biostudies-literatureENCODE Project ConsortiumIntramural NIH HHSNIDDK NIH HHSNHGRI NIH HHSNCI NIH HHSWellcome TrustNIGMS NIH HHS57-74https://www.ebi.ac.uk/biostudies/studies/S-EPMC3439153biostudies-literatureUnknown489(7414)The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variaNatureAn integrated encyclopedia of DNA elements in the human genome.PMC3439153R01 DK065806R01HG003541R01HG004456-03R01HG003700K99 HG006698U54HG004557U54HG004558U54HG004555T32 GM007205U54 HG004563U01 HG004561R01HG003988U54HG004576RC2HG005679U01HG004695095908U01HG004571U54HG004592U54HG004570P30 CA016086R37 DK044746U41HG004568R01HG003143RC2 HG005679RC2 HG005573U54 HG004570U54 HG004592U01 HG004695R01 HG003700U54 HG004576RC2 HG005591U01 HG004571R01 HG003988U54 HG004557U54 HG004558U54 HG004555U54HG004563R01 DK054369ZIA HG200341R01 HG003143U41 HG004568R01 HG003541U01HG004561R01 HG004456ZIA HG200323RC2HG005591P30 CA045508R01 HG005085Visel ALuo OJBickel PJStergachis ABCharos ABettinger KWhite KPYan KKGunter CRam OPepke SHussami NSchlesinger FMieczkowska JOFarnham PJRozowsky JRamirez LBowling KMO'Geen HChrast JMu XJMikkelsen TSXu XFisher-Aylor KIGiddings MCDreszer TRKeefe DBoychenko VLondon DParker SCPazin MJRaney BJKutyavin TVBrent MAbdelhamid RFPartridge ECFoissac SPenalva LOWold BGillespie SLochovsky LHoffman MMYu YStamatoyannopoulos JARisk BAEaton MLAldred SFLuscombe NMBhinge AAHarmanci ABansal ASahu ADSimon JMTrout DMiller WParker SLReed BSnyder MAbsher DMBirney EWong MCPei BRuan YVaquerizas JMRuan XDong XSchaner MRHoeckendorf BLoveland JKarczewski KJLowdon RFFrankish ANotredame CKhurana ESaunders GPetrykowska HMCentanin LChen XKim SKSuzuki AMHarte RLibbrecht MWGonzalez JMDunham ILassmann TBernstein BEKelly CJRosenbloom KRKundaje AGilbert JDunn DSafi AKasowski MKingswood CDespacio-Reyes GWilming LWashietl SMa LJohnson NJungreis IJohnson RBarrell DHeitner SGFullwood MJDillon LALiu ZReynolds APGertz JSearle SRaha DMieczkowski PACao ARSobral DDoyle FRobyr DDuttagupta RAlioto TFurey TSHansen RMalladi VSAkey JMPauli FPennachio LAGriffiths ELearned KWalters NSteward CTrinklein NDWrobel JMoran JHeermann SWilder SPMeadows SKAken BSandhu KSValencia AJohnson EMLong JCNavas PKent WHannon GJQu HENCODE Project ConsortiumLagarde JWeaver MABlow MJThomas SReddy TEKellner TIssner RKim MJDavis CALieb JDSchneider SBates DLWexler JRLacroute PDjebali SGist ERibeca PAddleman NXi HSBhanvadia RRTress MLMeyer LRBarson GKay MEbersol AKSkancke JBaker DLandt SGMin RGao HDerrien TLee BKZaleski CDekker JWeng ZIyer STanzer ARashid NUAdams LBShahab ABatzoglou SAltshuler RCDobin ADavidson CKapranov PHumbert RJohnson AKMudge JLevy SEKheradpour PManthravadi DDeSalvo GMoqtaderi ZStruhl KSchaub MAJin VXErnst JCline MSGiresi PGVernot BPusey BTakahashi HHarris RSCayting PEpstein CBHaussler DBanfai BYan YDiegel MJHendrix DATenenbaum SABhardwaj NThurman REGordon AMuratet MADurham TLin MFXue CBoatman LLin WLin XSanyal AMacCoss MJSandstrom RSTaylor JAlexander RPElnitski LLamarre-Vincent NReymond APark PJJain PVictorsen ABeal KRodriguez JMSchaeffer LJain GSheffield NCSidow AHardison RCGonzalez DDomanus MMonahan HBender MBrown JBGerstein MNewberry JKokocinski FFrum TGoren AAmrhein HDiekhans MRoach VMerkel AFlicek PMaier CWIyer VRChoudhury ABaer MTMyers RMBattenhouse AZhang ZZHaugen EKhatun JKellis MAntonarakis SEBoyle APKyriazopoulou-Panagiotopoulou SJha SMarinov GKCrawford GEPreall JBAdar SAuer TCurado JMargulies EHvan Baren MJTapanari ELotakis DGrubert FHowald CGreven MDrenkow JWeissman SMLi GMaddren MHunt TLi QNewberry KMNguyen EDEggleston TCarninci PBarber GPCanfield TKTilgner HPresaud KDumais EVarley KEDavis NSDumais JEzkurdia IGroudine MRynes EInoue DNeph SJChakrabortty SMiotto BVierstra JZheng MSboner AShoresh NStamatoyannopoulos GSnow CSisu CLukk MHerrero JGreen EDWitt HBalasundaram GBell IBell KGruhl FGunawardena HPAntoshechkin IZhang ZSinn RKaul RZhang XKharchenko PVKuiper HCLi JJEichenlaub MFastuca MShi MZhang JMaurano MTZhang MNesmith ASCollins PJMukherjee GKu MNeri FVVong SFeingold EARoder MMcDaniell RMSanchez MEZhuang JCoyne MJBilmes JANoble WSMueller CLajoie BRPatacsil DTruong TKirchmaier SHarrow JWard LDMortazavi AWong WHGrasfeder LLLee KWhitfield TWCheng YAnaya MEastman CZadissa AFrietze SFerreira PBussotti GHariharan MCheng CLindahl-Allen MBalasubramanian SKarolchik DWilliams BANi YGingeras TRShestak CGiardine BWu LLu ZHuang HWang HSabo PWang JWang LLian JGood PJWang PYip KYWang TBuske OJWu WBoley NPMcCue KGasper CBignell ABerry AXie LHabegger LKirkup VMGarg KPartridge EYang XReinhardt RSchertel LShowers KAEuskirchen GPark EHayashizaki YWittbrodt BGuigo RSloan CAMariotti MLeng JSong LFejes-Toth KSee LHBrazma AAbyzov AShafer AOVielmetter JAuerbach RKIyengar SKarmakar SSlifer THubbard TJKing BWinter DSammeth MCross MKDorschner MOOuyang ZLam HByron RFleming JDBatut PWittbrodt JfalseAn integrated encyclopedia of DNA elements in the human genome.The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this varia2012-01-01T00:00:00Z2012 Sep2026-04-29T13:49:04.492Z2019-03-27T00:57:50ZS-EPMC34391532295561610.1038/nature11247