Table 4.
GWAS Findings for Seven Traits (BMI, WHR, Glucose, Insulin, HOMA-B, HOMA-IR, HbA1c) for 109 MT-nDNA Candidate Genes
| No | SNV | Chrom | Position | Role | Gene | Full Gene Name (Cytogenetic Position) | BMI p | OBESITY p | WHR p | GLUC p | INS p | HOMA-B p | HOMAIR p | HbA1c p |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | rs622798 | 1 | 45549599 | upstream-2 kb | AKR1A1 | Aldo-Keto Reductase Family 1 Member A1 (1p34.1) | 8.56E−07 | – | – | – | – | – | – | – |
| 2 | rs1280316 | 1 | 66843725 | Intron | WDR78 | WD repeat domain 78 (1p31.3) | 6.81E−07 | – | – | – | – | – | – | – |
| 3 | rs1093013 | 1 | 75634658 | Intron | SLC44A5 | Solute carrier family 44 member 5 (1p31.1) | – | – | 4.86E−17 | – | – | – | – | – |
| 4 | rs6428792 | 1 | 119114244 | Intron | WARS2 | Tryptophanyl TRNA Synthetase 2, Mitochondrial (1p12) | – | – | 7.95E−18 | – | – | – | – | – |
| 5 | rs2301453 | 1 | 172389027 | Intron | DNM3 | Dynamin 3 (1q24.3) | – | – | 4.38E−17 | – | – | – | – | – |
| 6 | rs4844390 | 1 | 207761504 | Intron | CD46 | CD46 Molecule, Complement Regulatory Protein (1q32.2) | – | – | – | – | – | – | – | 6.90E−07 |
| 7 | rs11118296 | 1 | 219408638 | Intron | LYPLAL1 | Lysophospholipase Like 1 (1q41) | – | – | 3.00E−07 | – | – | – | – | – |
| 8 | rs6713865 | 2 | 23676937 | Intron | KLHL29 | Kelch like family member 29 (2p24.1) | – | – | – | – | – | – | – | 4.39E−13 |
| 9 | rs934778 | 2 | 25166355 | Intron | POMC | Proopiomelanocortin (2p23.3) | 7.15E−07 | – | – | – | – | – | – | |
| 10 | rs1107238 | 2 | 26235376 | Intron | HADHA | Hydroxyacyl-CoA Dehydrogenase/3-Ketoacyl-CoA Thiolase/Enoyl-CoA Hydratase (Trifunctional Protein), Alpha Subunit (2p23.3) | 8.86E−07 | – | – | – | – | – | – | |
| 11 | rs13404446 | 2 | 27296386 | intron | TRIM54 | Tripartite Motif Containing 54 (2p23.3) | – | – | – | 3.09E−09 | – | – | – | – |
| 12 | rs4665965 | 2 | 27313513 | intron | MPV17 | MPV17, Mitochondrial Inner Membrane Protein (2p23.3) | – | – | – | 1.83E−09 | – | – | – | – |
| 13 | rs3736594 | 2 | 27772914 | intron | MRPL33 | Mitochondrial Ribosomal Protein L33 (2p23.2) | – | – | – | 3.02E−13 | 4.67E−07 | – | – | – |
| 14 | rs4346434 | 2 | 43992607 | intron | LRPPRC | Leucine Rich Pentatricopeptide Repeat Containing (2p21) | – | – | 8.52E−08 | – | – | – | – | – |
| 15 | rs16843390 | 2 | 209655109 | intron | MAP2 | Microtubule Associated Protein 2 (2q34) | – | – | – | 3.32E−08 | – | – | – | – |
| 16 | rs715 | 2 | 210678331 | utr-3-prime | CPS1 | Carbamoyl-Phosphate Synthase 1 (2q34) | 5.81E−07 | – | – | – | – | – | – | – |
| 17 | rs933994 | 2 | 218785893 | intron | CYP27A1 | Cytochrome P450 Family 27 Subfamily A Member 1 (2q35) | 8.65E−07 | – | – | – | – | – | – | – |
| 18 | rs17036328 | 3 | 12348985 | intron | PPARG | Peroxisome Proliferator Activated Receptor Gamma (3p25.2) | 4.27E−07 | – | – | – | 3.59E−12 | – | – | – |
| 19 | rs3729931 | 3 | 12585017 | intron | RAF1 | Raf-1 Proto-Oncogene, Serine/Threonine Kinase (3p25.2) | – | – | 3.60E−10 | – | – | – | – | – |
| 20 | rs11715915 | 3 | 49417897 | nc-transcript | AMT | Aminomethyltransferase (3p21.31) | – | – | – | 4.90E−08 | – | – | – | – |
| 21 | rs12489828 | 3 | 52532998 | intron | NT5DC2 | 5′-Nucleotidase Domain Containing 2 (3p21.1) | – | – | 2.60E−10 | – | – | – | – | – |
| 22 | rs2365389 | 3 | 61250788 | intron | FHIT | Fragile Histidine Triad (3p14.2) | 3.75E−15 | – | – | – | – | – | – | – |
| 23 | rs332375 | 3 | 66377079 | intron | SLC25A26 | Solute Carrier Family 25 Member 26 (3p14.1) | – | – | 7.33E−07 | – | – | – | – | – |
| 24 | rs1735536 | 3 | 128377770 | intron | EEFSEC | Eukaryotic Elongation Factor, Selenocysteine-TRNA Specific (3q21.3) | 2.95E−10 | – | – | – | – | – | – | – |
| 25 | rs9844666 | 3 | 136255374 | intron | PCCB | Propionyl-CoA Carboxylase Beta Subunit (3q22.3) | 7.22E−07 | – | – | – | – | – | – | – |
| 26 | rs11924648 | 3 | 171000207 | intron | SLC2A2 | Solute Carrier Family 2 Member 2 (3q26.2) | – | – | – | 1.02E−17 | – | – | – | 4.05E−09 |
| 27 | rs10012946 | 4 | 6291623 | intron | WFS1 | Wolframin ER Transmembrane Glycoprotein (4p16.1) | – | – | – | 4.17E−07 | – | – | – | – |
| 28 | rs10518406 | 4 | 122841742 | intron | FGF2 | Fibroblast Growth Factor 2 (4q28.1) | 6.50E−07 | – | – | – | – | – | – | – |
| 29 | rs1458758 | 4 | 122914724 | intron | NUDT6 | Nudix Hydrolase 6 (4q28.1) | – | – | 6.22E−08 | – | – | – | – | – |
| 30 | rs303084 | 4 | 123145793 | intron | SPATA5 | Spermatogenesis associated 5 (4q28.1) | – | – | 3.40E−07 | – | – | – | – | – |
| 31 | rs12654264 | 5 | 75352778 | intron | HMGCR | 3-Hydroxy-3-Methylglutaryl-CoA Reductase (5q13.3) | 1.81E−08 | – | – | – | – | – | – | – |
| 32 | rs10478424 | 5 | 119453325 | intron | HSD17B4 | Hydroxysteroid 17-Beta Dehydrogenase 4 (5q23.1) | – | – | 1.40E−07 | – | – | – | – | – |
| 33 | rs2881156 | 5 | 135812973 | intron | SLC25A48 | Solute carrier family 25 member 48 (5q31.1) | – | 8.10E−07 | – | – | – | – | – | – |
| 34 | rs3828870 | 6 | 16743066 | intron | ATXN1 | Ataxin 1 (6p22.3) | – | – | – | – | – | – | – | 5.52E−07 |
| 35 | rs1800562 | 6 | 26092913 | intron | HFE | Hemochromatosis (6p22.2) | – | – | – | – | – | – | – | 4.67E−28 |
| 36 | rs1800629 | 6 | 31575254 | upstream-2KB | TNF | Tumor necrosis factor (6p21.33) | – | – | 7.30E−07 | – | – | – | – | – |
| 37 | rs6457796 | 6 | 34860776 | intron | UHRF1BP1 | UHRF1 binding protein 1 (6p21.31) | 1.15E−09 | – | – | – | – | – | – | – |
| 38 | rs10434 | 6 | 43785475 | utr-3-prime | VEGFA | Vascular endothelial growth factor A (6p21.1) | – | – | 8.80E−07 | – | – | – | – | – |
| 39 | rs1049354 | 6 | 88143732 | utr-3-prime | CNR1 | Cannabinoid receptor 1 (6q15) | 9.57E−07 | – | – | – | – | – | – | – |
| 40 | rs9400239 | 6 | 108656460 | intron | FOXO3 | Forkhead box O3 (6q21) | 1.61E−08 | – | – | – | – | – | – | – |
| 41 | rs1273733 | 6 | 121131419 | downstream-500B | TBC1D32 | TBC1 domain family member 32 (6q22.31) | 3.96E−12 | – | – | – | – | – | – | – |
| 42 | rs1049349 | 6 | 121449496 | utr-3-prime | GJA1 | Gap junction protein alpha 1; synonymous: CX43 (6q22.31) | 4.18E−15 | – | – | – | – | – | – | – |
| 43 | rs1293954 | 6 | 151669826 | intron | ESR1 | Estrogen receptor 1 (6q25.1-q25.2) | 4.41E−09 | – | – | – | – | – | – | – |
| 44 | rs1203576 | 7 | 40808233 | intron | SUGCT | C7orf10 (Succinyl-CoA:Glutarate-CoA Transferase, 7p14.1) | 1.48E−10 | – | – | – | – | – | – | – |
| 45 | rs2908289 | 7 | 44184343 | intron | GCK | Glucokinase (7p13) | – | – | – | 3.32E−88 | – | 6.00E−09 | – | 2.24E−19 |
| 46 | rs1088867 | 7 | 44705214 | intron | OGDH | Oxoglutarate dehydrogenase (7p13) | 7.90E−08 | – | – | – | – | – | – | – |
| 47 | rs16892421 | 8 | 106499705 | intron | OXR1 | Oxidation resistance 1 (8q23.1) | – | – | 6.94E−07 | – | – | – | – | – |
| 48 | rs7835803 | 8 | 120030213 | intron | DEPTOR | DEP domain containing MTOR interacting protein (8q24.12) | – | – | – | 4.97E−07 | – | – | – | – |
| 49 | rs2777795 | 9 | 104910084 | intron | ABCA1 | ATP binding cassette subfamily A member 1 (9q31.1) | – | – | 3.13E−08 | – | – | – | – | – |
| 50 | rs7023913 | 9 | 128255683 | downstream-500B | DNM1 | Dynamin 1 (9q34.11) | – | 7.30E−07 | – | – | – | – | – | – |
| 51 | rs3829109 | 9 | 136362314 | intron | DNLZ | DNL-Type Zinc Finger (9q34.3) | – | – | – | 1.13E−10 | – | – | – | – |
| 52 | rs1244497 | 10 | 7838019 | intron | TAF3 | TATA-box binding protein associated factor 3 (10p14) | 1.84E−11 | – | – | – | – | – | – | – |
| 53 | rs5030913 | 10 | 69246375 | intron | HKDC1 | Hexokinase domain containing 1 (10q22.1) | – | – | – | – | – | – | – | 3.56E−13 |
| 54 | rs4745982 | 10 | 69330087 | intron | HK1 | Hexokinase 1 (10q22.1) | – | – | – | – | – | – | – | 2.87E−65 |
| 55 | rs7899106 | 10 | 85651147 | intron | GRID1 | Glutamate Ionotropic Receptor Delta Type Subunit 1 (10q23.2) | 2.96E−08 | – | – | – | – | – | – | – |
| 56 | rs7917772 | 10 | 102727686 | intron | SFXN2 | Sideroflexin 2 (10q24.32) | – | – | 1.45E−09 | – | – | – | – | – |
| 57 | rs1004467 | 10 | 102834750 | intron | CYP17A1 | Cytochrome P450 Family 17 Subfamily A Member 1 (10q24.32) | 1.18E−07 | – | – | – | – | – | – | – |
| 58 | rs3740390 | 10 | 102878723 | intron | AS3MT | Arsenite Methyltransferase (10q24.32) | 4.82E−08 | – | – | – | – | – | – | – |
| 59 | rs4758633 | 11 | 219538 | intron | SIRT3 | Sirtuin 3 (11p15.5) | – | – | – | – | – | – | – | 3.44E−10 |
| 60 | rs757110 | 11 | 17396930 | missense | ABCC8 | ATP Binding Cassette Subfamily C Member 8 (11p15.1) | 4.23E−07 | – | – | – | – | – | – | – |
| 61 | rs10767664 | 11 | 27704439 | intron | BDNF | Brain Derived Neurotrophic Factor (11p14.1) | 5.53E−13 | – | – | – | – | – | – | – |
| 62 | rs11038913 | 11 | 46538180 | intron | AMBRA1 | Autophagy and beclin 1 regulator 1 (11p11.2) | – | – | – | 4.29E−08 | 4.91E−18 | – | – | – |
| 63 | rs11039149 | 11 | 47255124 | intron | NR1H3 | Nuclear Receptor Subfamily 1 Group H Member 3 (11p11.2) | – | – | – | 1.26E−12 | 4.13E−45 | – | – | – |
| 64 | rs7118178 | 11 | 47637583 | intron | MTCH2 | Mitochondrial carrier 2 (11p11.2) | 5.12E−08 | – | – | 3.84E−14 | 2.16E−29 | – | – | – |
| 65 | rs4246215 | 11 | 61796827 | utr-3-prime | FEN1 | Flap Structure-Specific Endonuclease 1 (11p12.2) | – | – | – | 4.46E−11 | – | – | – | – |
| 66 | rs174556 | 11 | 61813163 | intron | FADS1 | Fatty acid desaturase 1 (11q12.2) | – | – | – | 7.82E−18 | – | – | – | – |
| 67 | rs7943191 | 11 | 62561079 | intron | EEF1G | Eukaryotic translation elongation factor 1 gamma (11q12.3) | – | – | 4.36E−08 | – | – | – | – | – |
| 68 | rs11231150 | 11 | 62584330 | intron | TUT1 | Terminal uridylyl transferase 1, U6 snRNA-specific (11q12.3) | – | – | 5.20E−08 | – | – | – | – | – |
| 69 | rs1017639 | 11 | 68831066 | intron | CPT1A | Carnitine Palmitoyltransferase 1A (11q13.3) | 4.96E−10 | – | – | – | – | – | – | – |
| 70 | rs1296252 | 11 | 83273268 | intron | CCDC90B | Coiled-Coil Domain Containing 90B (11q13.3) | 7.60E−08 | – | – | – | – | – | – | – |
| 71 | rs2110073 | 12 | 6966719 | intron | PHB2 | Prohibitin 2 (12p13.31) | – | – | – | – | – | – | – | 4.44E−08 |
| 72 | rs7311050 | 12 | 7013532 | intron | LPCAT3 | Lysophosphatidylcholine Acyltransferase 3 (12p13.31) | – | – | – | – | – | – | – | 8.60E−08 |
| 73 | rs1049380 | 12 | 26336611 | downstream-500B | ITPR2 | Inositol 1,4,5-Trisphosphate Receptor Type 2 (12p11.23) | – | – | 1.42E−13 | – | – | – | – | – |
| 74 | rs2408955 | 12 | 48105348 | upstream-2KB | PFKM | Phosphofructokinase, muscle (12q13.11) | – | – | – | – | – | – | – | 1.42E−15 |
| 75 | rs35767 | 12 | 102481791 | missense | IGF1 | Insulin Like Growth Factor 1 (12q23.2) | – | – | – | – | 7.27E−08 | – | 7.57E−08 | – |
| 76 | rs4766578 | 12 | 111466567 | intron | ATXN2 | Ataxin 2 (12q24.12) | 2.85E−07 | – | – | – | – | – | – | 1.84E−07 |
| 77 | rs9581856 | 13 | 27451478 | upstream-2KB | MTIF3 | Mitochondrial Translational Initiation Factor 3 (13q12.2) | 1.03E−08 | – | – | – | – | – | – | – |
| 78 | rs1124607 | 13 | 27921083 | intron | PDX1 | Pancreatic And Duodenal Homeobox 1 (13q12.2) | – | – | – | 4.49E−07 | – | – | – | – |
| 79 | rs1325363 | 13 | 33192439 | intron | STARD13 | StAR related lipid transfer domain containing 13 (13q13.1-q13.2) | 7.25E−08 | – | – | – | – | – | – | – |
| 80 | rs1078892 | 13 | 40563883 | intron | FOXO1 | Forkhead Box O1 (13q14.11) | 5.11E−08 | – | – | – | – | – | – | – |
| 81 | rs7143963 | 14 | 102838088 | intron | TRAF3 | TNF Receptor Associated Factor 3 | 2.82E−07 | – | – | – | – | – | – | – |
| 82 | rs12908437 | 15 | 98744146 | intron | IGF1R | Insulin Like Growth Factor 1 Receptor | – | – | – | 6.32E−07 | – | – | – | – |
| 83 | rs740862 | 16 | 3639677 | intron | DNASE1 | Deoxyribonuclease 1 | 3.21E−07 | – | – | – | – | – | – | – |
| 84 | rs151181 | 16 | 28479196 | intron | CLN3 | CLN3, Battenin | 2.10E−07 | – | – | – | – | – | – | – |
| 85 | rs8055138 | 16 | 28880144 | intron | ATP2A1 | ATPase Sarcoplasmic/Endoplasmic Reticulum Ca2+ Transporting 1 | 8.17E−17 | – | – | – | – | – | – | – |
| 86 | rs749767 | 16 | 31113086 | downstream-500B | BCKDK | Branched Chain Ketoacid Dehydrogenase Kinase | 1.21E−09 | – | – | – | – | – | – | – |
| 87 | rs7186084 | 16 | 68782357 | intron | CDH1 | Cadherin 1 | – | – | – | – | – | – | – | 1.09E−07 |
| 88 | rs1847591 | 16 | 78908913 | intron | WWOX | WW domain containing oxidoreductase | – | – | 9.99E−07 | – | – | – | – | – |
| 89 | rs9904685 | 17 | 1352101 | intron | YWHAE | Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon | 6.27E−07 | – | – | – | – | – | – | – |
| 90 | rs4646404 | 17 | 17516885 | intron | PEMT | Phosphatidylethanolamine N-Methyltransferase | – | – | 5.30E−11 | – | – | – | – | – |
| 91 | rs9914988 | 17 | 28856086 | intron | ERAL1 | Era like 12S mitochondrial rRNA chaperone 1 | – | – | – | – | – | – | – | 2.77E−11 |
| 92 | rs242559 | 17 | 45948522 | intron | MAPT | Microtubule Associated Protein Tau | – | – | – | 8.29E−07 | – | – | – | – |
| 93 | rs1319247 | 17 | 63106279 | intron | TANC2 | Etratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 | – | – | 6.02E−08 | – | – | – | – | – |
| 94 | rs12940622 | 17 | 80641771 | intron | RPTOR | Regulatory Associated Protein Of MTOR Complex 1 | 2.49E−09 | – | – | – | – | – | – | – |
| 95 | rs1044661 | 17 | 82943144 | intron | B3GNTL1/TBCD | UDP-GlcNAc:BetaGal Beta-1,3-N-Acetylglucosaminyltransferase Like 1/Tubulin Folding CofactorD | – | – | – | – | – | 1.74E−46 | ||
| 96 | rs1788785 | 18 | 23562376 | intron | NPC1 | NPC Intracellular Cholesterol Transporter 1 | 1.98E−08 | – | – | – | – | – | – | – |
| 97 | rs17066842 | 18 | 60373391 | upstream-2KB | MC4R | Melanocortin 4 Receptor | 6.40E−14 | – | – | – | – | – | – | – |
| 98 | rs12454712 | 18 | 63178651 | intron | BCL2 | BCL2, Apoptosis Regulator | – | – | 1.10E−09 | – | 1.39E−07 | – | – | – |
| 99 | rs757318 | 19 | 18709498 | intron | CRTC1 | CREB Regulated Transcription Coactivator 1 | 8.76E−09 | – | – | – | – | – | – | – |
| 100 | rs2075650 | 19 | 44892362 | intron | TOMM40 | Translocase Of Outer Mitochondrial Membrane 40 | 1.25E−08 | – | – | – | – | – | – | – |
| 101 | rs405509 | 19 | 44905579 | upstream-2 kb | APOE | Apolipoprotein E | 2.65E−07 | – | – | – | – | – | – | – |
| 102 | rs2281361 | 20 | 32140338 | intron | TM9SF4 | ransmembrane 9 superfamily member 4 | 9.78E−07 | – | – | – | – | – | – | – |
| 103 | rs878639 | 20 | 35306660 | intron | UQCC1 | Ubiquinol-Cytochrome C Reductase Complex Assembly Factor 1 | – | – | 1.50E−11 | – | – | – | – | – |
| 104 | rs2076574 | 20 | 41092733 | intron | TOP1 | DNA topoisomerase I | – | – | 4.11E−07 | – | – | – | – | – |
| 105 | rs5750373 | 22 | 37028990 | intron | MPST | Mercaptopyruvate Sulfurtransferase | – | – | – | – | – | – | – | 2.17E−07 |
| 106 | rs2284099 | 22 | 43155830 | intron | TSPO | Translocator Protein | – | – | 6.65E−07 | – | – | – | – | – |
| 107 | rs1050828 | 23 | 154536002 | missense | G6PD | Glucose-6-phosphate dehydrogenase | – | – | – | – | – | – | – | 8.23E−135 |
| 108 | rs1448032 | 23 | 155052530 | intron | FUNDC2 | FUN14 domain containing 2 | – | – | – | – | – | – | – | 5.92E−17 |
| 109 | rs5940514 | 23 | 155559972 | intron | TMLHE | Trimethyllysine hydroxylase, epsilon | – | – | – | – | – | – | – | 2.22E−19 |
p values in italics annotate SNVs that associate as significant with more than one trait.