Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
Open accessAbstract
Regulatory and coding variants are known to be enriched with associations identified by genome-wide association studies (GWASs) of complex disease, but their contributions to trait heritability are currently unknown. We applied variance-component methods to imputed genotype data for 11 common diseases to partition the heritability explained by genotyped SNPs (hg(2)) across functional categories (while accounting for shared variance due to linkage disequilibrium). Extensive simulations showed that in contrast to current estimates from GWAS summary statistics, the variance-component approach partitions heritability accurately under a wide range of complex-disease architectures. Across the 11 diseases DNaseI hypersensitivity sites (DHSs) from 217 cell types spanned 16% of imputed SNPs (and 24% of genotyped SNPs) but explained an average of 79% (SE = 8%) of hg(2) from imputed SNPs (5.1× enrichment; p = 3.7 × 10(-17)) and 38% (SE = 4%) of hg(2) from genotyped SNPs (1.6× enrichment, p = 1.0 × 10(-4)). Further enrichment was observed at enhancer DHSs and cell-type-specific DHSs. In contrast, coding variants, which span 1% of the genome, explained <10% of hg(2) despite having the highest enrichment. We replicated these findings but found no significant contribution from rare coding variants in independent schizophrenia cohorts genotyped on GWAS and exome chips. Our results highlight the value of analyzing components of heritability to unravel the functional architecture of common disease.
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Most disease-associated variation in complex diseases lies in noncoding regulatory regions of the genome.
“Mapping genetic variants to gene expression and PPI networks has been fruitful, but most disease-associated variation in complex diseases lies in the noncoding regulatory regions of the genome188.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [188]
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- Authors
- Gusev, A., Lee, S. H., Trynka, G., Finucane, H., Vilhjálmsson, B. J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., Kähler, A. K., Hultman, C. M., Purcell, S. M., McCarroll, S. A., Daly, M., Pasaniuc, B., Sullivan, P. F., Neale, B. M., Wray, N. R., Raychaudhuri, S., Price, A. L., Ripke, S., Neale, B. M., Corvin, A., Walters, J. T. R., Farh, K.-H., Holmans, P. A., Lee, P., Bulik-Sullivan, B., Collier, D. A., Huang, H., Pers, T. H., Agartz, I., Agerbo, E., Albus, M., Alexander, M., Amin, F., Bacanu, S. A., Begemann, M., Belliveau, R. A., Bene, J., Bergen, S. E., Bevilacqua, E., Bigdeli, T. B., Black, D. W., Børglum, A. D., Bruggeman, R., Buccola, N. G., Buckner, R. L., Byerley, W., Cahn, W., Cai, G., Campion, D., Cantor, R. M., Carr, V. J., Carrera, N., Catts, S. V., Chambert, K. D., Chan, R. C. K., Chen, R. Y. L., Chen, E. Y. H., Cheng, W., Cheung, E. F. C., Chong, S. A., Cloninger, C. R., Cohen, D., Cohen, N., Cormican, P., Craddock, N., Crowley, J. J., Curtis, D., Davidson, M., Davis, K. L., Degenhardt, F., Del Favero, J., DeLisi, L. E., Demontis, D., Dikeos, D., Dinan, T., Djurovic, S., Donohoe, G., Drapeau, E., Duan, J., Dudbridge, F., Durmishi, N., Eichhammer, P., Eriksson, J., Escott-Price, V., Essioux, L., Fanous, A. H., Farrell, M. S., Frank, J., Franke, L., Freedman, R., Freimer, N. B., Friedl, M., Friedman, J. I., Fromer, M., Genovese, G., Georgieva, L., Gershon, E. S., Giegling, I., Giusti-Rodrguez, P., Godard, S., Goldstein, J. I., Golimbet, V., Gopal, S., Gratten, J., Grove, J., de Haan, L., Hammer, C., Hamshere, M. L., Hansen, M., Hansen, T., Haroutunian, V., Hartmann, A. M., Henskens, F. A., Herms, S., Hirschhorn, J. N., Hoffmann, P., Hofman, A., Hollegaard, M. V., Hougaard, D. M., Ikeda, M., Joa, I., Julià, A., Kahn, R. S., Kalaydjieva, L., Karachanak-Yankova, S., Karjalainen, J., Kavanagh, D., Keller, M. C., Kelly, B. J., Kennedy, J. L., Khrunin, A., Kim, Y., Klovins, J., Knowles, J. A., Konte, B., Kucinskas, V., Kucinskiene, Z. A., Kuzelova-Ptackova, H., Kähler, A. K., Laurent, C., Keong, J. L. C., Lee, S. H., Legge, S. E., Lerer, B., Li, M., Li, T., Liang, K.-Y., Lieberman, J., Limborska, S., Loughland, C. M., Lubinski, J., Lnnqvist, J., Macek, M., Magnusson, P. K. E., Maher, B. S., Maier, W., Mallet, J., Marsal, S., Mattheisen, M., Mattingsdal, M., McCarley, R. W., McDonald, C., McIntosh, A. M., Meier, S., Meijer, C. J., Melegh, B., Melle, I., Mesholam-Gately, R. I., Metspalu, A., Michie, P. T., Milani, L., Milanova, V., Mokrab, Y., Morris, D. W., Mors, O., Mortensen, P. B., Murphy, K. C., Murray, R. M., Myin-Germeys, I., Mller-Myhsok, B., Nelis, M., Nenadic, I., Nertney, D. A., Nestadt, G., Nicodemus, K. K., Nikitina-Zake, L., Nisenbaum, L., Nordin, A., O’Callaghan, E., O’Dushlaine, C., O’Neill, F. A., Oh, S.-Y., Olincy, A., Olsen, L., Van Os, J., Pantelis, C., Papadimitriou, G. N., Papiol, S., Parkhomenko, E., Pato, M. T., Paunio, T., Pejovic-Milovancevic, M., Perkins, D. O., Pietilinen, O., Pimm, J., Pocklington, A. J., Powell, J., Price, A., Pulver, A. E., Purcell, S. M., Quested, D., Rasmussen, H. B., Reichenberg, A., Reimers, M. A., Richards, A. L., Roffman, J. L., Roussos, P., Ruderfer, D. M., Salomaa, V., Sanders, A. R., Schall, U., Schubert, C. R., Schulze, T. G., Schwab, S. G., Scolnick, E. M., Scott, R. J., Seidman, L. J., Shi, J., Sigurdsson, E., Silagadze, T., Silverman, J. M., Sim, K., Slominsky, P., Smoller, J. W., So, H.-C., Spencer, C. C. A., Stahl, E. A., Stefansson, H., Steinberg, S., Stogmann, E., Straub, R. E., Strengman, E., Strohmaier, J., Stroup, T. S., Subramaniam, M., Suvisaari, J., Svrakic, D. M., Szatkiewicz, J. P., Sderman, E., Thirumalai, S., Toncheva, D., Tooney, P. A., Tosato, S., Veijola, J., Waddington, J., Walsh, D., Wang, D., Wang, Q., Webb, B. T., Weiser, M., Wildenauer, D. B., Williams, N. M., Williams, S., Witt, S. H., Wolen, A. R., Wong, E. H. M., Wormley, B. K., Wu, J. Q., Xi, H. S., Zai, C. C., Zheng, X., Zimprich, F., Wray, N. R., Stefansson, K., Visscher, P. M., Adolfsson, R., Andreassen, O. A., Blackwood, D. H. R., Bramon, E., Buxbaum, J. D., Brglum, A. D., Cichon, S., Darvasi, A., Domenici, E., Ehrenreich, H., Esko, T., Gejman, P. V., Gill, M., Gurling, H., Hultman, C. M., Iwata, N., Jablensky, A. V., Jönsson, E. G., Kendler, K. S., Kirov, G., Knight, J., Lencz, T., Levinson, D. F., Li, Q. S., Liu, J., Malhotra, A. K., McCarroll, S. A., McQuillin, A., Moran, J. L., Mortensen, P. B., Mowry, B. J., Nthen, M. M., Ophoff, R. A., Owen, M. J., Palotie, A., Pato, C. N., Petryshen, T. L., Posthuma, D., Rietschel, M., Riley, B. P., Rujescu, D., Sham, P. C., Sklar, P., St. Clair, D., Weinberger, D. R., Wendland, J. R., Werge, T., Daly, M. J., Sullivan, P. F., O’Donovan, M. C., Ripke, S., O’Dushlaine, C., Chambert, K., Moran, J. L., Kähler, A. K., Akterin, S., Bergen, S., Magnusson, P. K. E., Neale, B. M., Ruderfer, D., Scolnick, E., Purcell, S., McCarroll, S., Sklar, P., Hultman, C. M., & Sullivan, P. F.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Massachusetts Institute of Technology (US)
- The University of Queensland (AU)
- Karolinska Institutet (SE)
- University of North Carolina at Chapel Hill (US)
- University of California, Los Angeles (US)
- Corresponding author
- Gusev, Alexander
- ORCID
- Gusev, Alexander
- Trynka, Gosia
- Finucane, Hilary
- Vilhjálmsson, Bjarni J.
- Xu, Han
- Zang, Chongzhi
- Raychaudhuri, Soumya
- Corvin, Aiden
- Walters, James T.R.
- Holmans, Peter A.
- Lee, Phil
- Collier, David A.
- Huang, Hailiang
- Pers, Tune H.
- Agartz, Ingrid
- Agerbo, Esben
- Albus, Margot
- Bacanu, Silviu A.
- Begemann, Martin
- Bene, Judit
- Bigdeli, Tim B.
- Black, Donald W.
- Børglum, Anders D.
- Bruggeman, Richard
- Buccola, Nancy G.
- Buckner, Randy L.
- Cahn, Wiepke
- Campion, Dominique
- Cantor, Rita M.
- Carr, Vaughan J.
- Carrera, Noa
- Catts, Stanley V.
- Chan, Raymond C.K.
- Chen, Eric Y.H.
- Cheng, Wei
- Cheung, Eric F.C.
- Chong, Siow Ann
- Cloninger, C. Robert
- Cohen, David
- Cohen, Nadine
- Craddock, Nick
- Crowley, James J.
- Curtis, David
- Davidson, Michael
- Davis, Kenneth L.
- Degenhardt, Franziska
- DeLisi, Lynn E.
- Demontis, Ditte
- Dinan, Timothy
- Djurovic, Srdjan
- Donohoe, Gary
- Drapeau, Elodie
- Duan, Jubao
- Dudbridge, Frank
- Eriksson, Johan
- Fanous, Ayman H.
- Farrell, Martilias S.
- Frank, Josef
- Franke, Lude
- Freedman, Robert
- Freimer, Nelson B.
- Friedman, Joseph I.
- Fromer, Menachem
- Genovese, Giulio
- Gershon, Elliot S.
- Giegling, Ina
- Goldstein, Jacqueline I.
- Gopal, Srihari
- Gratten, Jacob
- Grove, Jakob
- Hammer, Christian
- Hamshere, Marian L.
- Hansen, Thomas
- Haroutunian, Vahram
- Hartmann, Annette M.
- Herms, Stefan
- Hirschhorn, Joel N.
- Hoffmann, Per
- Hollegaard, Mads V.
- Hougaard, David M.
- Ikeda, Masashi
- Joa, Inge
- Julià, Antonio
- Kahn, René S.
- Karachanak-Yankova, Sena
- Karjalainen, Juha
- Kavanagh, David
- Keller, Matthew C.
- Kelly, Brian J.
- Kennedy, James L.
- Kim, Yunjung
- Knowles, James A.
- Konte, Bettina
- Kuzelova-Ptackova, Hana
- Legge, Sophie E.
- Lerer, Bernard
- Li, Miaoxin
- Li, Tao
- Lieberman, Jeffrey
- Loughland, Carmel M.
- Maher, Brion S.
- Marsal, Sara
- Mattheisen, Manuel
- Mattingsdal, Morten
- McCarley, Robert W.
- McDonald, Colm
- McIntosh, Andrew M.
- Meier, Sandra
- Meijer, Carin J.
- Melle, Ingrid
- Metspalu, Andres
- Michie, Patricia T.
- Milani, Lili
- Milanova, Vihra
- Mokrab, Younes
- Morris, Derek W.
- Mors, Ole
- Murphy, Kieran C.
- Murray, Robin M.
- Nelis, Mari
- Nestadt, Gerald
- Nicodemus, Kristin K.
- O’Neill, F. Anthony
- Olsen, Line
- Pantelis, Christos
- Papadimitriou, George N.
- Papiol, Sergi
- Pato, Michele T.
- Paunio, Tiina
- Pejovic-Milovancevic, Milica
- Perkins, Diana O.
- Pocklington, Andrew J.
- Powell, John
- Quested, Digby
- Reichenberg, Abraham
- Reimers, Mark A.
- Richards, Alexander L.
- Roffman, Joshua L.
- Roussos, Panos
- Salomaa, Veikko
- Sanders, Alan R.
- Schall, Ulrich
- Schubert, Christian R.
- Schulze, Thomas G.
- Scott, Rodney J.
- Seidman, Larry J.
- Shi, Jianxin
- Silagadze, Teimuraz
- Sim, Kang
- Slominsky, Petr
- Smoller, Jordan W.
- So, Hon-Cheong
- Spencer, Chris C.A.
- Steinberg, Stacy
- Straub, Richard E.
- Strengman, Eric
- Strohmaier, Jana
- Stroup, T. Scott
- Subramaniam, Mythily
- Suvisaari, Jaana
- Szatkiewicz, Jin P.
- Toncheva, Draga
- Tooney, Paul A.
- Tosato, Sarah
- Veijola, Juha
- Waddington, John
- Wang, Dai
- Wang, Qiang
- Webb, Bradley T.
- Weiser, Mark
- Wildenauer, Dieter B.
- Williams, Nigel M.
- Williams, Stephanie
- Witt, Stephanie H.
- Wolen, Aaron R.
- Wu, Jing Qin
- Xi, Hualin Simon
- Zai, Clement C.
- Zheng, Xuebin
- Zimprich, Fritz
- Visscher, Peter M.
- Adolfsson, Rolf
- Andreassen, Ole A.
- Blackwood, Douglas H.R.
- Bramon, Elvira
- Buxbaum, Joseph D.
- Cichon, Sven
- Domenici, Enrico
- Ehrenreich, Hannelore
- Esko, Tõnu
- Gill, Michael
- Iwata, Nakao
- Jablensky, Assen V.
- Jönsson, Erik G.
- Kendler, Kenneth S.
- Kirov, George
- Knight, Jo
- Lencz, Todd
- Levinson, Douglas F.
- Li, Qingqin S.
- Liu, Jianjun
- Malhotra, Anil K.
- McQuillin, Andrew
- Mowry, Bryan J.
- Ophoff, Roel A.
- Owen, Michael J.
- Palotie, Aarno
- Pato, Carlos N.
- Petryshen, Tracey L.
- Rietschel, Marcella
- Riley, Brien P.
- Rujescu, Dan
- Sham, Pak C.
- Weinberger, Daniel R.
- Wendland, Jens R.
- Werge, Thomas
- O’Donovan, Michael C.
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2014-11
- Volume
- 95
- Issue
- 5
- Pages
- 535-552
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC4225595
- OpenAlex
- W2159417227
- Cited by
- 544
- References
- 88
- Citations by year
- 2026: 16 · 2025: 26 · 2024: 30 · 2023: 29 · 2022: 56 · 2021: 42 · 2020: 43 · 2019: 58 · 2018: 59 · 2017: 65 · 2016: 73 · 2015: 45 · 2014: 2
- FWCI
- 40.40
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (publishedVersion, other-oa)
- Research Explorer (The University of Manchester) (publishedVersion)
- VU Research Portal (publishedVersion, other-oa)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- EPubDev Repository (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Lancaster EPrints (Lancaster University) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion)
- Lirias (submittedVersion)
- GRO (submittedVersion)
- Pure Amsterdam UMC (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Research Portal (Queen's University Belfast) (submittedVersion)
- RUNE (Research UNE) (submittedVersion)
- Research Publications (Maastricht University) (submittedVersion, other-oa)
- NOVA (University of Newcastle Australia) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- UNC Libraries
- Funders
- Hertz Foundation
- Wellcome Trust (076113)
- Lundbeckfonden (R155-2014-1724)
- National Institutes of Health (5r01ar063759-07, 5u01mh094432-04)
- Medical Research Council (MR/L010305/1)
- Australian Research Council (FT0991360, DE130100614)
- National Health and Medical Research Council (613602)
- National Institute of Mental Health (U01MH096296, U01 MH094432, R01MH085548, T32MH020030, R01MH101244)
- National Human Genome Research Institute (R03HG006731, 1U01HG0070033)
- National Institute of General Medical Sciences (R01GM105857, F32GM106584)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01-AR063759)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- regulatory variants, enhancers, common complex diseases, variance components, linkage disequilibrium, coding variants, rare coding variants, schizophrenia, genome-wide association study
- MeSH terms
- Computer Simulation, Humans, Models, Genetic, Genetic Variation, Open Reading Frames, Genetic Diseases, Inborn, Inheritance Patterns, Regulatory Elements, Transcriptional, Genome-Wide Association Study
About these checks
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