mapped Gene(s)	Region^3	Disc^4 Pop	Rep^5 Pop	RAF^6	RAFEU^7	RAFEA^8	RAFSA^9	RAFAF^10	OR (95% CI)	𝑃 value
1	rs7542900 (C) [148]	F3-PGBD4P7	1p21.3	AA		0.56	0.80	0.72	0.79	0.56	1.16 (1.09–1.25)	6×10^−6
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)	4×10^−6
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)	7×10^−6
4	rs6426514 (A) [152]	RHOU	1q42.13	PS		0.06	0.09	0.03	0.02	0.12	1.51 (1.27–1.78)	2×10^−6
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)	4×10^−7
6	rs11677370 (T)[124]	DCDC2C	2p25.3	SEA (I)		0.4	0.68	0.71	—	0.78	1.35 (1.19–1.53)	3×10^−6
7	rs6712932 (C) [174]*	MRPS9-GPR45	2q12.1	EUR		NR	0.34	0.22	0.32	0.28	1.52 (1.27–1.82)	6×10^−6
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)	7×10^−8
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)	3×10^−6
10	rs13081389 (A) [116]	SYN2-GSTM5P1	3p25.2	EUR		NR	0.95	0.98	—	1.00	1.24 (1.15–1.35)	2×10^−7
11	rs17036101 (G) [109]	SYN2-GSTM5P1	3p25.2	EUR		0.93	0.95	0.98	—	0.98	1.15 (1.10–1.21)	2×10^−7
12	rs1801282 (C) [103]	PPARG	3p25.2	EUR		0.86	0.90	0.94	0.91	1.00	1.14 (1.08–1.20)	2×10^−6
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)	3×10^−6
14	rs3773506 (C) [124]	PLS1	3q23	SEA (I)		0.06	0.04	0.11	0.04	0.14	1.81 (1.39–2.35)	9×10^−6
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)	7×10^−6
16	rs1374910 (T) [149]	IGF2BP2	3q27.2	HIS		NR	0.02	0.08	—	0.15	1.24 (1.15–1.34)	1×10^−7
17	rs7659604 (T) [104]	ANXA5-TMEM155	4q27	EUR		0.38	0.44	0.36	0.45	0.71	1.35 (1.19–1.54)	9×10^−6
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)	9×10^−6
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)	4×10^−6
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)	7×10^−7
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)	4×10^−7
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)	4×10^−6
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)	1×10^−6
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)	9×10^−6
25	rs9465871 (C) [104]	CDKAL1	6p22.3	EUR		0.18	0.16	0.52	0.21	0.58	1.18 (1.04–1.34)	3×10^−7
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)	2×10^−6
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)	2×10^−6
28	rs6930576 (A) [121]	SASH1	6q24.3	AA		0.28	0.34	0.18	0.44	0.24	1.31 (1.18–1.45)	7×10^−7
29	rs741301 (C) [175]*	ELMO1	7p14.2	EA		NR	0.32	0.32	0.43	0.67	2.67 (1.71–4.16)	8×10^−6
30	rs1525739 (C) [176]*	LOC100287613	7p21	EUR		NR	0.49	0.16	0.27	0.33	NR	6×10^−6
31	rs7636 (A) [124]	ACHE	7q22.1	EA		0.06	0.04	0	0.05	0.33	1.85 (1.42–2.41)	5×10^−6
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)	2×10^−6
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)	1×10^−6
34	rs7020996 (C) [109]	CDKN2B-AS1-DMRTA1	9p21.3	EUR		NR	0.81	0.57	—	0.74	1.26 (1.15–1.38)	2×10^−7
35	rs649891 (C) [150]	PTPRD	9p23	MA		0.35	0.20	0.73	0.43	0.79	NR	6×10^−6
36	rs10993738 (C) [138]	SYK	9q22.2	EA		0.15	0.02	0.26	—	0	1.16 (1.09–1.23)	5×10^−6
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)	6×10^−6
38	rs10980508 (A) [176]*	SVEP1-RPS21P5	9q31	EUR		NR	0.86	0.97	0.97	0.94	NR	1×10^−6
39	rs1327796 (G) [138]	PALM2	9q31.3	EA		0.24	0.22	0.27	—	0.21	1.13 (1.08–1.20)	3×10^−6
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)	7×10^−6
41	rs10741243 (G) [124]	TCERG1L	10q26.3	SEA (I)		0.93	0.95	0.89	—	0.49	1.75 (1.38–2.23)	5×10^−6
42	rs9300039 (C) [98]	RPL9P23-HNRNPKP3	11p12	EUR		0.89	0.87	0.70	0.82	0.85	1.48 (1.28–1.71)	6×10^−8
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)	2×10^−6
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)	3×10^−7
45	rs12304921 (G) [104]	HIGD1C	12q13.12	EUR		0.15	0.16	0.50	0.36	0.15	2.5 (1.53–4.09)	7×10^−6
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)	2×10^−7
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)	4×10^−6
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)	7×10^−6
49	rs4760790 (A) [116]	TSPAN8-LGR5	12q21.1	EUR		NR	0.22	0.24	—	0.14	1.11 (1.06–1.16)	4×10^−6
50	rs730570 (G) [149]	BEGAIN-DLK1	14q32.2	HIS		NR	0.16	0.80	0.45	0.80	1.14 (1.08–1.21)	8×10^−6
51	rs1436953 (G) [145]	C2CD4A-C2CD4B	15q22.2	EA		0.64	0.43	0.57	0.57	0.24	1.14 (NR)	8×10^−6
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)	7×10^−7
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)	5×10^−7
54	rs17177078 (C) [176]*	TNRC6A	16p12	EUR		NR	0.93	1.00	0.97	1.00	NR	5×10^−6
55	rs16955379 (C) [127]	CMIP	16q23.2	EA		0.80	0.98	0.77	—	0.96	1.08 (1.05–1.12)	3×10^−7
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)	9×10^−7
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)	4×10^−6
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)	9×10^−6
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)	9×10^−6
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)	2×10^−6
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)	4×10^−6
62	rs2106294 (T) [121]	LIMK2	22q12.2	AA		0.94	0.70	0.86	0.75	1.00	1.75 (1.39–2.22)	4×10^−6
63	rs470089 (G) [176]*	SULT4A1	22q13.3	EUR		NR	0.8	0.93	0.76	0.60	NR	9×10^−6

¹𝑇ℎ𝑒 SNP-risk allele: SNP(s) most strongly associated with trait (risk allele).
2Reference for the largest study reporting association of the SNP with T2D or fasting plasma glucose at genome-wide significance (𝑃<5×10⁻⁸).
3Cytogenetic region associated with the SNP (NCBI).
4Discovery 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.
5Replication 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.
6Reported risk allele frequency (RAF) for the SNP; NR if not reported.
7RAF in HapMap population for Utah residents with Northern and Western European-ancestry from the CEPH collection; “—” denotes data not listed in HapMap.
8RAF in HapMap population for Han Chinese in Beijing, China; “—” denotes data not listed in HapMap.
9RAF in HapMap population for Gujarati Indians in Houston, Texas; “—” denotes data not listed in HapMap.
10RAF 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.