1

Identificationoftype2diabeteslociin433,540EastAsianindividuals12CassandraNSpracklen1,83,MomokoHorikoshi2,83,YoungJinKim3,83,KuangLin4,83,FionaBragg4,Sanghoon3Moon3,KenSuzuki2,5,6,7,ClaudiaHTTam8,9,YasuharuTabara10,Soo-HeonKwak11,FumihikoTakeuchi12,4JirongLong13,VictorJYLim14,Jin-FangChai14,Chien-HsiunChen15,MasahiroNakatochi16,JieYao17,Hyeok5SunChoi18,ApoorvaKIyengar1,HannahJPerrin1,SarahMBrotman1,MartijnvandeBunt19,20,AnnaL6Gloyn19,20,21,JenniferEBelow22,23,MichaelBoehnke24,DonaldWBowden25,26,JohnCChambers27,28,29,30,31,7AnubhaMahajan19,20,MarkIMcCarthy19,20,21,#,MaggieCYNg22,25,LaurenEPetty22,23,WeihuaZhang28,29,8AndrewPMorris20,32,33,LindaSAdair34,ZhengBian35,JulianaCNChan8,9,36,37,Li-ChingChang15,Miao-Li9Chee38,Yii-DerIdaChen17,Yuan-TsongChen15,ZhengmingChen4,Lee-MingChuang39,40,ShufaDu34,10PennyGordon-Larsen34,MyronGross41,XiuqingGuo17,YuGuo35,SoheeHan3,Annie-GreenHoward42,11WeiHuang43,Yi-JenHung44,45,MiYeongHwang3,Chii-MinHwu46,47,SahokoIchihara48,MasatoIsono12,12Hye-MiJang3,GuozhiJiang8,9,JostBJonas49,YoichiroKamatani5,50,TomohiroKatsuya51,52,Takahisa13Kawaguchi10,Chiea-ChuenKhor53,54,KatsuhikoKohara55,Myung-ShikLee56,NannetteRLee57,LimingLi58,14JianjunLiu53,59,AndreaOLuk8,9,JunLv58,YukinoriOkada7,60,MarkAPereira61,Charumathi15Sabanayagam38,62,63,JinxiuShi43,DongMunShin3,WingYeeSo8,36,AtsushiTakahashi5,64,Brian16Tomlinson8,Fuu-JenTsai65,RobMvanDam14,59,66,Yong-BingXiang67,KenYamamoto68,Toshimasa17Yamauchi6,KyungheonYoon3,CanqingYu58,Jian-MinYuan69,70,LiangZhang38,WeiZheng13,Michiya18Igase71,YoonShinCho18,JeromeIRotter72,Ya-XingWang73,WayneHHSheu45,47,74,MitsuhiroYokota75,19Jer-YuarnWu15,Ching-YuCheng38,62,63,Tien-YinWong38,62,63,Xiao-OuShu13,NorihiroKato12,Kyong-Soo20Park11,76,77,E-ShyongTai14,59,78,FumihikoMatsuda10,Woon-PuayKoh14,79,RonaldCWMa8,9,36,37,Shiro21Maeda2,80,81,IonaYMillwood4,82,JuyoungLee3,TakashiKadowaki6,84*,RobinGWalters4,82,84*,Bong-Jo22Kim3,84*,KarenLMohlke1,84*,XuelingSim14,84*23241 DepartmentofGenetics,UniversityofNorthCarolinaatChapelHill,ChapelHill,NC,USA252 LaboratoryforEndocrinology,MetabolismandKidneyDiseases,RIKENCentreforIntegrative26

MedicalSciences,Yokohama,Japan273 DivisionofGenomeResearch,CenterforGenomeScience,NationalInstituteofHealth,Cheongju-28

si,Korea294 NuffieldDepartmentofPopulationHealth,UniversityofOxford,Oxford,UK305 LaboratoryforStatisticalandTranslationalGenetics,RIKENCentreforIntegrativeMedical31

Sciences,Yokohama,Japan326 DepartmentofDiabetesandMetabolicDiseases,GraduateSchoolofMedicine,TheUniversityof33

Tokyo,Tokyo,Japan347 DepartmentofStatisticalGenetics,OsakaUniversityGraduateSchoolofMedicine,Osaka,Japan358 DepartmentofMedicineandTherapeutics,TheChineseUniversityofHongKong,HongKong,36

China379 ChineseUniversityofHongKong-ShanghaiJiaoTongUniversityJointResearchCentreinDiabetes38

GenomicsandPrecisionMedicine,TheChineseUniversityofHongKong,HongKong,China3910 CenterforGenomicMedicine,KyotoUniversityGraduateSchoolofMedicine,Kyoto,Japan4011 DepartmentofInternalMedicine,SeoulNationalUniversityHospital,Seoul,SouthKorea4112 DepartmentofGeneDiagnosticsandTherapeutics,ResearchInstitute,NationalCenterforGlobal42

HealthandMedicine,Tokyo,Japan4313 DivisionofEpidemiology,DepartmentofMedicine,VanderbiltUniversityMedicalCenter,44

Nashville,TN,USA4514 SawSweeHockSchoolofPublicHealth,NationalUniversityofSingaporeandNationalUniversity46

HealthSystem,Singapore,Singapore4715 InstituteofBiomedicalSciences,AcademiaSinica,Taipei,Taiwan48

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16 DepartmentofNursing,NagoyaUniversityGraduateSchoolofMedicine,NagoyaUniversity49Hospital,Nagoya,Japan50

17 DepartmentofPediatrics,TheInstituteforTranslationalGenomicsandPopulationSciences,51LABioMedatHarbor-UCLAMedicalCenter,Torrance,CA,USA52

18 BiomedicalScience,HallymUniversity,Chuncheon,SouthKorea5319 OxfordCentreforDiabetes,EndocrinologyandMetabolism,UniversityofOxford,Oxford,UK5420 WellcomeCentreforHumanGenetics,UniversityofOxford,Oxford,UK5521 OxfordNIHRBiomedicalResearchCentre,OxfordUniversityHospitalsNHSFoundationTrust,56

ChurchillHospital,Oxford,UK5722 VanderbiltGeneticsInstitute,DivisionofGeneticMedicine,VanderbiltUniversityMedicalCenter,58

Nashville,TN,USA5923 HumanGeneticsCenter,SchoolofPublicHealth,TheUniversityofTexasHealthScienceCenterat60

Houston,Houston,TX,USA6124 DepartmentofBiostatisticsandCenterforStatisticalGenetics,UniversityofMichigan,AnnArbor,62

MI,USA6325 CenterforGenomicsandPersonalizedMedicineResearch,CenterforDiabetesResearch,Wake64

ForestSchoolofMedicine,Winston-Salem,NC,USA6526 DepartmentofBiochemistry,WakeForestSchoolofMedicine,Winston-Salem,NC,USA6627 LeeKongChianSchoolofMedicine,NanyangTechnologicalUniversity,Singapore,Singapore6728 DepartmentofEpidemiologyandBiostatistics,ImperialCollegeLondon,London,UK6829 DepartmentofCardiology,EalingHospital,LondonNorthWestHealthcareNHSTrust,Middlesex,69

UK7030 ImperialCollegeHealthcareNHSTrust,ImperialCollegeLondon,London,UK7131 MRC-PHECentreforEnvironmentandHealth,ImperialCollegeLondon,London,UK7232 DepartmentofBiostatistics,UniversityofLiverpool,Liverpool,UK7333 SchoolofBiologicalSciences,UniversityofManchester,Manchester,UK7434 DepartmentofNutrition,GillingsSchoolofGlobalPublicHealth,UniversityofNorthCarolinaat75

ChapelHill,ChapelHill,NC,USA7635 ChineseAcademyofMedicalSciences,Beijing,China7736 HongKongInstituteofDiabetesandObesity,TheChineseUniversityofHongKong,HongKong,78

China7937 LiKaShingInstituteofHealthSciences,TheChineseUniversityofHongKong,HongKong,China8038 SingaporeEyeResearchInstitute,SingaporeNationalEyeCentre,Singapore,Singapore8139 DivisionofEndocrinology&Metabolism,DepartmentofInternalMedicine,NationalTaiwan82

UniversityHospital,Taipei,Taiwan8340 InstituteofPreventiveMedicine,SchoolofPublicHealth,NationalTaiwanUniversity,Taipei,84

Taiwan8541 DepartmentofLaboratoryMedicineandPathology,UniversityofMinnesota,Minneapolis,MN,86

USA8742 DepartmentofBiostatistics,CarolinaPopulationCenter,GillingsSchoolofGlobalPublicHealth,88

UniversityofNorthCarolinaatChapelHill,ChapelHill,NC,USA8943 DepartmentofGenetics,Shanghai-MOSTKeyLaboratoryofHealthandDiseaseGenomics,90

ChineseNationalHumanGenomeCenteratShanghai,Shanghai,China9144 DivisionofEndocrineandMetabolism,Tri-ServiceGeneralHospitalSongshanBranch,Taipei,92

Taiwan9345 SchoolofMedicine,NationalDefenseMedicalCenter,Taipei,Taiwan9446 SectionofEndocrinologyandMetabolism,DepartmentofMedicine,TaipeiVeteransGeneral95

Hospital,Taipei,Taiwan96

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47 SchoolofMedicine,NationalYang-MingUniversity,Taipei,Taiwan9748 DepartmentofEnvironmentalandPreventiveMedicine,JichiMedicalUniversitySchoolof98

Medicine,Shimotsuke,Japan9949 DepartmentofOphthalmology,MedicalFacultyMannheimoftheUniversityofHeidelberg,100

Mannheim,Germany10150 LaboratoryofComplexTraitGenomics,DepartmentofComputationalBiologyandMedical102

Sciences,GraduateSchoolofFrontierSciences,TheUniversityofTokyo,Tokyo,Japan10351 DepartmentofClinicalGeneTherapy,OsakaUniversityGraduateSchoolofMedicine,Osaka,104

Japan10552 DepartmentofGeriatricandGeneralMedicine,GraduateSchoolofMedicine,OsakaUniversity,106

Osaka,Japan10753 GenomeInstituteofSingapore,AgencyforScience,TechnologyandResearch,Singapore,108

Singapore10954 DepartmentofBiochemistry,NationalUniversityofSingapore,Singapore,Singapore11055 DepartmentofRegionalResourceManagement,EhimeUniversityFacultyofCollaborative111

RegionalInnovation,Ehime,Japan11256 SeveranceBiomedicalScienceInstituteandDepartmentofInternalMedicine,YonseiUniversity113

CollegeofMedicine,Seoul,SouthKorea11457 DepartmentofAnthropology,SociologyandHistory,UniversityofSanCarlos,CebuCity,115

Philippines11658 DepartmentsofEpidemiology&Biostatistics,PekingUniversityHealthScienceCentre,Peking117

University,Beijing,China11859 DepartmentofMedicine,YongLooLinSchoolofMedicine,NationalUniversityofSingaporeand119

NationalUniversityHealthSystem,Singapore,Singapore12060 LaboratoryofStatisticalImmunology,ImmunologyFrontierResearchCenter(WPI-IFReC),Osaka121

University,Osaka,Japan12261 DivisionofEpidemiologyandCommunityHealth,SchoolofPublicHealth,UniversityofMinnesota,123

Minneapolis,MN,USA12462 Ophthalmology&VisualSciencesAcademicClinicalProgram(EyeACP),Duke-NUSMedicalSchool,125

Singapore,Singapore12663 DepartmentofOphthalmology,YongLooLinSchoolofMedicine,NationalUniversityofSingapore127

andNationalUniversityHealthSystem,Singapore,Singapore12864 DepartmentofGenomicMedicine,NationalCerebralandCardiovascularCenter,Osaka,Japan12965 DepartmentofMedicalGeneticsandMedicalResearch,ChinaMedicalUniversityHospital,130

Taichung,Taiwan13166 DepartmentofNutrition,HarvardT.HChanSchoolofPublicHealth,Boston,MA,USA13267 StateKeyLaboratoryofOncogeneandRelatedGenes&DepartmentofEpidemiology,Shanghai133

CancerInstitute,RenjiHospital,ShanghaiJiaotongUniversitySchoolofMedicine,Shanghai,China13468 DepartmentofMedicalBiochemistry,KurumeUniversitySchoolofMedicine,Kurume,Japan13569 DivisionofCancerControlandPopulationSciences,UPMCHillmanCancerCenter,Universityof136

Pittsburgh,Pittsburgh,PA,USA13770 DepartmentofEpidemiology,GraduateSchoolofPublicHealth,UniversityofPittsburgh,138

Pittsburgh,PA,USA13971 DepartmentofAnti-agingMedicine,EhimeUniversityGraduateSchoolofMedicine,Ehime,Japan14072 DepartmentsofPediatricsandMedicine,TheInstituteforTranslationalGenomicsandPopulation141

Sciences,LABioMedatHarbor-UCLAMedicalCenter,Torrance,CA,USA14273 BeijingInstituteofOphthalmology,OphthalmologyandVisualSciencesKeyLaboratory,Beijing143

TongrenHospital,CapitalMedicalUniversity,Beijing,China144

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74 DivisionofEndocrinologyandMetabolism,DepartmentofMedicine,TaichungVeteransGeneral145Hospital,Taichung,Taiwan146

75 KurumeUniversitySchoolofMedicine,Kurume,Japan14776 DepartmentofInternalMedicine,SeoulNationalUniversityCollegeofMedicine,Seoul,South148

Korea14977 DepartmentofMolecularMedicineandBiopharmaceuticalSciences,GraduateSchoolof150

ConvergenceScienceandTechnology,SeoulNationalUniversity,Seoul,SouthKorea15178 Duke-NUSMedicalSchool,Singapore,Singapore15279 HealthServicesandSystemsResearch,Duke-NUSMedicalSchool,Singapore,Singapore15380 DepartmentofAdvancedGenomicandLaboratoryMedicine,GraduateSchoolofMedicine,154

UniversityoftheRyukyus,Okinawa,Japan15581 DivisionofClinicalLaboratoryandBloodTransfusion,UniversityoftheRyukyusHospital,Okinawa,156

Japan15782 MedicalResearchCouncilPopulationHealthResearchUnit,UniversityofOxford,Oxford,UK158# Currentaddress:Genentech,SanFrancisco,CA,USA15916083 Theseauthorscontributedequallytothiswork.16184 Theseauthorsjointlysupervisedthiswork.162* Correspondingauthor 163

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SUMMARY164Meta-analysesofgenome-wideassociationstudies(GWAS)haveidentified>240lociassociatedwith165type2diabetes(T2D),howevermostlocihavebeenidentifiedinanalysesofEuropean-ancestry166individuals.ToexamineT2DriskinEastAsianindividuals,wemeta-analyzedGWASdatain77,418cases167and356,122controls.Inthemainanalysis,weidentified298distinctassociationsignalsat178loci,and168acrossT2Dassociationmodelswithandwithoutconsiderationofbodymassindexandsex,weidentified16956locinewlyimplicatedinT2Dpredisposition.CommonvariantsassociatedwithT2DinbothEastAsian170andEuropeanpopulationsexhibitedstronglycorrelatedeffectsizes.Newassociationsincludesignals171in/nearGDAP1,PTF1A,SIX3,ALDH2,amicroRNAcluster,andgenesthataffectmuscleandadipose172differentiation.Atanotherlocus,eQTLsattwooverlappingT2Dsignalsactthroughtwogenes,NKX6-3173andANK1,indifferenttissues.Associationstudiesindiversepopulationsidentifyadditionallociand174elucidatediseasegenes,biology,andpathways.175176Type2diabetes(T2D)isacommonmetabolicdiseaseprimarilycausedbyinsufficientinsulinproduction177and/orsecretionbythepancreaticβcellsandinsulinresistanceinperipheraltissues1.Mostgeneticloci178associatedwithT2DhavebeenidentifiedinpopulationsofEuropean(EUR)ancestry,includingarecent179meta-analysisofgenome-wideassociationstudies(GWAS)ofnearly900,000individualsofEuropean180ancestrythatidentified>240lociinfluencingtheriskofT2D2.Differencesinallelefrequencybetween181ancestriesaffectthepowertodetectassociationswithinapopulation,particularlyamongvariantsrare182ormonomorphicinonepopulationbutmorefrequentinanother3,4.Althoughsmallerthanstudiesin183Europeanpopulations,arecentT2Dmeta-analysisinalmost200,000Japaneseindividualsidentified28184additionalloci4.TherelativecontributionsofdifferentpathwaystothepathophysiologyofT2Dmayalso185differbetweenancestrygroups.Forexample,inEastAsian(EAS)populations,T2Dprevalenceisgreater186thaninEuropeanpopulationsamongpeopleofsimilarbodymassindex(BMI)orwaistcircumference5.187Weperformedthelargestmeta-analysisofEastAsianindividualstoidentifynewgeneticassociations188andprovideinsightintoT2Dpathogenesis.189190RESULTS191Weconductedafixed-effectinverse-varianceweightedGWASmeta-analysiscombining23studies192imputedtothe1000GenomesPhase3referencepanelfromtheAsianGeneticEpidemiologyNetwork193(AGEN)consortium(SupplementaryTables1-3).Weperformedsex-combinedT2Dassociationwithout194BMIadjustmentin77,418T2Dcasesand356,122controls(effectivesamplesize,Neff=211,793)andwith195BMIadjustmentin54,481T2Dcasesand224,231controls(Neff=135,780).InthesetofstudieswithBMI-196adjustedanalyses,wealsotestedforT2Dassociationinmodelsstratifiedbysex(SupplementaryFigure1971).Wedefined“lead”variantsasthestrongestT2D-associatedvariantswithP<5x10-8anddefinedthe198region+/-500kbfromtheleadvariantasalocus.Alocuswasconsiderednoveliftheleadvariantwas199locatedatleast500kbawayfrompreviouslyreportedT2D-associatedvariantsinanyancestry.200201Usingsummaryassociationstatisticsfor~11.7millionvariantswithoutadjustmentforBMI202(SupplementaryFigure1;SupplementaryTables1-3),weidentifiedleadvariantsat178locitobe203associatedwithT2D,ofwhich49werenovel(Table1;SupplementaryFigure2;SupplementaryTable4).204Leadvariantsatallnovellociwerecommon(MAF≥5%;SupplementaryFigure3),exceptfortwolow-205frequencyleadvariantsnearGDAP1(MAF=2.4%),whichregulatesmitochondrialproteinsandmetabolic206fluxinskeletalmuscle6,andPTF1A(MAF=4.7%),whichencodesatranscriptionfactorrequiredfor207pancreaticacinarcelldevelopment7.LeadvariantsmetastricterP-valuethresholdforsignificancebased208onBonferronicorrectionfor11.7milliontests(P<4.3x10-9)at147ofthe178loci,including31ofthe49209novelloci.210211

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UsingGCTA8,weidentified298distinctsignalsthatmetalocus-widesignificancethresholdofP<1x10-5212(SupplementaryTable5),204ofwhichweregenome-widesignificant(P<5x10-8).Overall,weobserved2132-4signalsat50lociand≥5signalsat11loci.Amongthe49novelloci,9locihadtwosignalsandthe214locusatWNT7Bhadthreesignals.Amongthetenlociwiththemostsignificantmeta-analysisP-valuesof215association,sevencontained≥5distinctsignals(16signalsatINS/IGF2/KCNQ1;7signalsatCDKN2A/B216andGRM8/PAX4/LEP;5signalsatCDKAL1,HHEX/IDE,CDC123/CAMK1D,andTCF7L2;Supplementary217Figure4;SupplementaryTables5).ThesevendistinctassociationsignalsattheGRM8/PAX4/LEPlocus218span1.4Mb,andnoevidenceofT2Dassociationatthislocushasyetbeenreportedinnon-EastAsian219ancestrygroups2,9(SupplementaryFigure4C).Jointanalysesconfirmedindependentassociations(LD220r2=0.0025)attwopreviouslyreportedPAX4missensevariants10,rs2233580[Arg192His:riskallele221frequency(RAF)=8.6%,OR=1.31,95%CI1.27–1.34,PGCTA=3.0x10

-89]andrs3824004(Arg192Ser:222RAF=3.4%,OR=1.23,95%CI1.19-1.28,PGCTA=4.3x10

-29).Theassociationsignalsatthislocusalsoinclude223variantsnearLEP,whichencodesleptin,ahormonethatregulatesappetite11;increasedleptinlevelsare224associatedwithobesityandT2D,withgreaterincreaseinleptinlevelsperunitofBMIinChinese225individualscomparedtothoseofAfrican-American,European,andHispanicancestries12.226227AtthepreviouslyreportedANK1/NKX6-3locus2,13,14,weobservedthreedistinctT2Dassociationsignals,228twoofwhichoverlapandconsistofvariantsspanningonly~25kb(Figure1).Givenconflicting229interpretationofcandidategenes2,15,16,wecomparedtheT2D-associationsignalsidentifiedinEastAsian230individualstoeQTLsreportedatthislocusinislets2,16-18,subcutaneousadipose19,andskeletalmuscle15.231Atthestrongestsignal,theleadT2D-associatedvariant,rs33981001,isinhighLDwiththeleadcis-eQTL232variantforNKX6-3inpancreaticislets(rs12549902;EASLDr2=0.79,EURr2=0.83)16,andtheT2Drisk233alleleisassociatedwithdecreasedexpressionofNKX6-3(β=-0.36,P=6.1x10-7;Figure1)20.NKX6-3,or234NK6homeobox3,encodesapancreaticislettranscriptionfactorrequiredforthedevelopmentofalpha235andβcellsinthepancreas21andhasbeenshowntoinfluenceinsulinsecretion16.AtthesecondT2D-236associationsignal,rs62508166isinhighLDwiththeleadcis-eQTLvariantforANK1insubcutaneous237adiposetissue19andskeletalmuscle15(rs516946;EASLDr2=0.96,EURr2=0.80),andtheT2Driskalleleis238associatedwithincreasedexpressionofANK1(subcutaneousadipose:β=0.20,P=1.8x10-7;skeletal239muscle:β=1.01,P=2.8x10-22).ANK1belongstotheankyrinfamilyofintegralmembraneproteinsthathas240beenshowntoaffectglucoseuptakeinskeletalmuscle,andchangesinexpressionlevelsmayleadto241insulinresistance22.Together,theseGWASandeQTLsignalssuggestthatvariantswithinthis~25kb242regionacttoincreaseordecreaseexpressionlevelsoftwodifferentgenesindifferenttissuesto243increaseT2Drisk.244245InT2DassociationanalysesadjustedforBMI,weidentifiedanadditionaltenloci,fourofwhichwerenot246reportedpreviouslyforT2D,includinglocinearMYOM3/SRSF10,TSN,GRB10,andNID2(Supplementary247Figure5A;SupplementaryTable4).AttheNID2locus,theT2DriskalleleisassociatedwithlowerBMIin248EastAsianindividuals,consistentwithalipodystrophyphenotype23,24.Amongthecombined188loci249identifiedinmodelswithandwithoutadjustmentforBMI,effectsizeswerehighlycorrelated(Pearson250correlationr=0.99;SupplementaryFigures1and6).Thelocuswiththestrongestheterogeneitybetween251thetwomodelswasFTO(Phet=5.6x10

-3),althougheventhislocusfailedtosurpassaBonferroni-252correctedthresholdforsignificantheterogeneity(Phet<0.05/188=2.7x10

-4).253254Insex-stratifiedanalysesofmales(28,027casesand89,312controls)andfemales(27,370casesand255135,055controls),weidentifiedoneadditionalnovelmale-specificlocusnearIFT81andtwoadditional256novelfemale-specificlocinearCPS1andLMTK2(SupplementaryFigure5Band5C;SupplementaryTable2576).TheleadCPS1variantrs1047891(Thr1412Asn)hasbeenreportedpreviouslytohaveastronger258effectinfemalesthaninmalesforcardiovasculardiseaseandseveralbloodmetabolites25.Taken259

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together,weidentifiedatotalof56novellociacrossBMI-unadjusted,BMI-adjusted,andsex-stratified260models.261262AmongallT2D-associatedloci,aregionspanningalmost2Mbonchromosome12nearALDH2exhibited263thestrongestdifferencesbetweensexes(rs12231737,Phet=2.6x10

-19),withcompellingevidenceof264associationinmales(P=5.5x10-27)andnoevidenceforassociationinfemales(P=0.19)(Supplementary265Figure7;SupplementaryTable6).Further,jointconditionalanalysesrevealedtwoconditionallydistinct266signals(rs12231737,PGCTA=1.7x10

-21;rs557597782,PGCTA=4.7x10-7)inmalesonly.ALDH2encodes267

aldehydedehydrogenase2familymember,akeyenzymeinalcoholmetabolismthatconverts268acetaldehydeintoaceticacid.ThisstretchofT2DassociationsinmalesreflectsalongLDblockthat269aroseduetoarecentselectivesweepinEastAsianindividualsandresultsinflushing,nausea,and270headachefollowingalcoholconsumption26.Themostsignificantlyassociatedmissensevariantin271moderateLDwithrs12231737(r2=0.68)wascommonfunctionalvariantrs671(ALDH2Glu504Lys:272RAF=77.4%,OR=1.16,95%CI1.15–1.18,Pmales=4.2x10

-24),whichleadstoreducedALDH2activityand273reducedalcoholmetabolism,andhavepreviouslybeenreportedtobeassociatedwithcardiometabolic274traitsinEastAsianpopulations;theT2Driskalleleisassociatedwithbettertoleranceforalcoholand275increasedBMI,increasedsystolicanddiastolicbloodpressure,andincreasedtriglycerides,butincreased276high-densitylipoprotein,decreasedlow-densitylipoprotein,anddecreasedcardiovascularrisk27-31.The277strongsexualdimorphismobservedatthislocusmaybeduetodifferencesinalcoholconsumption278patternsbetweenmalesandfemales27,29and/ordifferencesintheeffectofalcoholoninsulin279sensitivity32.280281WithaneffectivesamplesizecomparabletothelargeststudyofT2DinEuropeanindividuals(EastAsian282Neff=211,793;EuropeanNeff=231,436)

2andimputationtoadense1000Genomesreferencepanel,our283resultsprovidethemostcomprehensiveandprecisecatalogueofEastAsianT2Deffectstodatefor284comparisonsacrossancestries(Figure2;SupplementaryTable7).For178EAST2Dlociand231EURT2D285loci(unadjustedforBMI)identifiedinaEuropeanmeta-analysis2,wecomparedtheper-alleleeffect286sizesforthe343variantsavailableinbothdatasets(i.e.polymorphicandpassedqualitycontrol),287includingleadvariantsfrombothancestriesatsharedsignals.Overall,theper-alleleeffectsizes288betweenthetwoancestriesweremoderatelycorrelated(r=0.54;Figure2A).Whenthecomparisonwas289restrictedtothe290variantsthatarecommon(MAF≥5%)inbothancestries,theeffectsizecorrelation290increasedtor=0.71(Figure2B;SupplementaryFigure8).Thiseffectsizecorrelationfurtherincreasedto291r=0.88for116variantssignificantlyassociatedwithT2D(P<5x10-8)inbothancestries.Whiletheoverall292effectsizesforall343variantsappear,onaverage,tobestrongerinEastAsianindividualsthan293European,thistrendisreducedwheneachlocusisrepresentedonlybytheleadvariantfromone294population(SupplementaryFigure9).Specifically,manyvariantsidentifiedwithlargereffectsizesinthe295Europeanmeta-analysisaremissingfromthecomparisonbecausetheywererare/monomorphicor296poorlyimputedintheEastAsianmeta-analysis,forwhichimputationreferencepanelsareless297comprehensivecomparedtotheEuropean-centricHaplotypeReferenceConsortiumpanel.298299Variantsexhibitingthelargestdifferencesineffectsizesacrossancestriesaregenerallyrare(MAF300≤0.1%)inEuropeanpopulationsbutcommon(e.g.PAX4,RANBP3L)orlowfrequency(e.g.ZNF257,301DGKD)inEastAsianpopulations.Forexample,rs142395395nearZNF257(RAF=96.9%,OR=1.24,95%CI3021.19-1.29,P=7.0x10-23)hasbeenreportedonlytwicein15,414individualsofnon-FinnishEuropean303ancestryfromthegnomADdatabase33.Thisvarianttagsapreviouslydescribedinversionof415kb304observedonlyinEastAsianindividualsthatdisruptsthecodingsequenceandexpressionofZNF257,as305wellaslymphoblastoidexpressionof81downstreamgenesandtranscripts34.Thesedatasuggestthat306ZNF257and/ordownstreamtargetgenesinfluenceT2Dsusceptibility(SupplementaryFigure10).307

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308Weidentifiedmanylociforwhichtheleadvariantsexhibitedsimilarallelefrequenciesandeffectsizesin309boththeEastAsianandEuropeanmeta-analyses,butonlyreachedgenome-widesignificanceintheEast310Asianmeta-analysis.Givensharedsusceptibilityacrossancestrygroups,theselocimaybedetectedin311non-EastAsianpopulationswhensamplesizesincrease.Amongthesevariantsisrs117624659,located312nearNKX6-1(PEAS=2.0x10

-16,PEUR=2.2x10-4).Thisleadvariantoverlapsahighlyconservedregionthat313

showsopenchromatinspecifictopancreaticislets.Weconductedtranscriptionalreporterassaysin314MIN6mouseinsulinomacellsandobservedthatrs117624659exhibitedsignificantallelicdifferencesin315enhanceractivity(Figure3;SupplementaryFigure11).Inthepancreas,NK6homeobox1(NKX6.1)is316requiredforthedevelopmentofinsulin-producingβcellsandisapotentbifunctionaltranscriptional317regulator35.Further,inactivationofNkx6.1inmicedemonstratedrapid-onsetdiabetesduetodefectsin318insulinbiosynthesisandsecretion36.Unexpectedly,theT2Driskalleleshowedincreasedtranscriptional319activity,suggestingthatthevariantdoesnotactinisolationorthatNXK6-1isnotthetargetgene.320321AtoneofthenovelT2D-associatedlocinearSIX3,theriskalleleofEastAsianleadvariantrs12712928322(RAF=40.2%,OR=1.06,95%CI1.04–1.07,P=3.2x10-14)iscommonacrossnon-EastAsianancestries,323rangingfrom16.0%inEuropeansto26.4%inSouthAsians;however,therewasnoevidenceof324associationintheotherancestrygroups(meta-analysis:OR=0.98,95%CI0.96–0.99,P=2.9x10-3)(Figure3254A;SupplementaryFigure12;SupplementaryTable8).WithintheEastAsianmeta-analysis,the326directionofeffectisconsistentacrossEastAsiancountries(Figure4B)andwithinthecontributing327cohorts(SupplementaryFigure13).TheT2Driskallelers12712928-Cisassociatedwithhigherfasting328glucoselevelsinEastAsianpopulations37,38,hasthestrongestassociationwithlowerexpressionlevelsof329bothSIX3andSIX2inpancreaticislets17,anddemonstratedallele-specificbindingtothetranscription330factorGABPAandsignificantlylowerlevelsoftranscriptionalactivity38.Whilelargerstudiesinother331ancestrygroupscouldimprovetheaccuracyoftheeffectestimate,currentevidencesuggeststhatthe332T2DassociationnearSIX3isspecifictoEastAsianpopulations.333334ToidentifypotentialcandidategenesunderlyingtheT2D-associationsignalsidentifiedinEastAsian335individuals,wefurthercharacterized88loci,includingknownandnovelloci,forwhichtheleadvariant336attheprimaryEastAsianassociationsignalislocated>500kbfromtheleadvariantofanyprimary337EuropeanT2Dassociationsignal2(SupplementaryTable9).Wecharacterizedlociusingpriortrait338associations,cis-regulatoryeffectsonexpression(colocalizedeQTL),predictedeffectsonprotein339sequence,andaliteraturesearch(SupplementaryTables10-13).Basedonassociationresultsfrom340cardiometabolictraitconsortia39,BiobankJapan40,andtheUKBiobank41,theleadT2D-associated341variantat19ofthe88lociwasassociated(P<5x10-8)withatleastoneadditionalcardiometabolictrait,342mostfrequentlyBMIorafatmass-relatedtrait(16loci;SupplementaryTables10and12).At12ofthe343examinedloci,T2Dsignalswerecolocalizedwithcis-eQTLsfortranscriptsinsubcutaneousadipose344tissue(n=5),skeletalmuscle(n=3),pancreas(n=2),pancreaticislets(n=3),orwholeblood(n=5;345SupplementaryTables11-12).At19loci,theleadT2D-associatedvariantoravariantinhighLDwithit346(EastAsianr2>0.80)altertheproteinsequence(SupplementaryTables12).Thesevariantsaffect347mesenchymalstemcelldifferentiationandadipogenesis(GIT2,STEAP2andJMJD1C),musclestemcell348biology(CALCR),glucosemetabolism(PGM1andSCTR),andinsulinsecretion(FGFR4;Supplementary349Table13).Whilemechanisticinferenceisrequired,thesepotentialmolecularmechanismssuggestnew350T2DsusceptibilitygenesprimarilydetectedbyanalysesinEastAsians.351352T2DlociwerealsoidentifiedatclustersofnoncodingRNAswithrolesinisletβcellfunction.Onelocus353includesasetofmicroRNAsspecificallyexpressedinisletβcells,thematernallyexpressednoncoding354RNAMEG3,andthepaternallyexpressedgeneDLK1.TargetsofthemicroRNAsatthislocusincreaseβ355

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cellapoptosis42,andreducedMeg3impairsinsulinsecretion43.DLK1inhibitsadipocytedifferentiation,356protectingfromobesity44,andpromotespancreaticductalcelldifferentiationintoβcells,increasing357insulinsecretion45,46.OthervariantsnearMEG3havebeenassociatedwithtype1diabetes(EASandEUR358LDr2=0withEASleadvariant)47.TheothernoncodingRNAlocusistheMIR17HGclusterofmiRNAsthat359regulateglucose-stimulatedinsulinsecretionandpancreaticβcellproliferationstress48;oneofthese360microRNAs,miR-19a,affectshepaticgluconeogenesis49.YetanotherindependentT2Dassociationlocus361islocatednearTRAF3,whichisadirecttargetoftheMIR17HGmicroRNAclusterandpromotes362hyperglycemiabyincreasinghepaticglucoseproduction50,51.TheT2Dassociationresultssuggestthat363thesenoncodingRNAsinfluencediseasesusceptibility.364365DISCUSSION366TheseT2DGWASmeta-analysesinthelargestnumberofEastAsianindividualsanalyzedtodate367identified56novelloci,providingadditionalinsightintothebiologicalbasisofT2D.Theresults368emphasizesubstantialsharedT2DsusceptibilitywithEuropeanindividuals,asshownbythestrong369correlationofeffectsizesamongT2D-associatedgeneticvariantswithcommonallelefrequenciesin370bothEastAsianandEuropeanancestrypopulations.TheresultsalsodetectnovelassociationsinEast371Asianindividuals,severalofwhichareidentifiedbecausetheyhavehigherallelefrequenciesinEast372Asianpopulations,exhibitlargereffectsizes,and/orareinfluencedbyotherenvironmentalriskfactors373orlifestylebehaviorssuchasalcoholconsumption.374375Theidentifiedlocipointtomultipleplausiblemolecularmechanismsandmanynewcandidategenes376linkingT2Dsusceptibilitytodiversebiologicalprocesses.AnnotationoflociidentifiedintheEastAsian377meta-analysissuggestsasubstantialroleforinsulinresistanceinT2DpathogenesisamongEastAsian378individualsthroughskeletalmuscle,adipose,andliverdevelopmentandfunction.Wealsoprovide379evidencethatmultipledistinctassociationsignalsinthesameregiondonotnecessarilyactthroughthe380samegene.Conditionallydistinctassociationsignalsincloseproximitycanaffectdifferentgenesthat381mayactindifferenttissuesbydifferentmechanisms,emphasizingthevalueofidentifyingfunctional382variantsthatenablevariant-to-genelinkstobeexamineddirectly.Ourresultsprovideafoundationfor383futurebiologicalresearchinT2Dpathogenesisandofferpotentialtargetsformechanismsfor384interventionsindiseaserisk.385386METHODS387Ethicsstatement388Allhumanresearchwasapprovedbytherelevantinstitutionalreviewboardsforeachstudyattheir389respectivesitesandconductedaccordingtotheDeclarationofHelsinki.Allparticipantsprovidedwritten390informedconsent.391392Studycohortsandqualitycontrol393TheEastAsiantype2diabetes(T2D)meta-analyseswereperformedwithstudiesparticipatinginthe394AsianGeneticEpidemiologyNetwork(AGEN),aconsortiumofgeneticepidemiologystudiesofT2Dand395relatedtraitsconductedinindividualsofEastAsianancestry,andtheDiabetesMeta-analysisofTrans-396ethnicAssociationStudies(DIAMANTE),aconsortiumexaminingthegeneticcontributiontoT2Dacross397diverseancestrypopulationsincludingAfrican-American,EastAsian,European,Hispanic,andSouth398Asian.TheEastAsianmeta-analysisincluded77,418T2Dcasesand356,122controlsfrom23GWAS,399includingthreebiobanks,CKB,KBA52,53,andBBJ4[effectivesamplesize(Neff)=211,793;Supplementary400Figure1].AsubsetofstudieswasanalyzedinBMI-adjustedandsex-specificmodels(54,481cases,401224,231cases;Neff=135,780).Foreachstudy,T2Dcasecontrolascertainmentisdescribedin402SupplementaryTable1andsummarystatisticsareprovidedinSupplementaryTable2.Includedstudies403

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weregenotypedoneithercommerciallyavailableorcustomizedAffymetrixorIlluminagenome-wide404genotypingarrays.Arrayqualitycontrolcriteriaimplementedwithineachstudy,includingvariantcall405rateandHardy-Weinbergequilibrium,aresummarizedinSupplementaryTable3.Toharmonizestudy-406levelgenotypescaffoldforimputationto1000Genomes(1000G)referencepanels,eachstudyadopted407auniformprotocolforpre-imputationqualitychecks.Eachstudyappliedtheprotocoltoexclude408variantswith:i)mismatchedchromosomalpositionsorallelesnotpresentinthereferencepanel;ii)409ambiguousalleles(AT/CG)withminorallelefrequency(MAF)>40%inthereferencepanel;oriii)410absoluteallelefrequencydifferences>20%comparedtoEastAsian-specificallelefrequencies.The411genotypescaffoldforeachstudywasthenimputedtothe1000GPhase1or3referencepanel54using412minimac355orIMPUTEv256.InBMI-unadjustedanalyses,allstudieswereimputedto1000GPhase3.In413BMI-adjustedandsex-stratifiedanalyses,allstudieswereimputedto1000GPhase3exceptforBiobank414Japan14,whichwasimputedtothe1000GPhase1referencepanel.415416Study-levelassociationanalyses417Withineachstudy,allvariantsweretestedforassociationwithT2Dassuminganadditivemodelof418inheritancewithinaregressionframework,includingage,sex,andotherstudy-specificcovariates419(SupplementaryTable3).Toaccountforpopulationstructureandrelatedness,associationanalyses420wereeitherperformedusingFIRTH57ormach2datwithadditionaladjustmentforprincipalcomponents421inunrelatedindividualsoralinearmixedmodelwithkinshipmatriximplementedinBOLT-LMM58.In422studiesanalyzedwiththelinearmixedmodel,alleliceffectsandstandarderrorswereconvertedtothe423log-oddsscalethataccountsforcase-controlimbalance59.Withineachstudy,variantswereremovedif424the:i)imputationqualityscorewaspoor(minimac3r2<0.30;IMPUTE2infoscore<0.40);ii)combined425casecontrolminorallelecount<5;oriii)standarderrorofthelog-OR>10.Forasubsetofthestudies,426BMIwasaddedasanadditionalcovariate,andassociationanalyseswerealsoperformedseparatelyin427malesandfemales.Foreachstudyandmodel,associationstatisticswerecorrectedwithgenomic428controlinflationfactor60calculatedfromcommonvariants(MAF≥5%)(SupplementaryTable3).ForBBJ,429weappliedthegenomiccontrolinflationfactor1.21asreported4.430431Sex-combinedmeta-analysis432Wecombinedstudy-levelassociationstatisticsusingfixedeffectsmeta-analysiswithinverse-variance433weightingoflog-ORsimplementedinMETAL61.Variantswithallelefrequencydifferences>20%between4341000GenomesPhase1and3panelswereexcludedfromthemeta-analysis.Toassessexcessinflation435arisingfromcrypticrelatednessandpopulationstructure,weappliedLDscoreregressiontothemeta-436analysissummarystatisticstoestimateresidualinflationofsummarystatistics,usingasetof1,889437unrelatedChineseindividualsfromtheSingaporeChineseEyeStudy62.TheLDscoreregression438interceptswere0.991forBMI-unadjusted,and1.0148forBMI-adjustedmodels.AstheLDscore439regressioninterceptsindicatedabsenceofexcessinflation,themeta-analysisresultswerecorrectedfor440inflationusingtheseLDscoreregressionintercepts.Forsubsequentanalyses,weconsideredonly441variantsthatwerepresentinatleast50%oftheeffectivesamplesizeNeff[computedas4/(1/Ncases+4421/Ncontrols)]

61.Heterogeneityinalleliceffectsizesbetweenstudieswereassessedwithfixedeffects443inversevarianceweightedmeta-analysisPhet.WefurthercomparedthegeneticeffectsfromBMI-444unadjustedandBMI-adjustedmodelsusingfixedeffectsinversevarianceweightedmeta-analysisPhet.445Lociweredefinedasnoveliftheleadvariantis:(1)atleast500kbawayandconfirmedbyGCTAtobe446conditionallyindependentfrompreviouslyreportedT2D-associatedvariantsinanyancestry,and(2)447assessedusingLocusZoomplotsanddetailedliteraturereviewtobeawayfromknownlociwith448extendedLD.449450Sex-differentiatedmeta-analysis451

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Themeta-analysesdescribedabovewererepeatedformalesandfemalesseparately.Themale-specific452meta-analysesincludedupto28,027casesand89,312controls(Neff=65,660)andthefemale-specific453analysesincludedupto27,370casesand135,055controls(Neff=70,332).LDscoreregressionintercepts454were1.0035forBMI-unadjustedand1.0034forBMI-adjustedmodelsinmalesand1.0035forBMI-455unadjustedand1.0034forBMI-adjustedmodelsinfemales.Wefurtherperformedatestfor456heterogeneityinalleliceffectsbetweenmalesandfemalesasimplementedinGWAMA63,64.457458Detectionofdistinctassociationsignals459Todetectmultipledistinctassociationsignalsateachassociatedlocus,wecombinedoverlappingloci460whenthedistancebetweenanypairofleadvariantswas<1Mb.Wethenperformedapproximate461conditionalanalysesusingGCTA8withgenome-widemeta-analysissummarystatisticsandLDestimated462from78,000samplesfromtheKoreanBiobankArray53.463464ComparinglocieffectsbetweenEastAsianandEuropeanpopulations465Wecomparedtheper-alleleeffectsizesofleadvariantsidentifiedfromtheEastAsianBMI-unadjusted466sex-combinedmeta-analysis(178leadvariants)andEuropeanBMI-unadjustedsex-combinedmeta-467analysis2(231leadvariants;SupplementaryTable7).Acrossthe409associatedvariantsfromthetwo468ancestries,11leadvariantsoverlapped,resultingin398uniquevariants.AsthevariantsintheEuropean469analysiswereimputedusingtheHaplotypeReferenceConsortiumreferencepanelanddidnotinclude470indelvariants,avariantinstrongLD(EastAsianr2>0.90)withtheleadEastAsianvariantwasusedwhen471theleadvariantwasanindel,whenpossible.IftheleadEastAsianvariantoravariantinstrongLD(East472Asianr2>0.90)wasnotavailableintheEuropeandatafromDIAMANTE,weusedresultsfromaprevious473Europeantype2diabetesmeta-analysis65.Theeffectsizecomparisonplotwasrestrictedto343variants474wheredatawasavailableforbothancestries(Figure2A).ForlocithatweresignificantinboththeEast475AsianandEuropeanmeta-analyses,iftheleadvariantsweredifferent,bothleadvariantswereplotted476(seeSupplementaryTable7).Effectsizeplotswerefurtherrestrictedto:i)290leadvariantswith477MAF≥5%inbothEastAsianandEuropeanmeta-analyses(SupplementaryFigure7);ii)162leadvariants478significantintheEastAsianmeta-analysis(SupplementaryFigure8A);andiii)192leadvariants479significantintheEuropeanmeta-analysis(SupplementaryFigure8B).480481Associationswithothermetabolictraitsandoutcomes482WeusedtheType2DiabetesKnowledgePortal39toexploreassociationsofthenewlyidentifiedlociwith483othermetabolictraitsandoutcomes.Associationstatisticsfromthefollowingconsortiawereavailable484forqueryontheportal(lastaccessedMarch18,2019):coronaryarterydiseasefromCARDIoGRAM66,485BMIandwaist-hip-ratiofromGIANT67,68,lipidtraitsfromGLGC69,andglycemictraitsfromMAGIC70,71.486Additionally,weusedavailabledatafromAGENEastAsianmeta-analysesforlipids72andadiponectin73,487alongwiththephenotypicdatafromtheUKBiobank74.Effectsizeswereobtainedfrompubliclyavailable488summarystatisticfiles.489490Colocalizationwithexpressionquantitativetraitloci(eQTL)491WesearchedpubliclyavailableeQTLdatabasessuchasGTEx75andtheParkerlabIsletBrowser17,to492identifycis-eQTLsatthenovellociinadipose(subcutaneousandvisceral),blood,pancreas,pancreatic493islet,andskeletalmuscletissue.Wealsosearchedforcis-eQTLsinsubcutaneousadiposetissuedata494fromtheMETSIMstudy19.ColocalizedeQTLswereidentifiediftheleadexpressionlevel-associated495variantandtheGWASleadvariantwereinhighLD(r2>0.80)inEuropeanstoaccommodatethe496predominantlyEuropeaneQTLdata.Reciprocalconditionalanalyseswerealsoperformedusingthe497METSIMdatatodetermineiftheGWASleadvariantandtheleadeSNPwerepartofthesameeQTL498signal.499

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500Literaturereview501WeconductedatraditionalliteraturereviewtoidentifycandidategenesateachnovellocususingNCBI502EntrezGene,PubMedandOMIM.Weincludedgenesymbolsandthefollowingkeywordsassearch503termsinPubMed:diabetes,glucose,insulin,islet,adipose,muscle,liver,obesity.Agenewasconsidered504apotentialcandidateifanapparentlinktoT2Dbiologyexistedbasedonpriorstudiesofgenefunction.505506FunctionalannotationandexperimentationatNKX6-1507WeusedENCODE76,ChromHMM77,andHumanEpigenomeAtlas78dataavailablethroughtheUCSC508GenomeBrowsertoidentifycandidatevariantsattheassociationsignalnearNKX6-1thatoverlapped509open-chromatinpeaks,ChromHMMchromatinstates,andchromatin-immunoprecipitationsequencing510(ChIP-seq)peaksofhistonemodificationsH4K4me1,H3K4me3,andH3K27ac,andtranscriptionfactors511inthepancreasandpancreaticislets.MIN6mouseinsulinomacells79and823/13ratinsulinomacells80512wereculturedinDMEM(Sigma)supplementedwith10%FBS,1mMsodiumpyruvate,and0.1mMbeta-513mercaptoethanol.Thecellculturesweremaintainedat37°Cwith5%CO2.Tomeasurevariantallelic514differencesinenhanceractivityattheNKX6-1locus,wedesignedoligonucleotideprimers(forward:515CCCTAGTAATGCCCTTTTTGTT;reverse:TCAGCCTGAGAAGTCTGTGA)withKpnIandXholrestrictionsites,516andamplifiedthe400-bpDNAregion(GRCh37/hg19-chr4:85,339,430-85,339,829)around517rs117624659.Aspreviouslydescribed80,weligatedamplifiedDNAfromindividualshomozygousforeach518alleleintothemultiplecloningsiteofthepGL4.23(Promega)minimalpromoterluciferasereporter519vectorinboththeforwardandreverseorientationswithrespecttothegenome.Cloneswereisolated520andsequencedforgenotypeandfidelity.2.1x105MIN6or3.0x105823/13cellswereseededperwell521andgrownto90%confluencein24-wellplates.Weco-transfectedfiveindependentluciferase522constructsandRenillacontrolreportervector(phRL-TK,Promega)usingLipofectamine2000(Life523Technologies)andincubated.48-hourspost-transfection,thecellswerelysedwithPassiveLysisBuffer524(Promega).LuciferaseactivitywasmeasuredusingtheDual-luciferaseReporterAssaySystem(Promega)525permanufacturerinstructionsandaspreviouslydescribed81.526 527

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18

ACKNOWLEDGEMENTS766Thisworkwassupportedbysubawards(toX.SandY.S.C.)fromNIDDKU01DK105554(JoseC.Florez).767Theauthorsthankallinvestigators,staffmembersandstudyparticipantsfortheircontributionstoall768participatingstudies.Afulllistoffunding,andindividualandstudyacknowledgementsareavailablein769SupplementaryMaterials.770771AUTHORCONTRIBUTIONS772Projectcoordination:K.L.M,X.S.Writing:C.N.S.,E.S.T,M.B.,M.H.,Y.J.K.,K.L.,K.L.M,X.S.Coreanalyses:773C.N.S.,M.H.,Y.J.K.,K.L.,A.K.I.,H.J.P.,S.M.B.,X.S.eQTLlookups:M.vdB,A.L.G.DIAMANTEanalysisgroup:774J.E.B.,M.B.,D.W.B.,J.C.C.,A.M.,M.I.M.,M.C.Y.N.,L.E.P.,W.Zhang.,A.P.M.Statisticalanalysisin775individualstudies:Y.T.,M.H.,K.S.,X.S.,F.T.,M.N.,C.N.S.,K.L.,F.B.,Y.J.K.,S.Moon.,C.H.T.T.,J.Y.,X.G.,776J.Long.,J.F.C.,V.J.Y.L.,S.H.K.,H.S.C.,C.H.C.Individualstudydesignandprincipalinvestigators:M.Igase.,777T.Kadowaki.,Y.X.W.,N.K.,M.Y.,K.L.M.,R.G.W.,E.S.T.,B.J.K.,R.C.W.M.,J.I.R.,F.M.,X.O.S.,C.Y.C.,W.P.K.,778T.Y.W.,K.S.P.,Y.S.C.,W.H.H.S.,J.Y.W.Genotypingandphenotyping:K.K.,A.T.,Y.K.,T.Y.,Y.O.,J.B.J.,779T.Katsuya.,M.Isono.,S.I.,K.Yamamoto.,A.H.,S.D.,W.H.,J.S.,P.G.L.,C.Y.,Y.G.,Z.B.,J.Lv.,L.L.,Z.C.,N.R.L.,780L.S.A.,J.Liu.,R.M.vD.,S.H.,K.Yoon.,H.M.J.,D.M.S.,G.J.,A.O.L.,B.T.,W.Y.S.,J.C.N.C.,M.Y.H.,Y.D.I.C.,781T.Kawaguchi.,Y.B.X.,W.Zheng.,L.Z.,C.C.K.,M.A.P.,M.G.,J.M.Y.,C.S.,M.L.C.,M.S.L.,C.M.H.,L.M.C.,782Y.J.H.,L.C.C.,Y.T.C.,F.J.T.,J.I.R.783784AUTHORINFORMATION785786Summary-levelstatisticswillbeavailableattheAGENconsortiumwebsite787https://blog.nus.edu.sg/agen/summary-statistics/andtheAcceleratingMedicinesPartnershipT2D788portalhttp://www.type2diabetesgenetics.org/.789790Theauthorsdeclarenocompetinginterest.791792Correspondenceandrequestsformaterialsshouldbeaddressedtomohlke@med.unc.eduand/or793ephsx@nus.edu.sg.794795WEBRESOURCES796Pre-imputationpreparationandqualitycontrol,http://www.well.ox.ac.uk/~wrayner/tools/797MichiganImputationServer,https://imputationserver.sph.umich.edu/index.html798EPACTS,https://github.com/statgen/EPACTS799RVTESTS,https://github.com/zhanxw/rvtests800METAL,http://csg.sph.umich.edu/abecasis/metal/801LDSC,https://github.com/bulik/ldsc802GWAMA,https://www.geenivaramu.ee/en/tools/gwama803Type2DiabetesKnowledgePortal,http://www.type2diabetesgenetics.org804GTExPortal,https://gtexportal.org/home/805ParkerlabIsletBrowser,http://theparkerlab.org/tools/isleteqtl/806807808809810811812813

.CC-BY 4.0 International licensecertified by peer review) is the author/funder. It is made available under aThe copyright holder for this preprint (which was notthis version posted June 28, 2019. . https://doi.org/10.1101/685172doi: bioRxiv preprint

19

Table1.Novelleadvariantsassociatedwithtype2diabetesinEastAsians814Locus Leadvariant Chr Pos RA NRA RAF Neff Cases

(N)

Controls

(N)

OR(95%CI) P

VWA5B1 rs60573766 1 20,688,352 C T 0.635 210,985 77,181 354,521 1.04(1.03-1.06) 4.30E-10MAST2 rs562138031 1 46,244,900 C CT 0.726 210,231 76,984 350,185 1.06(1.04-1.07) 8.66E-12PGM1 rs2269239 1 64,109,359 C G 0.813 211,039 77,221 351,786 1.06(1.04-1.07) 5.81E-10TSEN15 rs1327123 1 184,014,593 C G 0.460 210,985 77,181 354,521 1.04(1.03-1.05) 6.40E-09MDM4 rs201297151 1 204,474,581 CAAAAAAAA C 0.440 210,231 76,984 350,185 1.04(1.03-1.05) 4.64E-08SIX3 rs12712928 2 45,192,080 C G 0.402 211,321 77,275 355,448 1.06(1.04-1.07) 3.16E-14IKZF2 rs75179644 2 213,687,103 T C 0.899 210,985 77,181 354,521 1.08(1.05-1.10) 6.01E-10ZBTB20 rs6768463 3 114,964,264 T A 0.614 211,793 77,418 356,122 1.05(1.03-1.06) 3.19E-11TFRC rs9866168 3 195,830,310 T A 0.640 210,985 77,181 354,521 1.05(1.03-1.06) 1.31E-09RANBP3L rs16902871 5 36,257,018 G A 0.149 211,793 77,418 356,122 1.06(1.04-1.08) 3.34E-09PCSK1 rs11960326 5 95,850,807 C T 0.416 211,680 77,388 355,625 1.04(1.03-1.05) 3.74E-09REPS1 rs556058292 6 139,259,142 C CT 0.651 210,985 77,181 354,521 1.04(1.03-1.06) 1.42E-08HIVEP2 rs9390022 6 143,056,556 T C 0.800 211,793 77,418 356,122 1.05(1.03-1.07) 6.35E-09ZNF713 rs565050730 7 55,984,953 GA G 0.334 210,985 77,181 354,521 1.04(1.03-1.06) 4.78E-08STEAP1 rs62469016 7 89,752,238 C G 0.223 211,793 77,418 356,122 1.07(1.05-1.08) 1.52E-15CALCR rs2074120 7 93,107,093 A C 0.323 211,793 77,418 356,122 1.04(1.03-1.06) 8.38E-09GRM8/PAX4 rs117737118 7 126,526,991 G A 0.093 209,652 76,825 348,561 1.18(1.15-1.21) 1.01E-31ASAH1 rs34642578 8 17,927,609 T C 0.053 210,985 77,181 354,521 1.09(1.06-1.13) 1.67E-09ZNF703 rs12680217 8 37,397,803 T C 0.553 211,457 77,324 355,195 1.05(1.03-1.06) 1.64E-11GDAP1 rs149265787 8 75,214,398 G A 0.024 211,694 77,392 355,608 1.14(1.10-1.19) 5.68E-10TRIB1 rs10103720 8 126,471,770 C T 0.378 211,793 77,418 356,122 1.04(1.03-1.06) 3.33E-09EFR3A rs73708055 8 132,879,882 G A 0.252 211,793 77,418 356,122 1.04(1.03-1.06) 4.41E-08DMRT2 rs1016565 9 1,032,567 A G 0.421 211,793 77,418 356,122 1.04(1.02-1.05) 2.18E-08PTCH1 rs113154802 9 98,278,413 C T 0.888 210,985 77,181 354,521 1.06(1.04-1.08) 4.91E-08ABCA1 rs201375651 9 107,597,527 CA C 0.395 211,793 77,418 356,122 1.04(1.03-1.06) 2.56E-08PTF1A rs77065181 10 23,487,778 A G 0.047 211,098 77,211 355,018 1.09(1.06-1.13) 1.63E-08ARID5B rs141583966 10 63,712,602 G GGTGT 0.909 210,066 76,938 349,783 1.08(1.05-1.11) 6.58E-10JMJD1C rs148928116 10 64,976,133 T TA 0.795 210,985 77,181 354,521 1.06(1.05-1.08) 2.31E-13ARHGAP19 rs10736116 10 99,056,921 C G 0.306 211,793 77,418 356,122 1.05(1.03-1.06) 9.21E-11BBIP1 rs7895872 10 112,678,657 T G 0.579 210,985 77,181 354,521 1.05(1.03-1.06) 2.29E-11BDNF rs988748 11 27,724,745 G C 0.565 211,793 77,418 356,122 1.04(1.03-1.06) 1.62E-10FAIM2 rs77978149 12 50,269,863 T C 0.090 210,406 77,022 352,897 1.08(1.05-1.10) 3.89E-09ALDH2 rs149212747 12 111,836,771 A AC 0.795 210,231 76,984 350,185 1.07(1.05-1.09) 2.07E-11RBM19 rs7307263 12 114,123,722 G C 0.427 210,985 77,181 354,521 1.04(1.02-1.05) 3.96E-08FGF9 rs9316706 13 22,589,883 A G 0.351 211,793 77,418 356,122 1.04(1.03-1.06) 3.33E-09NYNRIN rs12437434 14 24,878,370 C T 0.713 211,039 77,221 351,786 1.05(1.03-1.06) 1.02E-09LRRC74A rs140431144 14 77,382,093 TA T 0.327 207,126 75,090 353,783 1.05(1.03-1.06) 9.21E-11DLK1/MEG3/

miRNA

cluster

rs73347525 14 101,255,172 A G 0.756 205,739 74,694 350,558 1.06(1.04-1.08) 5.54E-11

TRAF3 rs55700915 14 103,237,952 A G 0.434 211,039 77,221 351,786 1.04(1.03-1.06) 1.50E-08HERC2 rs76704029 15 28,546,173 T C 0.732 173,598 66,475 264,668 1.06(1.04-1.08) 3.03E-08MYO5C rs149336329 15 52,587,740 G T 0.949 210,231 76,984 350,185 1.11(1.07-1.14) 1.31E-09RGMA rs61021634 15 93,825,384 A G 0.438 210,985 77,181 354,521 1.05(1.03-1.06) 9.47E-12IGF1R rs79826452 15 99,366,409 A G 0.890 210,985 77,181 354,521 1.07(1.04-1.10) 3.80E-08PKD1L3 rs12600132 16 72,022,534 T C 0.432 211,793 77,418 356,122 1.04(1.03-1.05) 5.95E-09ZFHX3 rs6416749 16 73,100,308 C T 0.375 210,460 77,062 350,162 1.05(1.04-1.07) 3.40E-12SUMO2 rs35559984 17 73,187,031 CA C 0.652 206,547 74,931 352,159 1.05(1.03-1.07) 7.88E-09ZNF799 rs4604181 19 12,509,536 A C 0.514 209,652 76,825 348,561 1.04(1.03-1.06) 1.80E-08ZNRF3 rs147413364 22 29,380,119 T TA 0.357 210,874 77,175 351,384 1.04(1.03-1.06) 3.38E-08WNT7B rs28637892 22 46,313,618 T G 0.215 175,881 63,772 319,376 1.05(1.04-1.07) 3.66E-09SinglevariantassociationresultsfromEastAsianfixed-effectinverse-variancemeta-analysis(BMI-unadjustedsex-combinedmodeladjustedforage,sex,andstudy-specificcovariates)usingMETAL.Lociweredefinedasnoveliftheleadvariantis(1)atleast500kbawayandconfirmedbyGCTAtobeconditionallyindependentfrompreviouslyreportedT2D-associatedvariantsinanyancestry,and(2)assessedusinglocuszoomplotsandbiologylookupstobeawayfromknownlociwithextendedLD.Fouradditionalvariantsmetthedefinitionforanovellocusbutarelocatedwithinthepreviouslyreportedmajorhistocompatibilitycomplex(MHC)region;seeSupplementaryTableS5forthefulllistofdistinctassociationsignalsattheMHCregion.rs4804181was>500kbfromprimarysignalrs3111316inEuropeanmeta-analysis,but<500kbfromtheirsecondarysignalrs755734872.Genome-widesignificantassociationisdefinedasP<5.0E-08.Physicalpositionbasedonhg19.EffectallelesareassoicatedwithincreasedriskforT2D.OddsratiosreflectperalleleeffectsofvariantsonT2Drisk.Abbreviations:Chr,chromosome;Pos,position;RA,riskallele;NRA,non-riskallele;RAF,riskallelefrequency;Neff,effectivesamplesize;OR,oddsratio;CI,confidenceinterval;P,P-value

815816817818819

.CC-BY 4.0 International licensecertified by peer review) is the author/funder. It is made available under aThe copyright holder for this preprint (which was notthis version posted June 28, 2019. . https://doi.org/10.1101/685172doi: bioRxiv preprint

Figure 1: Two distinct T2D-association signals at the ANK1-NKX6-3 locus associated with expression levels of two transcripts in two tissues. (A) Regional association plot for East Asian sex-combined BMI-unadjusted meta-analysis at ANK1-NKX6-3 locus. Approximate conditional analysis using GTCA identified three distinct T2D-association signals at this locus (signal 1, rs33981001; signal 2, rs62508166; signal 3, rs144239281, in order of strength of association). Using 1000G Phase3 East Asian LD, variants are colored in red and blue with the first and second distinct signals respectively (lead variants represented as diamonds). (B) Variant rs12549902, in high LD (EAS LD r2=0.80, EUR r2=0.83) with T2D signal 1, shows the strongest association with expression levels of NXK6-3 in pancreatic islets in 118 individuals16. (C) Variant rs516946, in high LD (EAS LD r2=0.96, EUR r2=0.80) with T2D signal 2, shows the strongest association with expression levels of ANK1 in subcutaneous adipose tissue in 770 individuals19. As rs62508166 is not available in the subcutaneous adipose tissue data set, a variant in perfect LD (rs28591316) was used and is represented by the blue diamond variant.

.CC-BY 4.0 International licensecertified by peer review) is the author/funder. It is made available under aThe copyright holder for this preprint (which was notthis version posted June 28, 2019. . https://doi.org/10.1101/685172doi: bioRxiv preprint

SFRP1 GOLGA7

GINS4

AGPAT6

NKX6 3

ANK1

KAT6A AP3M2

PLAT

41.2 41.4 41.6 41.8 42Position on chr8 (Mb)

rs62508166 (Signal 2)

0

2

4

6

log 1

0(pva

lue)

ANK1 eQTL Results (Sub. Adipose)

0

2

4

6

log 1

0(pva

lue)

NKX6-3 eQTL Results (Pan. Islets)

rs33981001 (Signal 1)

Figure 1

rs33981001 (Signal 1)

rs62508166 (Signal 2)

0 0.2 0.4 0.6 0.8 1

r2with reference SNPAGEN T2D GWAS Results

0

5

10

15

20

25

log 1

0(pva

lue)

.CC-BY 4.0 International licensecertified by peer review) is the author/funder. It is made available under aThe copyright holder for this preprint (which was notthis version posted June 28, 2019. . https://doi.org/10.1101/685172doi: bioRxiv preprint

−0.25

0.0

0.25

0.50

0.0 0.1 0.2 0.3Per−allele effect size in EAS (SE)

Per−

alle

le e

ffect

siz

e in

EU

R (S

E)A

B

−0.1

0.0

0.1

0.2

0.00 0.05 0.10 0.15 0.20Per−allele effect size in EAS (SE)

Per−

alle

le e

ffect

siz

e in

EU

R (S

E)

EUR onlyEUR and EASEAS only

LEP

PAX4

RANBP3L

PTF1A

TCF7L2

NKX6-1

KCNQ1

ZNF257ZNF738

ATG16L1

P<5x10-8 in:

Figure 2: Effect size comparison of lead variants identified in this T2D GWAS BMI-unadjusted meta-analysis in East Asians and previous T2D GWAS meta-analysis in Europeans2. For 343 lead variants identified from the two BMI unadjusted meta-analyses, per-alleleeffect sizes (beta) from Europeans meta-analysis (y-axis) were plotted against per-allele effect sizes from this East Asians meta-analysis (x-axis). (A) All 343 lead variants; (B) 290 lead variants with minor allele frequency at least 5% in both ancestries. Variants are colored purple if they were significant (P<5x10-8) in East Asians only, green if they were significant in Europeans only, and blue if they were significant in both East Asians and Europeans (see Methods and Supplementary Table 7).

.CC-BY 4.0 International licensecertified by peer review) is the author/funder. It is made available under aThe copyright holder for this preprint (which was notthis version posted June 28, 2019. . https://doi.org/10.1101/685172doi: bioRxiv preprint

A B

C-log 1

0(P-

valu

e)

0

20

40

60

80

100

Recom

bination rate (cM/M

b)

0.20.40.60.8

r2

LOC101928978

85.2 85.4Position on chr4 (Mb) Forward Reverse

Rela

tive

Luci

fera

se A

ctivi

ty

P = 0.0003

EmptyVector

T C T C

P = 0.0001

0

10

20

30

40

85,340,000rs142390274 rs117624659

hg19 Chr4

DNA Element

Islet ChromHMM

100 Vertebrate

Conservation

Islet H3K4me3

Islet H3K4me1

Islet FAIRE

85,330,000

0

5

10

15

NKX6-1

Figure 3: rs117624659 at NKX6-1 locus exhibits allelic differences in transcriptional activity. (A)

rs117624659 (purple diamond) shows the strongest association with type 2 diabetes in the region. Variants are

colored based on 1000G Phase 3 East Asian LD with rs117624659. (B) rs117624659 and an additional candidate

variant rs142390274 in high pairwise LD (r2>0.80) span a 22 kb region approximately 75 kb upstream of NKX6-1.

rs117624659 overlaps a region of open chromatin in pancreatic islets and lies within a region conserved across

vertebrates. (C) rs117624659-T, associated with increased risk of T2D, showed greater transcriptional activity in

an element cloned in both forward and reverse orientations with respect to NKX6-1 in MIN6 cells compared to

rs117624659-C and an “empty vector” containing a minimal promoter.

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T2D Odds ratio

0.91 0.95 1.00 1.05

AFR

EAS

EUR

HIS

SAS

Combined

rs12712928

Ancestry OR (95% CI) P

2.9E-02

3.2E-14

1.0E-02

6.9E-02

7.8E-01

7.1E-04

0.95 (0.90-0.99)

1.06 (1.04-1.07)

0.98 (0.96-1.00)

0.97 (0.90-1.05)

1.00 (0.96-1.03)

1.02 (1.01-1.03)

T2D Odds ratio

Chinese

Japanese

Korean

Malay/Filipino

Combined

rs12712928

East AsianPopuations OR (95% CI) P

4.2E-06

3.0E-06

1.7E-04

1.6E-01

3.2E-14

1.06 (1.03-1.09)

1.05 (1.03-1.07)

1.06 (1.03-1.10)

1.10 (0.96-1.25)

1.06 (1.04-1.07)

A

B

0.98 1.02 1.07 1.12 1.17

Figure 4: Forest plots of BMI-unadjusted meta-analysis association results at SIX3-SIX2 locus. Odds ratios (black boxes) and 95% confidence intervals (horizontal lines) for T2D associations at the lead East Asian variant (rs12721928) are presented(A) across ancestries of African-American (AFR), East Asian (EAS), European (EUR)2, Hispanic (HIS), and South Asian (SAS) individuals, and (B) within East Asians by four major East Asian populations (Chinese, Japanese, Korean, and Malay/Filipino combined due to small sample sizes). The size of the box is proportional to the sample size of each contributing population.

.CC-BY 4.0 International licensecertified by peer review) is the author/funder. It is made available under aThe copyright holder for this preprint (which was notthis version posted June 28, 2019. . https://doi.org/10.1101/685172doi: bioRxiv preprint

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FIGURELEGENDS820821Figure1:TwodistinctT2D-associationsignalsattheANK1-NKX6-3locusassociatedwithexpression822levelsoftwotranscriptsintwotissues.(A)RegionalassociationplotforEastAsiansex-combinedBMI-823unadjustedmeta-analysisatANK1-NKX6-3locus.ApproximateconditionalanalysisusingGTCAidentified824threedistinctT2D-associationsignalsatthislocus(signal1,rs33981001;signal2,rs62508166;signal3,825rs144239281,inorderofstrengthofassociation).Using1000GPhase3EastAsianLD,variantsare826coloredinredandbluewiththefirstandseconddistinctsignalsrespectively(leadvariantsrepresented827asdiamonds).(B)Variantrs12549902,inhighLD(EASLDr2=0.80,EURr2=0.83)withT2Dsignal1,shows828thestrongestassociationwithexpressionlevelsofNXK6-3inpancreaticisletsin118individuals16.(C)829Variantrs516946,inhighLD(EASLDr2=0.96,EURr2=0.80)withT2Dsignal2,showsthestrongest830associationwithexpressionlevelsofANK1insubcutaneousadiposetissuein770individuals19.As831rs62508166isnotavailableinthesubcutaneousadiposetissuedataset,avariantinperfectLD832(rs28591316)wasusedandisrepresentedbythebluediamondvariant.833834Figure2:EffectsizecomparisonofleadvariantsidentifiedinthisEastAsianT2DGWASBMI-835unadjustedmeta-analysisandpreviousEuropeanT2DGWASmeta-analysis2.836For343leadvariantsidentifiedfromthetwoBMIunadjustedmeta-analyses,per-alleleeffectsizes(β)837fromtheEuropeanmeta-analysis(y-axis)wereplottedagainstper-alleleeffectsizesfromthisEastAsian838meta-analysis(x-axis).(A)All343leadvariants;(B)290leadvariantswithminorallelefrequency≥5%in839bothancestries.Variantsarecoloredpurpleiftheyweresignificant(P<5x10-8)intheEastAsiananalysis840only,greeniftheyweresignificantinEuropeananalysisonly,andblueiftheyweresignificantinboth841theEastAsianandEuropeananalysis(seeMethodsandSupplementaryTable7).Thedasheddiagonal842linerepresentsthetrendlineacrossallplottedvariants.843844Figure3:rs117624659atNKX6-1locusexhibitsallelicdifferencesintranscriptionalactivity.(A)845rs117624659(purplediamond)showsthestrongestassociationwithT2Dintheregion.Variantsare846coloredbasedon1000GPhase3EastAsianLDwithrs117624659.(B)rs117624659andanadditional847candidatevariantrs142390274inhighpairwiseLD(r2>0.80)spana22kbregionapproximately75kb848upstreamofNKX6-1.rs117624659overlapsaregionofopenchromatininpancreaticisletsandlies849withinaregionconservedacrossvertebrates.(C)rs117624659-T,associatedwithincreasedriskofT2D,850showedgreatertranscriptionalactivityinanelementclonedinbothforwardandreverseorientations851withrespecttoNKX6-1inMIN6cellscomparedtors117624659-Candan“emptyvector”containinga852minimalpromoter.853854Figure4:ForestplotsofBMI-unadjustedmeta-analysisassociationresultsatSIX3-SIX2locus.Odds855ratios(blackboxes)and95%confidenceintervals(horizontallines)forT2DassociationsattheleadEast856Asianvariant(rs12721928)arepresented(A)acrossancestriesofAfrican-American(AFR),EastAsian857(EAS),European(EUR)2,Hispanic(HIS),andSouthAsian(SAS)individuals,and(B)withinfourmajorEast858Asianpopulations(Chinese,Japanese,Korean,andMalay/Filipinocombinedduetosmallsamplesizes).859Thesizeoftheboxisproportionaltothesamplesizeofeachcontributingpopulation.860861SupplementaryFigure1:Flowchartofstudydesign,depictingthedifferentdataanalysesperformed.862863SupplementaryFigure2:ManhattanplotforEastAsianT2Dmeta-analysisassociationresultsinmodel864unadjustedforBMI.-log10(P)fromfixedeffectsinversevarianceweightedgenome-widemeta-analysis865associationresultsforeachvariant(y-axis)wasplottedagainstthegenomicposition(hg19;x-axis).866KnownT2Dlociachievinggenome-widesignificance(P<5.0x10-8)meta-analysisareshowninblue.Loci867

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achievinggenome-widesignificancethatarepreviouslyunreportedforT2Dassociationareshownin868red.869870SupplementaryFigure3:Therelationshipbetweeneffectsizeandminorallelefrequency.Oddsratios871(y-axis)andminorallelefrequencies(x-axis)for178primaryassociationsignalsfromtheT2DBMI-872unadjustedmodels.873874SupplementaryFigure4:RegionalassociationplotsatsevenT2Dassociatedlociwiththestrongest875associationP-valueandmorethanfivedistinctassociationsignalsinEastAsians.(A)INS/IGF2/KCNQ1,876(B)CDKN2A/B,(C)PAX4/LEP,(D)CDKAL1,(E)HHEX/IDE,(F)CDC123/CAMK1D,and(G)TCF7L2.Variants877arecoloredbasedonEastAsian1000GPhase3LDwiththeleadvariantsforeachassociationsignal,878shownasdiamonds.879880SupplementaryFigure5:MiamiplotsofEastAsianT2Dmeta-analysisassociationresultsadjustedfor881BMI.Foreachplot,-log10(P)fromfixedeffectsinverse-varianceweightedgenome-widemeta-analysis882associationresultsforeachvariant(y-axis)wasplottedagainstthegenomicposition(hg19;x-axis).(A)883Sex-combinedmeta-analysesinmodelsunadjustedforBMI(top)andadjustedforBMI(bottom).Both884sex-combinedmodelsincludethesamesetofstudiesforcomparablesamplesize.NovelT2D-associated885lociareshowninblue(modelsunadjustedforBMI),purple(modelsadjustedforBMI),orgreen(both);886(B)sex-specificmeta-analysesformales(top)andfemales(bottom)withoutBMIadjustment;and(C)887sex-specificmeta-analysesformales(top)andfemales(bottom)withBMIadjustment.For(B)and(C),888locisignificantlyassociatedwithT2Dinfemalesonlyareshowninpurpleandlocisignificantlyassociated889withT2Dinmalesonlyareshowninblue.890891SupplementaryFigure6:Effectsizecomparisonofleadvariantsinsex-combinedmodelsunadjusted892andadjustedforBMI.At178leadvariantsidentifiedintheEastAsianBMI-unadjustedsex-combined893T2Dmeta-analysis,per-alleleeffectsizes(β)fromBMI-adjustedsex-combinedmodelswereplotted894againstBMI-unadjustedsex-combinedmodel.Bothsex-combinedmodelsincludethesamesetof895studiesforcomparablesamplesize.Errorbarsindicate95%confidenceintervals.Effectsizesbetween896thetwomodelsarehighlycorrelatedwithaPearsoncorrelationcoefficientr=0.99(SupplementaryTable8974).898899SupplementaryFigure7:Regionalplotsofmale-specificT2D-associatedlocus,ALDH2.(A)Malesonly,900(B)sex-combined,and(C)femalesonly.Foreachplot,-log10(P)fromassociationresultsforeachvariant901(y-axis)wasplottedagainstthegenomicposition(hg19;x-axis).Theleadvariantrs12231737plottedis902theleadvariantfromBMI-unadjustedmale-specificmeta-analysis,andalsothesex-combinedmeta-903analysisfromthesamesubsetofindividualsincludedinthesex-stratifiedanalyses.Thisleadvariant904rs12231737isinhighLDwithrs77768175,identifiedfromthelargerBMI-unadjustedsex-combined905meta-analysis(EastAsianr2=0.80).VariantsareshadedbasedonEastAsian1000GPhase3LDwiththe906leadvariant,shownasapurplediamond.907908SupplementaryFigure8:Effectsizecomparisonofcommonleadvariants(MAF≥5%)identifiedinEast909Asianmeta-analysisandpreviouslypublishedEuropeanT2DGWASmeta-analysis2.910For290leadvariantswithMAF≥5%inbothEastAsianandEuropeanBMI-unadjustedmeta-analyses,911per-alleleeffectsizes(β)fromMahajanetal.2(y-axis)wereplottedagainstper-alleleeffectsizesfrom912thisEastAsianmeta-analysis(x-axis).VariantsarecoloredpurpleiftheyweresignificantintheEast913Asianmeta-analysisonly,greeniftheyweresignificantinEuropeanmeta-analysisonly,andblueifthey914

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weresignificantinboththeEastAsianandEuropeanmeta-analyses.Errorbarsindicate95%confidence915intervals.(seeMethodsandSupplementaryTable7).916917SupplementaryFigure9:EffectsizecomparisonofleadvariantsidentifiedinEastAsianBMI-918unadjustedmeta-analysisandpreviouslypublishedEuropeanT2DGWASmeta-analysis2.919For343leadvariantsidentifiedfromthetwoBMI-unadjustedmeta-analyses,per-alleleeffectsizes(β)920fromaEuropeanmeta-analysis(y-axis)wereplottedagainstper-alleleeffectsizesfromthisEastAsian921meta-analysis(x-axis).(A)162leadvariantssignificantintheEastAsianmeta-analysis(purple)orboth922theEastAsianandEuropeanmeta-analysis(blue)and(B)192leadvariantssignificantintheEuropean923meta-analysis(green)orboththeEastAsianandEuropeanmeta-analysis(blue).Theseplotsincludeonly924onevariantperlocus,incontrasttoFigure2andSupplementaryFigure8.925926SupplementaryFigure10:T2D-associationnearZNF257anditsrelationshipwithapreviouslyreported927ZNF257inversion.TheleadT2D-associatedvariantrs142395395nearZNF257tagsaninversionobserved928almostexclusivelyinEastAsianindividuals.Weobservedanassociationbetweenthevariantstagging929theinversionandadecreasedriskforT2D.Inthereferencehaplotype(“Reference”),thereisno930disruptiontoZNF257anditspromoter,thusthereisnormalZNF257functionandnormalexpressionof931downstreamtranscripts.Whenthealternateallelesarepresent(“Inversion”),aninversionisobserved,932markedbytheseparationofthepromoterandfirsttwoexonsofZNF257fromtherestofthegeneand933movingthemover400kbupstream.WhilethishasnotbeenobservedtoaffectexpressionofZNF208,934ZNF43,orZNF100,theinversionresultsinalossofZNF257functionandalteredexpressionof935downstreamtargets33.936937SupplementaryFigure11:rs117624659atNKX6-1exhibitsallelicdifferencesintranscriptionalactivity.938(A)ChromatinmarksinpancreaticisletsintheintergenicregionnearNKX6-1fromtheUCSCGenome939Browser(hg19)spanningtheleadT2Dassociatedvariant,rs117624659,andtheonlyothercandidate940variantrs142390274inhighLD(EastAsianr2>0.80)withrs117624659.NKX6-1istranscribedfromright941toleft.rs117624659overlapsregionsofaccessiblechromatininhumanpancreaticisletsdetectedby942isletFAIRE-seqalongwithH3K4me1andH3K4me3ChIP-seq.Italsooverlapsaconservedregionin943vertebrates.ThetestedcandidateregulatoryDNAelementisrepresentedbyahorizontalblack944rectangleintheupperportionofthefigure.(B)rs117624659attheNKX6-1locusexhibitedsignificant945allelicdifferencesintranscriptionalactivityinMIN6mouseinsulinomacellsonasecondday.(C-D)946rs11762465attheNKX6-1locusdidnotexhibitsignificantallelicdifferencesintranscriptionalactivityin947832/13ratinsulinomacellsonexperimentalday1(C)orday2(D).948949SupplementaryFigure12:Forestplotsof49novelT2D-associatedvariantsusingdatafromfive950ancestriesintheDIAMANTEconsortium.T2Dmeta-analysisresultsforthe49novelT2D-associated951variantsidentifiedinthisEastAsianmeta-analysiswereobtainedfromtheotherfourancestrygroups952withintheDIAMANTEconsortium(African-American,European,Hispanic,andSouthAsian)for953comparison.Oddsratios(blackboxes)and95%confidenceintervals(horizontallines)fortheassociation954betweentheleadEastAsianvariantsandT2Dfromeachancestryarepresented,alongwithacombined955oddsratioandP-value.Thesizeoftheboxisproportionaltothesamplesizeofeachcontributing956ancestrygroup.957958SupplementaryFigure13:ForestplotofBMI-unadjustedEastAsianmeta-analysisassociationresults959atSIX3-SIX2locusfromeachcontributingcohort.Oddsratios(blackboxes)and95%confidence960intervals(horizontallines)forT2DassociationsattheleadEastAsianvariant(rs12721928)arepresented961

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foreachEastAsiancontributingcohort.Thesizeoftheboxisproportionaltothesamplesizeofeach962dataset.FullstudynamescanbefoundinSupplementaryTable1.963

.CC-BY 4.0 International licensecertified by peer review) is the author/funder. It is made available under aThe copyright holder for this preprint (which was notthis version posted June 28, 2019. . https://doi.org/10.1101/685172doi: bioRxiv preprint