

, Soo Heon Kwak2*
, Ji Won Yoon3*
, Sanghun Lee4, Kyong Soo Park2,5,6


1Institute of Health and Environment, Seoul National University, Seoul, Korea
2Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
3Department of Internal Medicine, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
4Department of Bioconvergence & Engineering, Dankook University, Yongin, Korea
5Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
6Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
7Department of Public Health Sciences, Seoul National University, Seoul, Korea
8RexSoft Inc., Seoul, Korea
9Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Korea
Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea E-mail: kspark@snu.ac.kr
Department of Public Health Science, Seoul National University, 1 Gwanak-ro, Gwanakgu, Seoul 08826, Korea E-mail: won1@snu.ac.kr
Department of Preventive Medicine, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon 16499, Korea E-mail: chnaha@ajou.ac.kr Copyright © 2023 Korean Diabetes Association
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
PubReader
ePub Link
Cite this Article
| Study population | Total | Case | Control | Male | Age, yr | BMI, kg/m2 | Fasting glucose, mg/dL | Mean of F/U duration | Genotyping platform | SNP |
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genotyped |
Imputed |
Meta | ||||||||||
| KoGES | 6,122 | 790 (13) | 5,332 (87) | 2,847 (46) | 51.5±8.7 | 24.4±3.0 | 84.1±8.5 | 11 years (5.5 times) | Affymetrix SNP Array 5.0 | 399,013 | 3,758,649 | 2,713,317 |
| GENIE | 4,406 | 237 (5) | 4,169 (95) | 2,604 (59) | 45.7±8.6 | 23.1±2.9 | 93.9±9.9 | 6 years(5.7 times) | Affymetrix KOR_v1.0 | 344,632 | 3,692,736 | |
| SNP | Chr; position | A | Study |
Effect | SE | wAF | P value | ANNOVAR |
|---|---|---|---|---|---|---|---|---|
| rs78529720 | 2; 169777297 | T/C | KoGES | 1.008 | 0.155 | 7.11×10−11 | G6PC2, ABCB11 (intergenic) | |
| GENIE | 1.036 | 0.209 | 0.347 | 7.34×10−7 | ||||
| META | 1.017 | 0.124 | 2.90×10−16 | |||||
| rs895636 | 2; 45188353 | C/T | KoGES | 0.574 | 0.151 | 1.43×10−4 | SIX3, SIX2 (intergenic) | |
| GENIE | 0.831 | 0.198 | 0.375 | 2.75×10−5 | ||||
| META | 0.668 | 0.120 | 2.00×10−8 | |||||
| rs2971670 | 7; 44226101 | C/T | KoGES | 1.346 | 0.187 | 6.17×10−13 | GCK (intronic) | |
| GENIE | 1.400 | 0.250 | 0.185 | 2.18×10−8 | ||||
| META | 1.365 | 0.149 | 8.34×10−20 | |||||
| rs12222793 | 11; 92667047 | A/G | KoGES | 0.827 | 0.144 | 1.14×10−8 | FAT3, MTNR1B (intergenic) | |
| GENIE | 0.561 | 0.192 | 0.515 | 3.49×10−3 | ||||
| META | 0.731 | 0.115 | 4.30×10−10 |
| SNP | Chr; position | A | Study |
Effect | SE | wAF | P value | ANNOVAR |
|---|---|---|---|---|---|---|---|---|
| rs10947494 | 6; 34263743 | A/G | KoGES | 0.213 | 0.046 | 4.53×10−6 | NUDT3, RPS10-NUDT3 (intronic) | |
| GENIE | 0.120 | 0.068 | 0.203 | 7.96×10−2 | ||||
| META | 0.183 | 0.038 | 3.64×10−6 | |||||
| rs11187850 | 10; 96068480 | A/G | KoGES | 0.152 | 0.042 | 3.49×10−4 | PLCE1 (intronic) | |
| GENIE | 0.266 | 0.063 | 0.253 | 2.45×10−5 | ||||
| META | 0.187 | 0.034 | 4.85×10−8 | |||||
| rs2414772 | 15; 62654213 | G/A | KoGES | –0.163 | 0.039 | 3.26×10−5 | MIR6085, MGC15885 (intergenic) | |
| GENIE | –0.134 | 0.058 | 0.676 | 2.14×10−2 | ||||
| META | –0.153 | 0.032 | 6.30×10−6 | |||||
| rs16959641 | 16; 58054099 | C/G | KoGES | 0.222 | 0.068 | 1.09×10−3 | USB1 (exonic) | |
| GENIE | 0.366 | 0.107 | 0.077 | 6.00×10−4 | ||||
| META | 0.263 | 0.057 | 2.46×10−6 |
| Trait | SNP | Chr; position | A | Study |
Effect | SE | wAF | P value | ANNOVAR |
|---|---|---|---|---|---|---|---|---|---|
| T2DM | rs2296172 | 1; 39835817 | A/G | KoGES | 0.145 | 0.051 | 5.08×10−3 | MACF1 (exonic) | |
| GENIE | 0.097 | 0.079 | 0.144 | 2.21×10−1 | |||||
| META | 0.130 | 0.042 | 3.42×10−3 | ||||||
| rs243021 | 2; 60584819 | G/A | KoGES | 0.073 | 0.038 | 5.81×10−2 | LOC101927285, MIR4432H (intergenic) | ||
| GENIE | 0.060 | 0.057 | 0.667 | 2.94×10−1 | |||||
| META | 0.069 | 0.031 | 3.37×10−2 | ||||||
| rs864745 | 7; 28180556 | T/C | KoGES | 0.070 | 0.040 | 8.51×10−2 | JAZF1 (intronic) | ||
| GENIE | 0.062 | 0.061 | 0.272 | 3.11×10−1 | |||||
| META | 0.067 | 0.033 | 4.90×10−2 | ||||||
| rs10965250 | 9; 22133284 | G/A | KoGES | –0.094 | 0.036 | 9.85×10−3 | CDKN2B-AS1, DMRTA1 (intergenic) | ||
| GENIE | –0.086 | 0.055 | 0.436 | 1.19×10−1 | |||||
| META | –0.091 | 0.030 | 2.93×10−3 | ||||||
| rs9552911 | 13; 23864657 | G/A | KoGES | –0.084 | 0.044 | 5.66×10−2 | SGCG (intronic) | ||
| GENIE | –0.053 | 0.066 | 0.225 | 4.25×10−1 | |||||
| META | –0.074 | 0.036 | 4.89×10−2 | ||||||
| FPG | rs6943153 | 7; 50791579 | T/C | KoGES | –0.056 | 0.041 | 1.80×10−1 | GRB10 (intronic) | |
| GENIE | –0.105 | 0.062 | 0.737 | 9.07×10−2 | |||||
| META | –0.070 | 0.034 | 3.44×10−2 | ||||||
| rs10811661 | 9; 22134094 | T/C | KoGES | –0.090 | 0.036 | 1.23×10−2 | CDKN2B-AS1, DMRTA1 (intergenic) | ||
| GENIE | –0.076 | 0.055 | 0.438 | 1.67×10−1 | |||||
| META | –0.085 | 0.030 | 5.10×10−3 | ||||||
| rs2293941 | 13; 28491198 | G/A | KoGES | 0.084 | 0.037 | 2.41×10−2 | PDX1-AS1 (ncRNA_intronic) | ||
| GENIE | 0.039 | 0.055 | 0.466 | 4.73×10−1 | |||||
| META | 0.069 | 0.030 | 2.90×10−2 |
BMI, body mass index; F/U, follow-up; SNP, single nucleotide polymorphism; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype. Number of genotyped SNPs after quality control (QC): missingness per SNP <95%, minor allele frequency (MAF) <0.05, Hardy-Weinberg equilibrium (HWE) <1.00×10−6, and sex inconsistency, Number of imputed SNPs after QC: MAF <0.05, HWE <1.00×10−6, imputation quality scores <0.4.
SNP, single nucleotide polymorphism; Chr, chromosome; A, reference/alternative allele; SE, standard error; wAF, weighted alternative allele frequency; ANNOVAR, ANNOtate VARiation; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype; META, meta-analysis. Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.
SNP, single nucleotide polymorphism; Chr, chromosome; A, reference/alternative allele; SE, standard error; wAF, weighted alternative allele frequency; ANNOVAR, ANNOtate VARiation; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype; META, meta-analysis. Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.
FPG, fasting plasma glucose; T2DM, type 2 diabetes mellitus; SNP, single nucleotide polymorphism; Chr, chromosome; A, reference/alternative allele; SE, standard error; wAF, weighted alternative allele frequency; ANNOVAR, ANNOtate VARiation; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype; META, meta-analysis. Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.
