Supplementary Methods
Laboratory assays. For the Hong Kong population, plasma glucose (PG), total cholesterol (TC), triglyceride (TG) and HDL-C were measured enzymatically on a Roche Modular Analytics system (Roche Diagnostics GmbH, Mannheim, Germany). Plasma insulin was measured by enzyme linked immunosorbent assay (DAKOCytomation, Cambridgeshire, UK). For the SNUH population, PG, TC, TG and HDL-C were measured enzymatically on a TBA-200FR autoanalyzer (Toshiba Medical Systems Co., Ltd., Tokyo, Japan). Plasma insulin was measured by radioimmunoassay (BioSource Europe S.A., Belgium). For the KHGS population, PG was measured using a glucose oxidase method (YSI 2300-STAT; YSI Life Sciences, Yellow Springs, OH). TC and TG were measured enzymatically on a Beckman analyser (Beckman Instruments, Brea, CA). HDL-C was measured using the direct Sigma EZ-HDL assay (Sigma Diagnostics, St. Louis, MO). Plasma insulin was measured by radioimmunoassay (Linco Research Inc., St Louis, MO). For all populations, these measurements were performed using standard reagent kits supplied by the manufacturers and the precision performances of these assays were within the manufacturer’s specifications. Both intra- and inter-assay coefficient of variations were <2% for glucose, <3% for TC, <4% for TG, <3% for HDL and <8% for insulin.

Genotyping. We genotyped 13 SNPs in seven T2D genes using genomic DNA. For Hong Kong samples, SNPs were genotyped using primer extension of multiplex products with detection by MALDI-TOF mass spectroscopy using a Sequenom MassARRAY platform (San Diego, CA, USA) at the McGill University and Genome Quebec Innovation Centre. For Korea SNUH & KHGS samples, SNPs were genotyped using Assay-on-Demand TaqMan assays (Applied Biosystems, Foster City, CA, USA). Allele calling was detected by ABI PRISM 7900HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA). All alleles are reported for forward strand at NCBI build 36.

Quality Control. Hardy-Weinberg equilibrium (HWE) for each SNP was assessed by the exact test using PLINK (v.0.99, http://pngu.mgh.harvard.edu/~purcell/plink). In each population, HWE P values were > 0.001 in the control subjects for all SNPs. The average genotype call rates were 99.5%, 99.4% and 98.0% for Hong Kong, SNUH and KHGS samples, respectively. The average concordance rate based on blind duplicate comparisons (64 Hong Kong and 23 SNUH samples) was 98.0% for Hong Kong and 99.6% for SNUH samples. 

Statistical test for heterogeneity of effect. For disease association studies, a general method with inverse-variance weighting was used to derive the Q statistic for the comparison of the odds ratios (ORs) amongst studies, based on their natural logarithms of the ORs. Standard errors were directly estimated or imputed from the confidence intervals. The inverse of the variance of each estimate was taken as its weight, thus the summary logarithm of the odds ratio (lnORSUM) was: 
 , i = 1,2,…,s, where s = number of study
The Q statistic for assessment of heterogeneity was calculated as follows. This statistic followed a 2 distribution with df equals to number of studies -1:

For quantitative trait association studies, Q statistic for heterogeneity of standardized mean differences (SMDs) was calculated using inverse of the variance of each estimate as its weight and followed a 2 distribution with df equals to number of studies -1:
 , i = 1, 2, …, s

Power calculation. Posterior study powers were calculated using genetic power calculator (1). By using the observed effect sizes and assuming a multiplicative model for T2D association in our study, our current sample size had 77% and 43% power, respectively, to detect a genotype relative risk (GRR) of 1.13 with risk allele frequency of 0.13 (as of FTO) for  levels at 0.05 (unadjusted) and 0.0038 (Bonferroni correction). The respective power for GRR of 1.35 with risk allele frequency of 0.02 (as of TCF7L2) are 84% and 52%, respectively, for  levels at 0.05 and 0.0038. For quantitative trait associations, our current sample size had 74% and 38% power, respectively, to detect a difference of 0.09 SD per risk allele and risk allele frequency of 0.13 as observed in BMI for FTO for  levels at 0.05 and 0.0038. For a difference of 0.02 SD per risk allele and at risk allele frequency of 0.13 as observed in HOMA- for TCF7L2, the respective power are 6% and 0.6% for  levels at 0.05 and 0.0038.

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Supplementary Table 1. List of SNPs selected for replication in this study.

Gene	Associated SNPs	Referencesa	SNPs selected in this study	
IGF2BP2	rs1470579, rs4402960 
	DGI, FUSION, WTCCC	rs4402960	
CDKAL1

	rs10946398, rs7754840, rs7756992	Icelandic, DGI, FUSION, WTCCC	rs7754840, rs7756992	
SLC30A8

	rs13266634	French, Icelandic, DGI, FUSION, WTCCC	rs13266634	
CDKN2A/B	rs564398, rs10116277, rs1333040, rs10757274, rs2383206, rs10757278, rs1333049, rs10811661
	DGI, FUSION, WTCCC, CHD/MI	rs564398, rs1333040, rs10757278, rs10811661	
HHEX	rs1111875, rs5015480, rs7923837

	French, Icelandic, DGI, FUSION, WTCCC	rs1111875, rs5015480, rs7923837
	
TCF7L2

	rs7901695, rs7903146	French, Icelandic, DGI, FUSION, WTCCC	rs7903146	
FTO	rs8050136	FUSION, WTCCC	rs8050136	
aReferences: French (2); Icelandic (3); DGI (4); FUSION (5); WTCCC (6); coronary heart disease (CHD) / myocardial infraction (MI) (7-9)

Supplementary Table 2. Linkage disequilibrium structure of three T2D susceptibility genes in combined Chinese and Korean samples. Pairwise LD are indicated in upper right (D’) and lower left triangle (r2) for a) CDKAL1; b) CDKN2A/B; and c) HHEX 

a) 
Gene	SNP	rs7754840	rs7756992	
CDKAL1	rs7754840		0.884	
	rs7756992	0.564		

b)
Gene	SNP	rs564398	rs1333040	rs10757278	rs10811661	
CDKN2A/B	rs564398		0.936	0.825	0.195	
	rs1333040	0.262		0.844	0.242	
	rs10757278	0.088	0.309		0.044	
	rs10811661	0.004	0.020	0.002		

c)
Gene	SNP	rs1111875	rs5015480	rs7923837	
HHEX	rs1111875		0.994	0.645	
	rs5015480	0.520		0.799	
	rs7923837	0.253	0.549		

Supplementary Table 3. Haplotype association of CDKAL1, CDKN2A/B and HHEX in Chinese and Korean populations.

		Hong Kong	Korea SNUH	Korea KHGS	
Total N 
(cases/ controls)		3011 
(1481 / 1530)	1393 
(761 / 632)	2315
(799/ 1516)	
Gene	SNPs	P	P	P	
CDKAL1	rs7754840, rs7756992	2.1 x 10-6	0.006	2.2 x 10-5	
CDKN2A/B	rs564398, rs1333040, rs10757278, rs10811661	8.3 x 10-4	5.1 x 10-6	0.032	
HHEX	rs1111875, rs5015480, rs7923837	0.024	0.006	0.002	
Haplotypes with frequency ≥ 5% were compared in case-control samples by omnibus test.

Supplementary Table 4. Effects of body mass index adjustment for T2D association in the combined Chinese and Korean samples.

Gene	SNP	Risk allele/		P	
		non-risk allele	OR (95%CI)		
IGF2BP2	rs4402960	T/G	1.18 (1.08 - 1.28)	2.1 x 10-4	
CDKAL1	rs7756992	G/A	1.30 (1.21 - 1.41)	1.2 x 10-11	
SLC30A8	rs13266634	C/T	1.14 (1.05 - 1.23)	0.001	
CDKN2A/B	rs10811661	T/C	1.36 (1.26 - 1.47)	2.1 x 10-14	
HHEX	rs7923837	G/A	1.29 (1.18 - 1.42)	9.6 x 10-8	
TCF7L2	rs7903146	T/C	1.43 (1.13 - 1.80)	0.002	
FTO	rs8050136	A/C	1.09 (0.97 - 1.23)	0.130	
OR and 95%CI are reported with respect to risk allele using an additive model in logistic regression in combined samples with adjustment for BMI, age, gender and study population.
BMI, body mass index

Supplementary Table 5. Genotype frequency distribution and T2D association under different genetic models of seven genes in the combined Chinese and Korean samples.

		Case Frequency	Control Frequency	Additive	Dominance	Dominant	Recessive	
Gene	SNP	11	12	22a	11	12	22a	OR
(95% CI)b	P	Pc	OR
(95% CI)b	P	OR
(95% CI)b	P	
IGF2BP2	rs4402960	0.085	0.411	0.504	0.075	0.381	0.544	1.14 
(1.06 - 1.23)	8.7 x 10-4	0.461	1.18 
(1.07 - 1.31)	8.3 x 10-4	1.17 
(0.97 - 1.40)	0.095	
CDKAL1	rs7756992	0.325	0.462	0.213	0.256	0.489	0.255	1.27 
(1.18 - 1.36)	1.1 x 10-11	0.074	1.30 
(1.16 - 1.46)	9.6 x 10-6	1.45 
(1.30 - 1.61)	2.6 x 10-11	
SLC30A8	rs13266634	0.355	0.471	0.174	0.311	0.501	0.188	1.13 
(1.05 - 1.21)	6.6 x 10-4	0.110	1.11 
(0.98 - 1.26)	0.106	1.22 
(1.10 - 1.35)	1.8 x 10-4	
CDKN2A/B	rs10811661	0.378	0.469	0.154	0.303	0.493	0.204	1.29 
(1.20 - 1.38)	1.9 x 10-12	0.658	1.40 
(1.23 - 1.59)	3.0 x 10-7	1.39 
(1.26 - 1.55)	3.1 x 10-10	
HHEX	rs7923837	0.057	0.350	0.593	0.042	0.320	0.639	1.22 
(1.12 - 1.33)	3.8 x 10-6	0.895	1.25 
(1.13 - 1.38)	1.9 x 10-5	1.40 
(1.12 - 1.76)	0.004	
TCF7L2	rs7903146	0.001	0.062	0.937	0.001	0.045	0.953	1.34 
(1.09 - 1.65)	0.005	-	1.38 
(1.11 - 1.71)	0.003	0.87 
(0.23 - 3.25)	0.830	
FTO	rs8050136	0.017	0.252	0.731	0.014	0.224	0.762	1.14 
(1.03 - 1.26)	0.015	0.658	1.15 
(1.03 - 1.29)	0.014	1.16 
(0.78 - 1.72)	0.476	
a1: risk allele; 2: non-risk allele as defined according to Table 2. 
bOR & 95%CI are reported with respect to risk allele by logistic regression under additive, dominant and recessive (all 1 df test) models. 
cDominance P value is reported from a general models (2df test) with an additive and a dominance factor.

Supplementary Table 6. Associations of seven genes with T2D in Chinese and Korean populations after removal of young case and control subjects from the Hong Kong population. 
					Hong Kong	Korea SNUH	Korea KHGS	Combined	
Total N
(cases / controls)				1311
(589 / 722)	1393
(761 / 632)	2315
(799/ 1516)	5019
(2282 / 2737)	
Gene	SNP	Chr	Position
(bp)	Risk /
non-risk allelesa	Case
risk AF	Control risk AF	OR
(95%CI)b	P	Case
risk AF	Control risk AF	OR
(95%CI)b	P	Case
risk AF	Control risk AF	OR
(95%CI)b	P	OR
(95%CI)c	P	Pempirical	
IGF2BP2	rs4402960	3	186994381	T/G	0.255	0.235	1.11
(0.93 - 1.33)	0.252	0.331	0.296	1.18
(1.00 - 1.39)	0.049	0.318	0.273	1.24 
(1.09 - 1.42)	0.001	1.19
(1.09 - 1.3)	1.4 x 10-4	0.002	
CDKAL1	rs7754840	6	20769229	C/G	0.418	0.357	1.28
(1.10 - 1.50)	0.002	0.519	0.464	1.24
(1.07 - 1.44)	0.005	0.529	0.468	1.27 
(1.13 - 1.44)	1.0 x 10-4	1.27
(1.17 - 1.38)	7.9 x 10-9	1.0 x 10-4	
CDKAL1	rs7756992	6	20787688	G/A	0.513	0.458	1.24
(1.06 - 1.44)	0.006	0.586	0.526	1.26
(1.09 - 1.47)	0.002	0.601	0.530	1.33
 (1.17 - 1.50)	8.2 x 10-6	1.29
(1.19 - 1.40)	7.7 x 10-10	1.0 x 10-4	
SLC30A8d	rs13266634	8	118253964	C/T	0.550	0.534	1.07
(0.91 - 1.24)	0.425	0.627	0.585	1.18
(1.02 - 1.38)	0.029	0.590	0.582	1.03 
(0.91 - 1.17)	0.636	1.08
(1.00 - 1.18)	0.054	0.489	
CDKN2A/B	rs564398	9	22019547	C/T	0.101	0.099	1.02
(0.79 - 1.33)	0.870	0.156	0.128	1.24
(1.01 - 1.54)	0.044	0.127	0.135	0.93 
(0.77 - 1.11)	0.421	1.04
(0.92 - 1.18)	0.486	0.999	
CDKN2A/B	rs1333040	9	22073404	T/C	0.701	0.666	1.17
(0.99 - 1.38)	0.058	0.664	0.684	0.91
(0.77 - 1.07)	0.250	0.690	0.680	1.05 
(0.92 - 1.20)	0.477	1.04
(0.95 - 1.13)	0.403	0.996	
CDKN2A/B	rs10757278	9	22114477	G/A	0.525	0.485	1.17
(1.00 - 1.37)	0.045	0.449	0.453	0.98
(0.85 - 1.14)	0.834	0.477	0.449	1.12 
(0.99 - 1.27)	0.069	1.09
(1.01 - 1.19)	0.032	0.319	
CDKN2A/B	rs10811661	9	22124094	T/C	0.602	0.551	1.23
(1.05 - 1.44)	0.009	0.619	0.512	1.55
(1.33 - 1.81)	2.0 x 10-8	0.601	0.546	1.25 
(1.10 - 1.41)	4.4 x 10-4	1.33
(1.22 - 1.44)	1.2 x 10-11	1.0 x 10-4	
HHEX	rs1111875	10	94452862	C/T	0.303	0.274	1.15
(0.97 - 1.37)	0.106	0.347	0.305	1.21
(1.03 - 1.43)	0.019	0.352	0.309	1.23 
(1.08 - 1.41)	0.002	1.20
(1.10 - 1.31)	4.7 x 10-5	0.001	
HHEX	rs5015480	10	94455539	C/T	0.183	0.160	1.17
(0.95 - 1.45)	0.140	0.219	0.186	1.22
(1.02 - 1.47)	0.034	0.227	0.183	1.32 
(1.13 - 1.54)	3.7 x 10-4	1.25
(1.13 - 1.39)	1.7 x 10-5	3.0 x 10-4	
HHEX	rs7923837	10	94471897	G/A	0.206	0.168	1.28
(1.05 - 1.56)	0.015	0.262	0.210	1.33
(1.12 - 1.59)	0.002	0.252	0.224	1.17 
(1.01 - 1.35)	0.033	1.24
(1.13 - 1.37)	1.0 x 10-5	3.0 x 10-4	
TCF7L2	rs7903146	10	114748339	T/C	0.035	0.022	1.58
(0.98 - 2.55)	0.059	0.037	0.025	1.53
(0.98 - 2.39)	0.063	0.031	0.024	1.29 
(0.90 - 1.87)	0.169	1.44
(1.13 - 1.83)	0.003	0.039	
FTO	rs8050136	16	52373776	A/C	0.144	0.125	1.18
(0.93 - 1.48)	0.175	0.138	0.122	1.15
(0.92 - 1.44)	0.228	0.124	0.118	1.06 
(0.88 - 1.28)	0.535	1.12
(0.99 - 1.26)	0.077	0.620	
aAll alleles were indexed to the forward strand of NCBI Build 36. Risk alleles were defined according to association results from combined samples. 
bOR and 95%CI were reported with respect to the risk allele using a log additive model in logistic regression. 
cFixed effects Cochran-Mantel-Haenszel test was shown for meta-analysis in the combined samples.
AF, allele frequency; Chr, chromosome; 95% CI: 95% confidence intervals; OR, odds ratio.

Supplementary Figure 1. Effect of increasing number of risk alleles and T2D risk in the combined Chinese and Korean samples. Seven significant SNPs (rs4402960, rs7756992, rs13266634, rs10811661, rs7923837, rs7903146 and rs8050136) were selected to calculate the number of risk alleles under an additive model (except that only one risk allele was counted for homozygous and heterozygous risk carriers of TCF7L2). Odds ratio and 95% CI are shown. Numbers in parenthesis indicate sample size in each category.

Supplementary Figure 2. Meta-analysis of seven genes for T2D association in European and Asian populations.  The studies included French (2), Icelandic (3), DGI (4), FUSION (5), WTCCC (6), Japanese (10) and the present study (Hong Kong, Korea SNUH and Korea KHGS).

Supplementary Figure 3. Meta-analysis of FTO association with BMI for European and Asian populations. The studies included those from Frayling et al. (nondiabetic controls [EFSOCH and UKT2D GCC Controls], population based studies [ALSPAC mothers, NFBC1966 age 31, Oxford Biobank, Caerphilly, EPIC-Norfolk, BWHHS and InCHIANTI]) (11), Scuteri et al. (Sardinia and European Americans) (12), Li et al. (Chinese) (13), Horikoshi et al. (Japanese) (10) and the present study (Hong Kong adults and adolescents, Korea SNUH and Korea KHGS)