Search – Common Metabolic Diseases Genome Atlas

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Publication
released
Systematic Functional Characterization of Candidate Causal Genes for Type 2 Diabetes Risk Variants
Thomsen SK, Ceroni A, van de Bunt M, et al.
December 2016;(65(12)):3805-3811.
- PMID:27554474
- doi:10.2337/db16-0361
Publication
released
Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes
Norbert Bittner, Chenfu Shi, Danyun Zhao, et al.
Ann Rheum Dis. 2024-03-13;:ard-2023-224945.
- PMID:38479789
- doi:10.1136/ard-2023-224945
Publication
released
An integrated map of cell type-specific gene expression in pancreatic islets
Ruth M Elgamal, Parul Kudtarkar, Rebecca L Melton, et al.
Diabetes. 2023-15-08;(db230130)
- PMID:37582230
- doi:10.2337/db23-0130
Publication
released
Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes
Fan Zhang, Anna Helena Jonsson, Aparna Nathan, et al.
Nature. 2023-11-08;623(7987):616-624.
URL: https://doi.org/10.7303/syn52297840
Data summary: CITE-seq single-cell expression matrices and sequencing and bulk expression matrices are available…
URL: https://arkportal.synapse.org/Explore/Datasets/DetailsPage?id=syn52297840
Data summary: Associated genotype and clinical data are available through the Arthritis and Autoimmune and…
URL: https://immunogenomics.io/ampra2/
Data summary: A cell browser website is available to visualize our data and results.
Data summary: AMP Phase 1 single-cell data from ref. 8 are available on Immport (SDY998). PEAC clinical trial…
URL: https://github.com/Immunogenomics/RA_Atlas_CITEseq/
Data summary: The source code for the analyses is available at GitHub
URL: https://zenodo.org/record/8118599
Data summary: The source code for the analyses is available at zenodo
Publication
released
Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression
Katia K. Mattis, Nicole A. J. Krentz, Christoph Metzendorf, et al.
Diabetologia. 2023-01-12;
- doi:10.1007/s00125-022-05856-6
- PMID:36633628
Publication
released
Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
Paola Benaglio, Han Zhu, Mei-Lin Okino, et al.
Cell Genomics. 2022-12-14;2(12):100214.
Publication
released
Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk
Ricardo D’Oliveira Albanus, Xuming Tang, Henry J. Taylor, et al.
bioRxiv. 2022-11-14;
- doi:10.1101/2022.11.12.516291
Publication
released
The developmental impacts of natural selection on human pelvic morphology
Mariel Young, Daniel Richard, Mark Grabowski, et al.
Sci Adv. 2022-08-19;8(33):eabq4884.
Publication
released
A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids
Shweta Ramdas,Jonathan Judd,Sarah E Graham,Stavroula Kanoni,Yuxuan Wang,Ida Surakka,Brandon Wenz,Shoa L Clarke,Alessandra Chesi,Andrew Wells,Konain Fatima Bhatti,Sailaja Vedantam,Thomas W Winkler,Adam E Locke,Eirini Marouli,Greg J M Zajac,Kuan-Han H Wu,Ioanna Ntalla,Qin Hui,Derek Klarin,Austin T Hilliard,Zeyuan Wang,Chao Xue,Gudmar Thorleifsson,Anna Helgadottir,Daniel F Gudbjartsson,Hilma Holm,Isleifur Olafsson,Mi Yeong Hwang,Sohee Han,Masato Akiyama,Saori Sakaue,Chikashi Terao,Masahiro Kanai,Wei Zhou,Ben M Brumpton,Humaira Rasheed,Aki S Havulinna,Yogasudha Veturi,Jennifer Allen Pacheco,Elisabeth A Rosenthal,Todd Lingren,QiPing Feng,Iftikhar J Kullo,Akira Narita,Jun Takayama,Hilary C Martin,Karen A Hunt,Bhavi Trivedi,Jeffrey Haessler,Franco Giulianini,Yuki Bradford,Jason E Miller,Archie Campbell,Kuang Lin,Iona Y Millwood,Asif Rasheed,George Hindy,Jessica D Faul,Wei Zhao,David R Weir,Constance Turman,Hongyan Huang,Mariaelisa Graff,Ananyo Choudhury,Dhriti Sengupta,Anubha Mahajan,Michael R Brown,Weihua Zhang,Ketian Yu,Ellen M Schmidt,Anita Pandit,Stefan Gustafsson,Xianyong Yin,Jian'an Luan,Jing-Hua Zhao,Fumihiko Matsuda,Hye-Mi Jang,Kyungheon Yoon,Carolina Medina-Gomez,Achilleas Pitsillides,Jouke Jan Hottenga,Andrew R Wood,Yingji Ji,Zishan Gao,Simon Haworth,Ruth E Mitchell,Jin Fang Chai,Mette Aadahl,Anne A Bjerregaard,Jie Yao,Ani Manichaikul,Wen-Jane Lee,Chao Agnes Hsiung,Helen R Warren,Julia Ramirez,Jette Bork-Jensen,Line L Kårhus,Anuj Goel,Maria Sabater-Lleal,Raymond Noordam,Pala Mauro,Floris Matteo,Aaron F McDaid,Pedro Marques-Vidal,Matthias Wielscher,Stella Trompet,Naveed Sattar,Line T Møllehave,Matthias Munz,Lingyao Zeng,Jianfeng Huang,Bin Yang,Alaitz Poveda,Azra Kurbasic,Sebastian Schönherr,Lukas Forer,Markus Scholz,Tessel E Galesloot,Jonathan P Bradfield,Sanni E Ruotsalainen,E Warwick Daw,Joseph M Zmuda,Jonathan S Mitchell,Christian Fuchsberger,Henry Christensen,Jennifer A Brody,Phuong Le,Mary F Feitosa,Mary K Wojczynski,Daiane Hemerich,Michael Preuss,Massimo Mangino,Paraskevi Christofidou,Niek Verweij,Jan W Benjamins,Jorgen Engmann,Tsao L Noah,Anurag Verma,Roderick C Slieker,Ken Sin Lo,Nuno R Zilhao,Marcus E Kleber,Graciela E Delgado,Shaofeng Huo,Daisuke D Ikeda,Hiroyuki Iha,Jian Yang,Jun Liu,Ayşe Demirkan,Hampton L Leonard,Jonathan Marten,Carina Emmel,Börge Schmidt,Laura J Smyth,Marisa Cañadas-Garre,Chaolong Wang,Masahiro Nakatochi,Andrew Wong,Nina Hutri-Kähönen,Xueling Sim,Rui Xia,Alicia Huerta-Chagoya,Juan Carlos Fernandez-Lopez,Valeriya Lyssenko,Suraj S Nongmaithem,Alagu Sankareswaran,Marguerite R Irvin,Christopher Oldmeadow,Han-Na Kim,Seungho Ryu,Paul R H J Timmers,Liubov Arbeeva,Rajkumar Dorajoo,Leslie A Lange,Gauri Prasad,Laura Lorés-Motta,Marc Pauper,Jirong Long,Xiaohui Li,Elizabeth Theusch,Fumihiko Takeuchi,Cassandra N Spracklen,Anu Loukola,Sailalitha Bollepalli,Sophie C Warner,Ya Xing Wang,Wen B Wei,Teresa Nutile,Daniela Ruggiero,Yun Ju Sung,Shufeng Chen,Fangchao Liu,Jingyun Yang,Katherine A Kentistou,Bernhard Banas,Anna Morgan,Karina Meidtner,Lawrence F Bielak,Jennifer A Smith,Prashantha Hebbar,Aliki-Eleni Farmaki,Edith Hofer,Maoxuan Lin,Maria Pina Concas,Simona Vaccargiu,Peter J van der Most,Niina Pitkänen,Brian E Cade,Sander W van der Laan,Kumaraswamy Naidu Chitrala,Stefan Weiss,Amy R Bentley,Ayo P Doumatey,Adebowale A Adeyemo,Jong Young Lee,Eva R B Petersen,Aneta A Nielsen,Hyeok Sun Choi,Maria Nethander,Sandra Freitag-Wolf,Lorraine Southam,Nigel W Rayner,Carol A Wang,Shih-Yi Lin,Jun-Sing Wang,Christian Couture,Leo-Pekka Lyytikäinen,Kjell Nikus,Gabriel Cuellar-Partida,Henrik Vestergaard,Bertha Hidalgo,Olga Giannakopoulou,Qiuyin Cai,Morgan O Obura,Jessica van Setten,Karen Y He,Hua Tang,Natalie Terzikhan,Jae Hun Shin,Rebecca D Jackson,Alexander P Reiner,Lisa Warsinger Martin,Zhengming Chen,Liming Li,Takahisa Kawaguchi,Joachim Thiery,Joshua C Bis,Lenore J Launer,Huaixing Li,Mike A Nalls,Olli T Raitakari,Sahoko Ichihara,Sarah H Wild,Christopher P Nelson,Harry Campbell,Susanne Jäger,Toru Nabika,Fahd Al-Mulla,Harri Niinikoski,Peter S Braund,Ivana Kolcic,Peter Kovacs,Tota Giardoglou,Tomohiro Katsuya,Dominique de Kleijn,Gert J de Borst,Eung Kweon Kim,Hieab H H Adams,M Arfan Ikram,Xiaofeng Zhu,Folkert W Asselbergs,Adriaan O Kraaijeveld,Joline W J Beulens,Xiao-Ou Shu,Loukianos S Rallidis,Oluf Pedersen,Torben Hansen,Paul Mitchell,Alex W Hewitt,Mika Kähönen,Louis Pérusse,Claude Bouchard,Anke Tönjes,Yii-Der Ida Chen,Craig E Pennell,Trevor A Mori,Wolfgang Lieb,Andre Franke,Claes Ohlsson,Dan Mellström,Yoon Shin Cho,Hyejin Lee,Jian-Min Yuan,Woon-Puay Koh,Sang Youl Rhee,Jeong-Taek Woo,Iris M Heid,Klaus J Stark,Martina E Zimmermann,Henry Völzke,Georg Homuth,Michele K Evans,Alan B Zonderman,Ozren Polasek,Gerard Pasterkamp,Imo E Hoefer,Susan Redline,Katja Pahkala,Albertine J Oldehinkel,Harold Snieder,Ginevra Biino,Reinhold Schmidt,Helena Schmidt,Stefania Bandinelli,George Dedoussis,Thangavel Alphonse Thanaraj,Patricia A Peyser,Norihiro Kato,Matthias B Schulze,Giorgia Girotto,Carsten A Böger,Bettina Jung,Peter K Joshi,David A Bennett,Philip L De Jager,Xiangfeng Lu,Vasiliki Mamakou,Morris Brown,Mark J Caulfield,Patricia B Munroe,Xiuqing Guo,Marina Ciullo,Jost B Jonas,Nilesh J Samani,Jaakko Kaprio,Päivi Pajukanta,Teresa Tusié-Luna,Carlos A Aguilar-Salinas,Linda S Adair,Sonny Augustin Bechayda,H Janaka de Silva,Ananda R Wickremasinghe,Ronald M Krauss,Jer-Yuarn Wu,Wei Zheng,Anneke I den Hollander,Dwaipayan Bharadwaj,Adolfo Correa,James G Wilson,Lars Lind,Chew-Kiat Heng,Amanda E Nelson,Yvonne M Golightly,James F Wilson,Brenda Penninx,Hyung-Lae Kim,John Attia,Rodney J Scott,D C Rao,Donna K Arnett,Mark Walker,Laura J Scott,Heikki A Koistinen,Giriraj R Chandak,Josep M Mercader,Clicerio Gonzalez Villalpando,Lorena Orozco,Myriam Fornage,E Shyong Tai,Rob M van Dam,Terho Lehtimäki,Nish Chaturvedi,Mitsuhiro Yokota,Jianjun Liu,Dermot F Reilly,Amy Jayne McKnight,Frank Kee,Karl-Heinz Jöckel,Mark I McCarthy,Colin N A Palmer,Veronique Vitart,Caroline Hayward,Eleanor Simonsick,Cornelia M van Duijn,Zi-Bing Jin,Fan Lu,Haretsugu Hishigaki,Xu Lin,Winfried März,Vilmundur Gudnason,Jean-Claude Tardif,Guillaume Lettre,Leen M T Hart,Petra J M Elders,Daniel J Rader,Scott M Damrauer,Meena Kumari,Mika Kivimaki,Pim van der Harst,Tim D Spector,Ruth J F Loos,Michael A Province,Esteban J Parra,Miguel Cruz,Bruce M Psaty,Ivan Brandslund,Peter P Pramstaller,Charles N Rotimi,Kaare Christensen,Samuli Ripatti,Elisabeth Widén,Hakon Hakonarson,Struan F A Grant,Lambertus Kiemeney,Jacqueline de Graaf,Markus Loeffler,Florian Kronenberg,Dongfeng Gu,Jeanette Erdmann,Heribert Schunkert,Paul W Franks,Allan Linneberg,J Wouter Jukema,Amit V Khera,Minna Männikkö,Marjo-Riitta Jarvelin,Zoltan Kutalik,Cucca Francesco,Dennis O Mook-Kanamori,Ko Willems van Dijk,Hugh Watkins,David P Strachan,Niels Grarup,Peter Sever,Neil Poulter,Wayne Huey-Herng Sheu,Jerome I Rotter,Thomas M Dantoft,Fredrik Karpe,Matt J Neville,Nicholas J Timpson,Ching-Yu Cheng,Tien-Yin Wong,Chiea Chuen Khor,Hengtong Li,Charumathi Sabanayagam,Annette Peters,Christian Gieger,Andrew T Hattersley,Nancy L Pedersen,Patrik K E Magnusson,Dorret I Boomsma,Eco J C de Geus,L Adrienne Cupples,Joyce B J van Meurs,Arfan Ikram,Mohsen Ghanbari,Penny Gordon-Larsen,Wei Huang,Young Jin Kim,Yasuharu Tabara,Nicholas J Wareham,Claudia Langenberg,Eleftheria Zeggini,Jaakko Tuomilehto,Johanna Kuusisto,Markku Laakso,Erik Ingelsson,Goncalo Abecasis,John C Chambers,Jaspal S Kooner,Paul S de Vries,Alanna C Morrison,Scott Hazelhurst,Michèle Ramsay,Kari E North,Martha Daviglus,Peter Kraft,Nicholas G Martin,John B Whitfield,Shahid Abbas,Danish Saleheen,Robin G Walters,Michael V Holmes,Corri Black,Blair H Smith,Aris Baras,Anne E Justice,Julie E Buring,Paul M Ridker,Daniel I Chasman,Charles Kooperberg,Gen Tamiya,Masayuki Yamamoto,David A van Heel,Richard C Trembath,Wei-Qi Wei,Gail P Jarvik,Bahram Namjou,M Geoffrey Hayes,Marylyn D Ritchie,Pekka Jousilahti,Veikko Salomaa,Kristian Hveem,Bjørn Olav Åsvold,Michiaki Kubo,Yoichiro Kamatani,Yukinori Okada,Yoshinori Murakami,Bong-Jo Kim,Unnur Thorsteinsdottir,Kari Stefansson,Jifeng Zhang,Y Eugene Chen,Yuk-Lam Ho,Julie A Lynch,Philip S Tsao,Kyong-Mi Chang,Kelly Cho,Christopher J O'Donnell,John M Gaziano,Peter Wilson,Karen L Mohlke,Timothy M Frayling,Joel N Hirschhorn,Sekar Kathiresan,Michael Boehnke,Million Veterans Program; Global Lipids Genetics Consortium; Struan Grant,Pradeep Natarajan,Yan V Sun,Andrew P Morris,Panos Deloukas,Gina Peloso,Themistocles L Assimes,Cristen J Willer,Xiang Zhu,Christopher D Brown.
Am J Hum Genet. 2022-08-04;109(8):1366-1387.
Publication
released
Characterizing cis-regulatory elements using single-cell epigenomics
Sebastian Preissl, Kyle J Gaulton, Bing Ren.
Nat Rev Genet. 2022-07-15;
- doi:10.1038/s41576-022-00509-1
- PMID:35840754
Publication
released
Cohesin-mediated loop anchors confine the locations of human replication origins
Daniel J Emerson # 1 2 3 , Peiyao A Zhao # 4 , Ashley L Cook # 1 2 3 , et al.
Nature. 2022-06-08;606(7915):812-819.
Data summary: All new raw data created in this manuscript have been uploaded to the 4D Nucleome portal and will…
Publication
released
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity
Steven Gazal, Omer Weissbrod, Farhad Hormozdiari, et al.
Nature Genetics. 2022-06-06;(2022)
- doi:10.1101/2021.08.02.21261488
URL: https://doi.org/10.5281/zenodo.6354007
Data summary: The list of 19,995 genes, summary statistics of the 63 independent traits, training and validation…
Data summary: Links for all data sets used to create S2G strategies are provided in Supplementary Table 26.
URL: http://www.ukbiobank.ac.uk/
Data summary: Access to the UK Biobank resource is available via application
URL: https://www.ebi.ac.uk/gwas/api/search/downloads/full
Data summary: The GWAS Catalog is available
URL: https://raw.githubusercontent.com/opentargets/genetics-gold-standards/master/gold_standards/processed/gwas_gold_standards.191108.tsv
Data summary: Open Targets SNP–gene pairs are available
URL: https://www.dropbox.com/s/kz2c49rpm2yanf5/all_byCS_rev1.txt?dl=0
Data summary: SNP–gene pairs from ref48 are available
URL: https://alkesgroup.broadinstitute.org/cS2G/code
Data summary: The code to estimate precision and recall of S2G strategies and the code to create combined S2G…
URL: https://doi.org/10.5281/zenodo.6415925
Data summary: The code to estimate precision and recall of S2G strategies and the code to create combined S2G…
Publication
released
Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk
Adam W Turner, Shengen Shawn Hu, Jose Verdezoto Mosquera, et al.
Nat Genet.. 2022-06-01;54(6):804-816.
File format: TSV
URL: https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-022-01069-0/MediaObjects/41588_2022_1069_MOESM10_ESM.xlsx
Data summary: Supplementary Data 6 Chromatin accessibility QTLs within individual coronary artery cell types,…
File format: TSV
URL: https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-022-01069-0/MediaObjects/41588_2022_1069_MOESM11_ESM.xlsx
Data summary: Supplementary Data 7 Chromatin accessibility QTLs from bulk coronary artery ATAC-seq data,…
Publication
released
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells
Kousuke Mouri, Michael H. Guo, Carl G. de Boer, et al.
Nat Genet. 2022-05-01;54(5):603-612.
- doi:10.1038/s41588-022-01056-5
- PMID:35513721
Publication
released
A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells
Sen Li, Xiaolin Zong, Liheng Zhang, et al.
Adipocyte. 2022-04-17;11(1):239-249.
Publication
released
Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions
Jiang Xu, Sanjeev Kumar, Nan Hua, et al.
bioRxiv. 2022-02-12;
- doi:10.1101/2022.02.03.478915
Publication
released
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
Peter Orchard, Nandini Manickam, Christa Ventresca, et al.
Genome Res. 2021-11-23;31(12):2258-2275.
URL: https://zenodo.org/search?page=1&size=20&q=5009200
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178735
Publication
released
Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits
Matthew C. Pahl, Claudia A. Doege, Kenyaita M. Hodge, et al.
Nat Commun. 2021-11-19;12(1):6749.
Publication
released
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
Hannah J Perrin, Kevin W Currin, Swarooparani Vadlamudi, et al.
PLoS Genet. 2021-10-26;17(10):e1009865.
Publication
released
Systematic analysis of binding of transcription factors to noncoding variants
Jian Yan, Yunjiang Qiu, André M. Ribeiro dos Santos, et al.
Nature. 2021-1-27;
- doi:10.1038/s41586-021-03211-0
- PMID:33505025
Publication
released
Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
Shubham Khetan, Susan Kales, Romy Kursawe, et al.
Nat Commun. 2021-09-02;12(1):5242.
URL: https://cmdga.org/publications/63f879cd-f426-4495-a12d-103fdac5867c/
URL: https://zenodo.org/record/4974390#.YzHqHi-B39A
Data summary: Linked to Zenodo
Publication
released
Joint disease-specificity at the regulatory base-pair level
Pushpanathan Muthuirulan, Dewei Zhao, Mariel Young, et al.
Nat Commun. 2021-07-06;12(1):4161.
Publication
released
Genetic effects on liver chromatin accessibility identify disease regulatory variants
Kevin W Currin, Michael R Erdos, Narisu Narisu, et al.
Am J Hum Genet.. 2021-05-20;S0002-9297(21):00185-3.
Publication
released
Large-scale genetic association and single cell accessible chromatin mapping defines cell type-specific mechanisms of type 1 diabetes risk
Joshua Chiou, Ryan J Geusz, Mei-Lin Okino, et al.
Nature. 2021-05-19;594(7863):398-402.
- doi:10.1038/s41586-021-03552-w
- PMID:34012112
Publication
released
Cardiac cell type-specific gene regulatory programs and disease risk association
James D Hocker, Olivier B Poirion, Fugui Zhu, et al.
Sci Adv.. 2021-05-14;7(20):eabf1444.

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Showing 25 of 187 results