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BLUEPRINT EpiVar Whole Genome Sequencing

BLUEPRINT EpiVar Whole Genome Sequencing

Type: Other
Archiver: European Genome-phenome Archive (EGA)

4 Datasets 12 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001002663	BLUEPRINT: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells (WGS)	Illumina HiSeq 2000	197
EGAD00001005192	BLUEPRINT EpiVar Whole Genome Sequencing Phase 2 genotypes		197
EGAD00001005199	BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 full summary statistics data include five molecular traits (eQTL, hQTL(H3K27ac), hQTL(H3K4me1), mQTL, and psiQTL) for three primary blood cells (Monocytes, Neutrophils, and T-cells). Each full summary statistics file contains the associations for all tested variants for each phenotype ID.		197
EGAD00001005200	BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 summary statistics of most significant association data include five molecular traits (eQTL, hQTL(H3K27ac), hQTL(H3K4me1), mQTL, and psiQTL) for three primary blood cells (Monocytes, Neutrophils, and T-cells). Each summary statistics file contains the most significant association for each phenotype ID.		197

Publications	Citations
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Cell 167: 2016 1398-1414.e24	559
Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells. Chen L, Yang R, Kwan T, Tang C, Watt S, Zhang Y, Bourque G, Ge B, Downes K, Frontini M, Ouwehand WH, Lin JW, Soranzo N, Pastinen T, Chen L. Sci Data 7: 2020 376	31
Functional annotation of genetic associations by transcriptome-wide association analysis provides insights into neutrophil development regulation. Yao Y, Yang J, Qin Q, Tang C, Li Z, Chen L, Li K, Ren C, Chen L, Rao S. Commun Biol 3: 2020 790	2
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ, Burdett T, Jupp S, Parkinson H, Papatheodorou I, Yates AD, Zerbino DR, Alasoo K. Nat Genet 53: 2021 1290-1299	367
Proximal and distal effects of genetic susceptibility to multiple sclerosis on the T cell epigenome. Roostaei T, Klein HU, Ma Y, Felsky D, Kivisäkk P, Connor SM, Kroshilina A, Yung C, Kaskow BJ, Shao X, Rhead B, Ordovás JM, Absher DM, Arnett DK, Liu J, Patsopoulos N, Barcellos LF, Weiner HL, De Jager PL. Nat Commun 12: 2021 7078	17
HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors. Ishigaki K, Lagattuta KA, Luo Y, James EA, Buckner JH, Raychaudhuri S. Nat Genet 54: 2022 393-402	83
Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity. Avalos D, Rey G, Ribeiro DM, Ramisch A, Dermitzakis ET, Delaneau O. Commun Biol 6: 2023 335	12
A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data. Little P, Liu S, Zhabotynsky V, Li Y, Lin DY, Sun W. Nat Commun 14: 2023 3030	17
Non-coding variants impact cis-regulatory coordination in a cell type-specific manner. Pushkarev O, van Mierlo G, Kribelbauer JF, Saelens W, Gardeux V, Deplancke B. Genome Biol 25: 2024 190	5
Fine-mapping and molecular characterisation of primary sclerosing cholangitis genetic risk loci. Goode EC, Fachal L, Panousis N, Moutsianas L, McIntyre RE, Bai BYH, Kawasaki N, Wittmann A, Raine T, Rushbrook SM, Anderson CA. Nat Commun 15: 2024 9594	2
Predicting cell type-specific epigenomic profiles accounting for distal genetic effects. Murphy AE, Beardall W, Rei M, Phuycharoen M, Skene NG. Nat Commun 15: 2024 9951	7
Integrating natural and engineered genetic variations to decode regulatory influence on blood traits. Tardaguila M, Von Schiller D, Colombo M, Gori I, Coomber EL, Vanderstichele T, Benaglio P, Chiereghin C, Gerety S, Vuckovic D, Landini A, Clerici G, Casiraghi A, Albers P, Ray-Jones H, Burnham KL, Tokolyi A, Persyn E, Spivakov M, Sankaran VG, Walter K, Kundu K, Pirastu N, Inouye M, Paul DS, Davenport EE, Sahlén P, Watt S, Soranzo N. Cell Rep 45: 2026 116937	0