Abdulla S, Aevermann B, Assis P, Badajoz S, Bell SM, Bezzi E, Cakir B, Chaffer J, Chambers S, Cherry JM et al (2025) CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data. Nucl Acids Res 53:D886-d900. https://doi.org/10.1093/nar/gkae1142

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aghamohammadi A, Abolhassani H, Biglari M, Abolmaali S, Moazzami K, Tabatabaeiyan M, Asgarian-Omran H, Parvaneh N, Mirahmadian M, Rezaei N (2011) Analysis of switched memory B cells in patients with IgA deficiency. Int Arch Allergy Immunol 156:462–468. https://doi.org/10.1159/000323903

Article  CAS  PubMed  Google Scholar 

Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine J-C, Geurts P, Aerts J et al (2017) SCENIC: single-cell regulatory network inference and clustering. Nat Methods 14:1083–1086. https://doi.org/10.1038/nmeth.4463

Article  CAS  PubMed  PubMed Central  Google Scholar 

Amaya-Uribe L, Rojas M, Azizi G, Anaya JM, Gershwin ME (2019) Primary immunodeficiency and autoimmunity: A comprehensive review. J Autoimmun 99:52–72. https://doi.org/10.1016/j.jaut.2019.01.011

Article  CAS  PubMed  Google Scholar 

Auton A, Abecasis GR, Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Donnelly P, Eichler EE et al (2015) A global reference for human genetic variation. Nature 526:68–74. https://doi.org/10.1038/nature15393

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bronson PG, Chang D, Bhangale T, Seldin MF, Ortmann W, Ferreira RC, Urcelay E, Pereira LF, Martin J, Plebani A (2016) Common variants at PVT1, ATG13–AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency. Nature genetics 48:1425–1429

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bulik-Sullivan BK, Loh P-R, Finucane HK, Ripke S, Yang J, Patterson N, Daly MJ, Price AL, Neale BM, Schizophrenia Working Group of the Psychiatric Genomics, C (2015) LD score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat Genet 47:291–295. https://doi.org/10.1038/ng.3211

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bulik-Sullivan B, Finucane HK, Anttila V, Gusev A, Day FR, Loh PR, Duncan L, Perry JR, Patterson N, Robinson EB et al (2015) An atlas of genetic correlations across human diseases and traits. Nat Genet 47:1236–1241. https://doi.org/10.1038/ng.3406

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chiou J, Geusz RJ, Okino M-L, Han JY, Miller M, Melton R, Beebe E, Benaglio P, Huang S, Korgaonkar K (2021) Interpreting type 1 diabetes risk with genetics and single-cell epigenomics. Nature 594:398–402

Article  CAS  PubMed  PubMed Central  Google Scholar 

Consortium G (2020) The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369:1318–1330

Article  Google Scholar 

International IBD Genetics Consortium (IIBDGC), Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G (2013) Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Gent 45:1353–1360

Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor S-S, Gervais O (2021) An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs. J Hepatol 75:572–581

Article  CAS  PubMed  PubMed Central  Google Scholar 

De Lange KM, Moutsianas L, Lee JC, Lamb CA, Luo Y, Kennedy NA, Jostins L, Rice DL, Gutierrez-Achury J, Ji S-G (2017) Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nat Genet 49:256–261

Article  CAS  PubMed  PubMed Central  Google Scholar 

de Leeuw CA, Mooij JM, Heskes T, Posthuma D (2015) MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput Biol 11:e1004219. https://doi.org/10.1371/journal.pcbi.1004219

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong X, Antao OQ, Song W, Sanchez GM, Zembrzuski K, Koumpouras F, Lemenze A, Craft J, Weinstein JS (2021) Type I Interferon-activated STAT4 regulation of follicular helper T cell-dependent cytokine and immunoglobulin production in lupus. Arthritis Rheumatol 73:478–489. https://doi.org/10.1002/art.41532

Article  CAS  PubMed  PubMed Central  Google Scholar 

Eldjarn GH, Ferkingstad E, Lund SH, Helgason H, Magnusson OT, Gunnarsdottir K, Olafsdottir TA, Halldorsson BV, Olason PI, Zink F et al (2023) Large-scale plasma proteomics comparisons through genetics and disease associations. Nature 622:348–358. https://doi.org/10.1038/s41586-023-06563-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Elmentaite R, Kumasaka N, Roberts K, Fleming A, Dann E, King HW, Kleshchevnikov V, Dabrowska M, Pritchard S, Bolt L et al (2021) Cells of the human intestinal tract mapped across space and time. Nature 597:250–255. https://doi.org/10.1038/s41586-021-03852-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Finucane HK, Reshef YA, Anttila V, Slowikowski K, Gusev A, Byrnes A, Gazal S, Loh PR, Lareau C, Shoresh N et al (2018) Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat Genet 50:621–629. https://doi.org/10.1038/s41588-018-0081-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Foley CN, Staley JR, Breen PG, Sun BB, Kirk PDW, Burgess S, Howson JMM (2021) A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits. Nat Commun 12:764. https://doi.org/10.1038/s41467-020-20885-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gazal S, Weissbrod O, Hormozdiari F, Dey KK, Nasser J, Jagadeesh KA, Weiner DJ, Shi H, Fulco CP, O’Connor LJ (2022) Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity. Nat Genet 54:827–836

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ghoussaini M, Mountjoy E, Carmona M, Peat G, Schmidt EM, Hercules A, Fumis L, Miranda A, Carvalho-Silva D, Buniello A (2021) Open targets genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. Nucleic Acids Res 49:D1311–D1320

Article  CAS  PubMed  PubMed Central  Google Scholar 

Giambartolomei C, Vukcevic D, Schadt EE, Franke L, Hingorani AD, Wallace C, Plagnol V (2014) Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet 10:e1004383. https://doi.org/10.1371/journal.pgen.1004383

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grosserichter-Wagener C, Franco-Gallego A, Ahmadi F, Moncada-Vélez M, Dalm VA, Rojas JL, Orrego JC, Correa Vargas N, Hammarström L, Schreurs MW et al (2020) Defective formation of IgA memory B cells, Th1 and Th17 cells in symptomatic patients with selective IgA deficiency. Clin Transl Immun 9:e1130. https://doi.org/10.1002/cti2.1130

Article  CAS  Google Scholar 

Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx BW, Jansen R, de Geus EJ, Boomsma DI, Wright FA et al (2016) Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet 48:245–252. https://doi.org/10.1038/ng.3506

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hemani G, Zheng J, Elsworth B, Wade KH, Haberland V, Baird D, Laurin C, Burgess S, Bowden J, Langdon R et al (2018) The MR-Base platform supports systematic causal inference across the human phenome. Elife. https://doi.org/10.7554/eLife.34408

Article  PubMed  PubMed Central  Google Scholar 

Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC (2022) Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nature Genet 54:1640–1651

Article  CAS  PubMed  PubMed Central