Search – Common Metabolic Diseases Genome Atlas

Showing 25 of 101 results

View All

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
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
Kevin W Currin, Hannah J Perrin, Gautam K Pandey, et al.
Genome Res. 2025-05-20;
- doi:10.1101/gr.279741.124
- PMID:40393811
Publication
released
A comprehensive spatio-cellular map of the human hypothalamus
John A. Tadross, Lukas Steuernagel, Georgina K. C. Dowsett, et al.
Nature. 2025-02-05;639(8055):708-716.
URL: https://www.nature.com/articles/s41586-024-08504-8
Publication
released
Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2
Sheridan H Littleton, Khanh B Trang, Christina M Volpe, et al.
Cell Genomics. 2024-05-08;
Data summary: Hi-C, RNA-seq, ATAC-seq, single-nucleus RNA-seq, and single-nucleus ATAC-seq data have been…
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241592
Data summary: Raw and processed Hi-C data GEO: GSE241592
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241050
Data summary: Raw and processed RNA-seq data GEO: GSE241050
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241591
Data summary: Raw and processed ATAC-seq data GEO: GSE241591
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241594
Data summary: Raw and processed single-nucleus RNA-seq data GEO: GSE241594
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241593
Data summary: Raw and processed single-nucleus ATAC-seq data GEO: GSE241593;
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
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation
Arushi Varshney Arushi Varshney, Nandini Manickam, Peter Orchard, et al.
bioRxiv. 2023-12-15;
URL: https://www.biorxiv.org/content/10.1101/2023.12.15.571696v2
Publication
released
Cell-Type Composition Affects Adipose Gene Expression Associations With Cardiometabolic Traits
Sarah M Brotman, Anniina Oravilahti, Jonathan D Rosen, et al.
Diabetes. 2023-11-01;72(11):1707-1718.
Publication
released
A comparative atlas of single-cell chromatin accessibility in the human brain
Yang Eric Li, Sebastian Preissl, Michael Miller, et al.
Science. 2023-10-13;382(6667)
Publication
released
An atlas of healthy and injured cell states and niches in the human kidney
Blue B. Lake, Rajasree Menon, Seth Winfree, et al.
Nature. 2023-07-19;619(7970):585-594.
URL: https://www.nature.com/articles/s41586-023-05769-3
Publication
released
Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes
Kristina M. Garske, Asha Kar, Caroline Comenho, et al.
Nat Commun. 2023-07-14;14(1):4214.
Publication
released
Lineage-specific differences and regulatory networks governing human chondrocyte development
Daniel Richard, Steven Pregizer, Divya Venkatasubramanian, et al.
Elife. 2023-03-15;15:12:e79925
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
Long-range chromosomal interactions increase and mark repressed gene expression during adipogenesis
Kristina M Garske, Caroline Comenho, David Z Pan, et al.
Epigenetics. 2022-12-01;17(13):1849-1862.
Available supplemental data: website
File format: other format
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129574
Data summary: Assay for transposase accessible chromatin (ATAC) -seq libraries were produced from human primary…
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
Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution
Charles A Herring, Rebecca K Simmons, Saskia Freytag, et al.
Cell. 2022-10-31;185(23):4428-4447.
- doi:10.1016/j.cell.2022.09.039
- PMID:36318921
Available supplemental data: website
File format: other format
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168408
Data summary: Single-nuclei RNA-seq and single-nuclei ATAC-seq data have been deposited at GEO under accession…
Available supplemental data: website
URL: http://brain.listerlab.org/
Data summary: Accompanying interactive browsers for this study are available at http://brain.listerlab.org.
Available supplemental data: website
URL: http://development.psychencode.org/
Data summary: All data for the Velmeshev et al. study is publicly available through the Sequence Read Archive,…
Available supplemental data: website
URL: https://www.sciencedirect.com/science/article/pii/S0092867422012582?via%3Dihub#sec4.1
Data summary: All original code has been deposited at Zenodo and is publicly available as of the date of…
Available supplemental data: website
URL: https://www.sciencedirect.com/science/article/pii/S0092867422012582?via%3Dihub#sec4.2.1
Data summary: Any additional information required to reanalyze the data reported in this work paper is available…
Publication
released
Genetic regulation of RNA splicing in human pancreatic islets
Goutham Atla, Silvia Bonàs-Guarch, Mirabai Cuenca-Ardura, et al.
Genome Biol. 2022-09-15;23(1):196.
URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02757-0#Sec36
Available supplemental data: website
File format: text
URL: https://zenodo.org/record/6546807#.Y-wbZi-B39B
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
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease
Hongbo Liu, Tomohito Doke, Dong Guo, et al.
Nature Genetics. 2022-06-16;54:950–962.
- PMID:35710981
- doi:10.1038/s41588-022-01097-w
Available supplemental data: website
URL: https://github.com/hbliu/Kidney_Epi_Pri
Data summary: Customized code used in the present study is available at github
Available supplemental data: website
URL: https://doi.org/10.5281/zenodo.6392494
Data summary: Zenodo
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
A single-cell atlas of human and mouse white adipose tissue
Margo P. Emont, Christopher Jacobs, Adam L. Essene, et al.
Nature. 2022-03-16;603(7903):926-933.
URL: https://www.nature.com/articles/s41586-022-04518-2
Publication
released
A mechanistic framework for cardiometabolic and coronary artery diseases
Simon Koplev, Marcus Seldin, Katyayani Sukhavasi, et al.
Nat Cardiovasc Res. 2022-01-12;1(1):85-100.
Available supplemental data: website
URL: http://starnet.mssm.edu
Data summary: The website was developed with a Python Flask backend and a sqlite3 database, with an application…
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 status

Available supplemental data

Publication year

Journal

Published by

Has dataset

publication_year!!

published_by!

published_by!!!

Showing 25 of 101 results