{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T10:32:21Z","timestamp":1794479541402,"version":"4.9.1"},"reference-count":110,"publisher":"Springer Science and Business Media LLC","issue":"8140","license":[{"start":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T00:00:00Z","timestamp":1793145600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T00:00:00Z","timestamp":1793145600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2026,11,12]]},"DOI":"10.1038\/s41586-026-10721-2","type":"journal-article","created":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T16:02:03Z","timestamp":1793203323000},"page":"417-428","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Rare and common genetic variants shape single-cell immune gene expression"],"prefix":"10.1038","volume":"659","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5168-6979","authenticated-orcid":false,"given":"Anna S. E.","family":"Cuomo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-5543-2810","authenticated-orcid":false,"given":"Eleanor","family":"Spenceley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4561-305X","authenticated-orcid":false,"given":"Hope A.","family":"Tanudisastro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Blake","family":"Bowen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7422-2288","authenticated-orcid":false,"given":"Albert","family":"Henry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao Lawrence","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0285-0426","authenticated-orcid":false,"given":"Angli","family":"Xue","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7719-0859","authenticated-orcid":false,"given":"Wei","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew J.","family":"Welland","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samantha J.","family":"Bryen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oscar A.","family":"Dong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arthur S.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey M.","family":"Pullin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristof","family":"Wing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Owen","family":"Tang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1154-3011","authenticated-orcid":false,"given":"Michael P.","family":"Gray","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Franklin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Harper","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Silk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katalina","family":"Bobowik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Stuckey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1216-5457","authenticated-orcid":false,"given":"John","family":"Marshall","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vivian","family":"Bakiris","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caitlin","family":"Uren","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rachael A.","family":"McCloy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bindu Swapna","family":"Madala","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2084-9477","authenticated-orcid":false,"given":"Amy","family":"Miniter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caitlin","family":"Bartie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Drew R.","family":"Neavin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Qiao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0514-0400","authenticated-orcid":false,"given":"Eyal","family":"Ben-David","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1326-4069","authenticated-orcid":false,"given":"Ling","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6947-8537","authenticated-orcid":false,"given":"Kyle Kai-How","family":"Farh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stuart M.","family":"Grieve","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1294-7739","authenticated-orcid":false,"given":"Tung","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Wallace","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1091-8734","authenticated-orcid":false,"given":"Jennifer","family":"Piscionere","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2840-4851","authenticated-orcid":false,"given":"Owen M.","family":"Siggs","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hannah","family":"Nicholas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrina M.","family":"de Lange","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5123-5999","authenticated-orcid":false,"given":"Alex W.","family":"Hewitt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gemma A.","family":"Figtree","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5771-2290","authenticated-orcid":false,"given":"Daniel G.","family":"MacArthur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5070-4124","authenticated-orcid":false,"given":"Joseph E.","family":"Powell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,10,28]]},"reference":[{"key":"10721_CR1","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1038\/s43586-022-00188-6","volume":"3","author":"F Aguet","year":"2023","unstructured":"Aguet, F. et al. Molecular quantitative trait loci. Nat. Rev. Methods Prim. 3, 4 (2023).","journal-title":"Nat. Rev. Methods Prim."},{"key":"10721_CR2","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.tig.2020.08.009","volume":"37","author":"BD Umans","year":"2021","unstructured":"Umans, B. D., Battle, A. & Gilad, Y. Where are the disease-associated eQTLs?\u00a0Trends Genet. 37, 109\u2013124 (2021).","journal-title":"Trends Genet."},{"key":"10721_CR3","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1038\/s41576-023-00599-5","volume":"24","author":"ASE Cuomo","year":"2023","unstructured":"Cuomo, A. S. E., Nathan, A., Raychaudhuri, S., MacArthur, D. G. & Powell, J. E. Single-cell genomics meets human genetics. Nat. Rev. Genet. 24, 535\u2013549 (2023).","journal-title":"Nat. Rev. Genet."},{"key":"10721_CR4","doi-asserted-by":"publisher","first-page":"D998","DOI":"10.1093\/nar\/gkae1070","volume":"53","author":"M Cerezo","year":"2025","unstructured":"Cerezo, M. et al. The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity. Nucleic Acids Res. 53, D998\u2013D1005 (2025).","journal-title":"Nucleic Acids Res."},{"key":"10721_CR5","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1038\/s41588-021-00913-z","volume":"53","author":"U V\u00f5sa","year":"2021","unstructured":"V\u00f5sa, U. et al. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. Nat. Genet. 53, 1300\u20131310 (2021).","journal-title":"Nat. Genet."},{"key":"10721_CR6","doi-asserted-by":"publisher","first-page":"1398","DOI":"10.1016\/j.cell.2016.10.026","volume":"167","author":"L Chen","year":"2016","unstructured":"Chen, L. et al. Genetic drivers of epigenetic and transcriptional variation in human immune cells. Cell 167, 1398\u20131414 (2016).","journal-title":"Cell"},{"key":"10721_CR7","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1038\/s41588-021-00800-7","volume":"53","author":"MJ Bonder","year":"2021","unstructured":"Bonder, M. J. et al. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat. Genet. 53, 313\u2013321 (2021).","journal-title":"Nat. Genet."},{"key":"10721_CR8","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1126\/science.aaz1776","volume":"369","author":"GTEx Consortium","year":"2020","unstructured":"GTEx Consortium The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318\u20131330 (2020).","journal-title":"Science"},{"key":"10721_CR9","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1038\/nature22403","volume":"546","author":"H Kilpinen","year":"2017","unstructured":"Kilpinen, H. et al. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 546, 370\u2013375 (2017).","journal-title":"Nature"},{"key":"10721_CR10","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1016\/j.cell.2018.10.022","volume":"175","author":"BJ Schmiedel","year":"2018","unstructured":"Schmiedel, B. J. et al. Impact of genetic polymorphisms on human immune cell gene expression. Cell 175, 1701\u20131715 (2018).","journal-title":"Cell"},{"key":"10721_CR11","doi-asserted-by":"publisher","first-page":"n214","DOI":"10.1136\/bmj.n214","volume":"372","author":"W Mn","year":"2021","unstructured":"Weedon, M. N. et al. Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation. BMJ\u00a0372, n214 (2021).","journal-title":"BMJ"},{"key":"10721_CR12","doi-asserted-by":"publisher","first-page":"e1006643","DOI":"10.1371\/journal.pgen.1006643","volume":"13","author":"S Kasela","year":"2017","unstructured":"Kasela, S. et al. Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells. PLoS Genet. 13, e1006643 (2017).","journal-title":"PLoS Genet."},{"key":"10721_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04365-8","volume":"9","author":"Y Momozawa","year":"2018","unstructured":"Momozawa, Y. et al. IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes. Nat. Commun. 9, 2427 (2018).","journal-title":"Nat. Commun."},{"key":"10721_CR14","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-61670-9","volume":"16","author":"NI Panousis","year":"2025","unstructured":"Panousis, N. I. et al. Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases. Nat. Commun. 16, 7204 (2025).","journal-title":"Nat. Commun."},{"key":"10721_CR15","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-00366-1","volume":"8","author":"S Kim-Hellmuth","year":"2017","unstructured":"Kim-Hellmuth, S. et al. Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. Nat. Commun. 8, 266 (2017).","journal-title":"Nat. Commun."},{"key":"10721_CR16","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf3041","volume":"376","author":"S Yazar","year":"2022","unstructured":"Yazar, S. et al. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease. Science 376, eabf3041 (2022).","journal-title":"Science"},{"key":"10721_CR17","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41586-022-04713-1","volume":"606","author":"A Nathan","year":"2022","unstructured":"Nathan, A. et al. Single-cell eQTL models reveal dynamic T cell state dependence of disease loci. Nature 606, 120\u2013128 (2022).","journal-title":"Nature"},{"key":"10721_CR18","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1038\/s41588-022-01066-3","volume":"54","author":"B Soskic","year":"2022","unstructured":"Soskic, B. et al. Immune disease risk variants regulate gene expression dynamics during CD4 T cell activation. Nat. Genet. 54, 817\u2013826 (2022).","journal-title":"Nat. Genet."},{"key":"10721_CR19","doi-asserted-by":"publisher","first-page":"2739","DOI":"10.1038\/s41588-024-02019-8","volume":"56","author":"C Tian","year":"2024","unstructured":"Tian, C. et al. Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases. Nat. Genet. 56, 2739\u20132752 (2024).","journal-title":"Nat. Genet."},{"key":"10721_CR20","doi-asserted-by":"publisher","first-page":"1104","DOI":"10.1038\/s41593-022-01128-z","volume":"25","author":"J Bryois","year":"2022","unstructured":"Bryois, J. et al. Cell-type-specific cis-eQTLs in eight human brain cell types identify novel risk genes for psychiatric and neurological disorders. Nat. Neurosci. 25, 1104\u20131112 (2022).","journal-title":"Nat. Neurosci."},{"key":"10721_CR21","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1038\/s41588-024-01702-0","volume":"56","author":"HM Natri","year":"2024","unstructured":"Natri, H. M. et al. Cell-type-specific and disease-associated expression quantitative trait loci in the human lung. Nat. Genet. 56, 595\u2013604 (2024).","journal-title":"Nat. Genet."},{"key":"10721_CR22","doi-asserted-by":"crossref","unstructured":"Alegbe, T. et al. Cell-type-resolved genetic variation shapes inflammatory bowel disease risk. Nature 656, 129\u2013139 (2026).","DOI":"10.1038\/s41586-026-10627-z"},{"key":"10721_CR23","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1038\/s41588-021-00801-6","volume":"53","author":"J Jerber","year":"2021","unstructured":"Jerber, J. et al. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nat. Genet. 53, 304\u2013312 (2021).","journal-title":"Nat. Genet."},{"key":"10721_CR24","doi-asserted-by":"publisher","unstructured":"Tanudisastro, H. A. et al. Tandem repeat variation shapes immune cell type-specific gene expression. Nature https:\/\/doi.org\/10.1038\/s41586-026-10438-2 (2026).","DOI":"10.1038\/s41586-026-10438-2"},{"key":"10721_CR25","unstructured":"Henry, A. et al. Single-cell genetics identifies cell-type-specific causal mechanisms in complex traits and diseases. Nat. Genet. (in press)."},{"key":"10721_CR26","doi-asserted-by":"publisher","unstructured":"Xue, A. et al. Genetic variants shape single-cell chromatin accessibility and disease risk. Nature https:\/\/doi.org\/10.1038\/s41586-026-11173-4 (2026).","DOI":"10.1038\/s41586-026-11173-4"},{"key":"10721_CR27","doi-asserted-by":"publisher","unstructured":"Zhou, W. et al. Efficient and accurate mixed model association tool for single-cell eQTL analysis. Nat. Genet. https:\/\/doi.org\/10.1038\/s41588-026-02798-2 (in press).","DOI":"10.1038\/s41588-026-02798-2"},{"key":"10721_CR28","doi-asserted-by":"crossref","unstructured":"van der Wijst, M. et al. The single-cell eQTLGen consortium. eLife 9, e52155 (2020).","DOI":"10.7554\/eLife.52155"},{"key":"10721_CR29","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.1111\/rssb.12388","volume":"82","author":"G Wang","year":"2020","unstructured":"Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. A simple new approach to variable selection in regression, with application to genetic fine mapping. J. R. Stat. Soc. Ser. B 82, 1273\u20131300 (2020).","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"10721_CR30","doi-asserted-by":"crossref","unstructured":"Brown, M., Greenwood, E., Zeng, B., Powell, J. E. & Gibson, G. Effect of all-but-one conditional analysis for eQTL isolation in peripheral blood. Genetics 223, iyac162 (2023).","DOI":"10.1093\/genetics\/iyac162"},{"key":"10721_CR31","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/s41588-024-01982-6","volume":"57","author":"SM Brotman","year":"2025","unstructured":"Brotman, S. M. et al. Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits. Nat. Genet. 57, 180\u2013192 (2025).","journal-title":"Nat. Genet."},{"key":"10721_CR32","doi-asserted-by":"publisher","DOI":"10.1126\/science.ads7373","volume":"389","author":"K Jaganathan","year":"2025","unstructured":"Jaganathan, K. et al. Predicting expression-altering promoter mutations with deep learning. Science 389, eads7373 (2025).","journal-title":"Science"},{"key":"10721_CR33","doi-asserted-by":"crossref","unstructured":"Ferraro, N. M. et al. Transcriptomic signatures across human tissues identify functional rare genetic variation. Science 369, eaaz5900 (2020).","DOI":"10.1101\/786053"},{"key":"10721_CR34","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1016\/j.ajhg.2011.05.029","volume":"89","author":"MC Wu","year":"2011","unstructured":"Wu, M. C. et al. Rare-variant association testing for sequencing data with the sequence kernel association test. Am. J. Hum. Genet. 89, 82\u201393 (2011).","journal-title":"Am. J. Hum. Genet."},{"key":"10721_CR35","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.cell.2018.12.015","volume":"176","author":"K Jaganathan","year":"2019","unstructured":"Jaganathan, K. et al. Predicting splicing from primary sequence with deep learning. Cell 176, 535\u2013548 (2019).","journal-title":"Cell"},{"key":"10721_CR36","doi-asserted-by":"publisher","first-page":"1415","DOI":"10.1038\/s41588-021-00931-x","volume":"53","author":"S Sakaue","year":"2021","unstructured":"Sakaue, S. et al. A cross-population atlas of genetic associations for 220 human phenotypes. Nat. Genet. 53, 1415\u20131424 (2021).","journal-title":"Nat. Genet."},{"key":"10721_CR37","doi-asserted-by":"publisher","first-page":"3318","DOI":"10.1038\/s41388-021-01765-x","volume":"40","author":"W-T Yang","year":"2021","unstructured":"Yang, W.-T., Chen, M., Xu, R. & Zheng, P.-S. PRDM4 inhibits cell proliferation and tumorigenesis by inactivating the PI3K\/AKT signaling pathway through targeting of PTEN in cervical carcinoma. Oncogene 40, 3318\u20133330 (2021).","journal-title":"Oncogene"},{"key":"10721_CR38","doi-asserted-by":"crossref","unstructured":"Avsec, \u017d. et al. Advancing regulatory variant effect prediction with AlphaGenome. Nature 649, 1206\u20131218 (2026).","DOI":"10.1038\/s41586-025-10014-0"},{"key":"10721_CR39","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/s41588-018-0268-8","volume":"51","author":"SM Urbut","year":"2019","unstructured":"Urbut, S. M., Wang, G., Carbonetto, P. & Stephens, M. Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nat. Genet. 51, 187\u2013195 (2019).","journal-title":"Nat. Genet."},{"key":"10721_CR40","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2023.100458","volume":"3","author":"J Margoliash","year":"2023","unstructured":"Margoliash, J. et al. Polymorphic short tandem repeats make widespread contributions to blood and serum traits. Cell Genom. 3, 100458 (2023).","journal-title":"Cell Genom."},{"key":"10721_CR41","doi-asserted-by":"publisher","first-page":"1239732","DOI":"10.3389\/fimmu.2023.1239732","volume":"14","author":"CL Wolf","year":"2023","unstructured":"Wolf, C. L., Pruett, C., Lighter, D. & Jorcyk, C. L. The clinical relevance of OSMin inflammatory diseases: a comprehensive review. Front. Immunol. 14, 1239732 (2023).","journal-title":"Front. Immunol."},{"key":"10721_CR42","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31626-4","volume":"13","author":"JJ Gilchrist","year":"2022","unstructured":"Gilchrist, J. J. et al. Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity. Nat. Commun. 13, 4073 (2022).","journal-title":"Nat. Commun."},{"key":"10721_CR43","doi-asserted-by":"publisher","first-page":"228","DOI":"10.4240\/wjgs.v16.i1.228","volume":"16","author":"Y Yang","year":"2024","unstructured":"Yang, Y., Fu, K.-Z. & Pan, G. Role of Oncostatin M in the prognosis of inflammatory bowel disease: a meta-analysis. World J. Gastrointest. Surg. 16, 228\u2013238 (2024).","journal-title":"World J. Gastrointest. Surg."},{"key":"10721_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22479-4","volume":"12","author":"K Kim","year":"2021","unstructured":"Kim, K. et al. Therapeutic B-cell depletion reverses progression of Alzheimer\u2019s disease. Nat. Commun. 12, 2185 (2021).","journal-title":"Nat. Commun."},{"key":"10721_CR45","doi-asserted-by":"publisher","DOI":"10.1002\/mco2.662","volume":"5","author":"J-C Liu","year":"2024","unstructured":"Liu, J.-C. et al. Immunoglobulin class-switch recombination: mechanism, regulation, and related diseases. MedComm. 5, e662 (2024).","journal-title":"MedComm."},{"key":"10721_CR46","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1093\/hmg\/ddac269","volume":"32","author":"RY Cordero","year":"2023","unstructured":"Cordero, R. Y. et al. Trans-ancestry, Bayesian meta-analysis discovers 20 novel risk loci for inflammatory bowel disease in an African American, East Asian and European cohort. Hum. Mol. Genet. 32, 873\u2013882 (2023).","journal-title":"Hum. Mol. Genet."},{"key":"10721_CR47","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1056\/NEJMoa2314076","volume":"391","author":"BE Sands","year":"2024","unstructured":"Sands, B. E. et al. Phase 2 trial of anti-TL1A monoclonal antibody tulisokibart for ulcerative colitis. N. Engl. J. Med. 391, 1119\u20131129 (2024).","journal-title":"N. Engl. J. Med."},{"key":"10721_CR48","doi-asserted-by":"publisher","first-page":"e1007458","DOI":"10.1371\/journal.pgen.1007458","volume":"14","author":"AC Richard","year":"2018","unstructured":"Richard, A. C. et al. Reduced monocyte and macrophage TNFSF15\/TL1A expression is associated with susceptibility to inflammatory bowel disease. PLoS Genet. 14, e1007458 (2018).","journal-title":"PLoS Genet."},{"key":"10721_CR49","doi-asserted-by":"publisher","DOI":"10.15252\/msb.202110663","volume":"18","author":"ASE Cuomo","year":"2022","unstructured":"Cuomo, A. S. E. et al. CellRegMap: a statistical framework for mapping context-specific regulatory variants using scRNA-seq. Mol. Syst. Biol. 18, e10663 (2022).","journal-title":"Mol. Syst. Biol."},{"key":"10721_CR50","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1038\/s41588-024-02050-9","volume":"57","author":"A Haglund","year":"2025","unstructured":"Haglund, A. et al. Cell state-dependent allelic effects and contextual Mendelian randomization analysis for human brain phenotypes. Nat. Genet. 57, 358\u2013368 (2025).","journal-title":"Nat. Genet."},{"key":"10721_CR51","doi-asserted-by":"publisher","first-page":"1947","DOI":"10.1093\/hmg\/ddt582","volume":"23","author":"C Yao","year":"2014","unstructured":"Yao, C. et al. Sex- and age-interacting eQTLs in human complex diseases. Hum. Mol. Genet. 23, 1947\u20131956 (2014).","journal-title":"Hum. Mol. Genet."},{"key":"10721_CR52","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.1038\/s41590-024-01883-0","volume":"25","author":"L Rebuffet","year":"2024","unstructured":"Rebuffet, L. et al. High-dimensional single-cell analysis of human natural killer cell heterogeneity. Nat. Immunol. 25, 1474\u20131488 (2024).","journal-title":"Nat. Immunol."},{"key":"10721_CR53","doi-asserted-by":"publisher","DOI":"10.1126\/science.adj1182","volume":"385","author":"A Verma","year":"2024","unstructured":"Verma, A. et al. Diversity and scale: genetic architecture of 2068 traits in the VA Million Veteran Program. Science 385, eadj1182 (2024).","journal-title":"Science"},{"key":"10721_CR54","doi-asserted-by":"crossref","unstructured":"Gschwind, A. R. et al. An encyclopedia of human enhancer\u2013gene regulatory interactions. Nature 657, 179\u2013190 (2026).","DOI":"10.1038\/s41586-026-10781-4"},{"key":"10721_CR55","doi-asserted-by":"publisher","first-page":"609532","DOI":"10.3389\/fcell.2021.609532","volume":"9","author":"A Ben-Shmuel","year":"2021","unstructured":"Ben-Shmuel, A., Sabag, B., Biber, G. & Barda-Saad, M. The role of the cytoskeleton in regulating the natural killer cell immune response in health and disease: from signaling dynamics to function. Front. Cell Dev. Biol. 9, 609532 (2021).","journal-title":"Front. Cell Dev. Biol."},{"key":"10721_CR56","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1038\/s41588-024-01909-1","volume":"56","author":"L Rumker","year":"2024","unstructured":"Rumker, L. et al. Identifying genetic variants that influence the abundance of cell states in single-cell data. Nat. Genet. 56, 2068\u20132077 (2024).","journal-title":"Nat. Genet."},{"key":"10721_CR57","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms13850","volume":"8","author":"M Mangino","year":"2017","unstructured":"Mangino, M., Roederer, M., Beddall, M. H., Nestle, F. O. & Spector, T. D. Innate and adaptive immune traits are differentially affected by genetic and environmental factors. Nat. Commun. 8, 13850 (2017).","journal-title":"Nat. Commun."},{"key":"10721_CR58","doi-asserted-by":"publisher","first-page":"1214","DOI":"10.1016\/j.cell.2020.08.008","volume":"182","author":"D Vuckovic","year":"2020","unstructured":"Vuckovic, D. et al. The polygenic and monogenic basis of blood traits and diseases. Cell 182, 1214\u20131231 (2020).","journal-title":"Cell"},{"key":"10721_CR59","doi-asserted-by":"publisher","first-page":"14792","DOI":"10.1074\/jbc.M313127200","volume":"279","author":"ASJ Marshall","year":"2004","unstructured":"Marshall, A. S. J. et al. Identification and characterization of a novel human myeloid inhibitory C-type lectin-like receptor (MICL) that is predominantly expressed on granulocytes and monocytes. J. Biol. Chem. 279, 14792\u201314802 (2004).","journal-title":"J. Biol. Chem."},{"key":"10721_CR60","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1016\/j.immuni.2013.12.015","volume":"40","author":"K Neumann","year":"2014","unstructured":"Neumann, K. et al. Clec12a is an inhibitory receptor for uric acid crystals that regulates inflammation in response to cell death. Immunity 40, 389\u2013399 (2014).","journal-title":"Immunity"},{"key":"10721_CR61","doi-asserted-by":"publisher","first-page":"1866","DOI":"10.1038\/s41588-023-01529-1","volume":"55","author":"H Mostafavi","year":"2023","unstructured":"Mostafavi, H., Spence, J. P., Naqvi, S. & Pritchard, J. K. Systematic differences in discovery of genetic effects on gene expression and complex traits. Nat. Genet. 55, 1866\u20131875 (2023).","journal-title":"Nat. Genet."},{"key":"10721_CR62","doi-asserted-by":"publisher","first-page":"1036","DOI":"10.1038\/s41588-020-0684-4","volume":"52","author":"V Orr\u00f9","year":"2020","unstructured":"Orr\u00f9, V. et al. Complex genetic signatures in immune cells underlie autoimmunity and inform therapy. Nat. Genet. 52, 1036\u20131045 (2020).","journal-title":"Nat. Genet."},{"key":"10721_CR63","doi-asserted-by":"publisher","DOI":"10.1136\/bmjopen-2018-028649","volume":"9","author":"KA Kott","year":"2019","unstructured":"Kott, K. A. et al. Biobanking for discovery of novel cardiovascular biomarkers using imaging-quantified disease burden: protocol for the longitudinal, prospective, BioHEART-CT cohort study. BMJ Open 9, e028649 (2019).","journal-title":"BMJ Open"},{"key":"10721_CR64","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"10721_CR65","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1038\/s41592-023-01943-7","volume":"20","author":"SJ Fleming","year":"2023","unstructured":"Fleming, S. J. et al. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender. Nat. Methods 20, 1323\u20131335 (2023).","journal-title":"Nat. Methods"},{"key":"10721_CR66","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03224-8","volume":"25","author":"D Neavin","year":"2024","unstructured":"Neavin, D. et al. Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods. Genome Biol. 25, 94 (2024).","journal-title":"Genome Biol."},{"key":"10721_CR67","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1865-2","volume":"20","author":"Y Huang","year":"2019","unstructured":"Huang, Y., McCarthy, D. J. & Stegle, O. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. Genome Biol. 20, 273 (2019).","journal-title":"Genome Biol."},{"key":"10721_CR68","doi-asserted-by":"publisher","first-page":"1150","DOI":"10.1093\/bioinformatics\/btz698","volume":"36","author":"AS Bais","year":"2020","unstructured":"Bais, A. S. & Kostka, D. scds: computational annotation of doublets in single-cell RNA sequencing data. Bioinformatics 36, 1150\u20131158 (2020).","journal-title":"Bioinformatics"},{"key":"10721_CR69","doi-asserted-by":"publisher","first-page":"979","DOI":"10.12688\/f1000research.73600.1","volume":"10","author":"P-L Germain","year":"2021","unstructured":"Germain, P.-L., Lun, A., Garcia Meixide, C., Macnair, W. & Robinson, M. D. Doublet identification in single-cell sequencing data using. F1000Res. 10, 979 (2021).","journal-title":"F1000Res."},{"key":"10721_CR70","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1862-5","volume":"20","author":"J Alquicira-Hernandez","year":"2019","unstructured":"Alquicira-Hernandez, J., Sathe, A., Ji, H. P., Nguyen, Q. & Powell, J. E. scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data. Genome Biol. 20, 264 (2019).","journal-title":"Genome Biol."},{"key":"10721_CR71","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23196-8","volume":"12","author":"L Michielsen","year":"2021","unstructured":"Michielsen, L., Reinders, M. J. T. & Mahfouz, A. Hierarchical progressive learning of cell identities in single-cell data. Nat. Commun. 12, 2799 (2021).","journal-title":"Nat. Commun."},{"key":"10721_CR72","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","volume":"184","author":"Y Hao","year":"2021","unstructured":"Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573\u20133587 (2021).","journal-title":"Cell"},{"key":"10721_CR73","doi-asserted-by":"crossref","unstructured":"Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888\u20131902.e21 (2019).","DOI":"10.1016\/j.cell.2019.05.031"},{"key":"10721_CR74","doi-asserted-by":"publisher","first-page":"5876","DOI":"10.1016\/j.cell.2023.11.026","volume":"186","author":"C Xu","year":"2023","unstructured":"Xu, C. et al. Automatic cell-type harmonization and integration across Human Cell Atlas datasets. Cell 186, 5876\u20135891 (2023).","journal-title":"Cell"},{"key":"10721_CR75","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl5197","volume":"376","author":"C Dom\u00ednguez Conde","year":"2022","unstructured":"Dom\u00ednguez Conde, C. et al. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 376, eabl5197 (2022).","journal-title":"Science"},{"key":"10721_CR76","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0","volume":"19","author":"FA Wolf","year":"2018","unstructured":"Wolf, F. A., Angerer, P. & Theis, F. J. Scanpy: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).","journal-title":"Genome Biol."},{"key":"10721_CR77","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1016\/j.ajhg.2019.01.002","volume":"104","author":"Y Liu","year":"2019","unstructured":"Liu, Y. et al. ACAT: a fast and powerful P value combination method for rare-variant analysis in sequencing studies. Am. J. Hum. Genet. 104, 410\u2013421 (2019).","journal-title":"Am. J. Hum. Genet."},{"key":"10721_CR78","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"10721_CR79","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"ENCODE Project Consortium","year":"2012","unstructured":"ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57\u201374 (2012).","journal-title":"Nature"},{"key":"10721_CR80","doi-asserted-by":"publisher","first-page":"D882","DOI":"10.1093\/nar\/gkz1062","volume":"48","author":"Y Luo","year":"2020","unstructured":"Luo, Y. et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 48, D882\u2013D889 (2020).","journal-title":"Nucleic Acids Res."},{"key":"10721_CR81","doi-asserted-by":"publisher","unstructured":"Hitz, B. C. et al. The ENCODE uniform analysis pipelines. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.04.04.535623 (2023).","DOI":"10.1101\/2023.04.04.535623"},{"key":"10721_CR82","doi-asserted-by":"publisher","first-page":"D1243","DOI":"10.1093\/nar\/gkae974","volume":"53","author":"G Perez","year":"2025","unstructured":"Perez, G. et al. The UCSC Genome Browser database: 2025 update. Nucleic Acids Res. 53, D1243\u2013D1249 (2025).","journal-title":"Nucleic Acids Res."},{"key":"10721_CR83","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1038\/s41588-019-0538-0","volume":"51","author":"CP Fulco","year":"2019","unstructured":"Fulco, C. P. et al. Activity-by-contact model of enhancer\u2013promoter regulation from thousands of CRISPR perturbations. Nat. Genet. 51, 1664\u20131669 (2019).","journal-title":"Nat. Genet."},{"key":"10721_CR84","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1038\/s41586-021-03446-x","volume":"593","author":"J Nasser","year":"2021","unstructured":"Nasser, J. et al. Genome-wide enhancer maps link risk variants to disease genes. Nature 593, 238\u2013243 (2021).","journal-title":"Nature"},{"key":"10721_CR85","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0560-6","volume":"16","author":"M Lizio","year":"2015","unstructured":"Lizio, M. et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 16, 22 (2015).","journal-title":"Genome Biol."},{"key":"10721_CR86","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nmeth.1906","volume":"9","author":"J Ernst","year":"2012","unstructured":"Ernst, J. & Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215\u2013216 (2012).","journal-title":"Nat. Methods"},{"key":"10721_CR87","doi-asserted-by":"publisher","first-page":"D88","DOI":"10.1093\/nar\/gkl822","volume":"35","author":"A Visel","year":"2007","unstructured":"Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browser\u2013a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88\u201392 (2007).","journal-title":"Nucleic Acids Res."},{"key":"10721_CR88","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"10721_CR89","doi-asserted-by":"publisher","unstructured":"Cuomo, A. S. E. Data from: impact of rare and common genetic variation on cell type-specific gene expression in human blood. Zenodo https:\/\/doi.org\/10.5281\/zenodo.18221260 (2026).","DOI":"10.5281\/zenodo.18221260"},{"key":"10721_CR90","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02664-4","volume":"23","author":"T Zeng","year":"2022","unstructured":"Zeng, T. & Li, Y. I. Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol. 23, 103 (2022).","journal-title":"Genome Biol."},{"key":"10721_CR91","doi-asserted-by":"crossref","unstructured":"Viechtbauer, W. Conducting meta-analyses in R with the metafor package. J. Stat. Softw. 36, (2010).","DOI":"10.18637\/jss.v036.i03"},{"key":"10721_CR92","doi-asserted-by":"publisher","first-page":"e1004383","DOI":"10.1371\/journal.pgen.1004383","volume":"10","author":"C Giambartolomei","year":"2014","unstructured":"Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014).","journal-title":"PLoS Genet."},{"key":"10721_CR93","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1038\/s41588-022-01024-z","volume":"54","author":"C Bellenguez","year":"2022","unstructured":"Bellenguez, C. et al. New insights into the genetic etiology of Alzheimer\u2019s disease and related dementias. Nat. Genet. 54, 412\u2013436 (2022).","journal-title":"Nat. Genet."},{"key":"10721_CR94","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2022.100212","volume":"2","author":"K Tsuo","year":"2022","unstructured":"Tsuo, K. et al. Multi-ancestry meta-analysis of asthma identifies novel associations and highlights the value of increased power and diversity. Cell Genom. 2, 100212 (2022).","journal-title":"Cell Genom."},{"key":"10721_CR95","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/nature24284","volume":"551","author":"K Michailidou","year":"2017","unstructured":"Michailidou, K. et al. Association analysis identifies 65 new breast cancer risk loci. Nature 551, 92\u201394 (2017).","journal-title":"Nature"},{"key":"10721_CR96","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1038\/s41431-020-0636-6","volume":"28","author":"COVID-19 Host Genetics Initiative","year":"2020","unstructured":"COVID-19 Host Genetics Initiative The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic. Eur. J. Hum. Genet. 28, 715\u2013718 (2020).","journal-title":"Eur. J. Hum. Genet."},{"key":"10721_CR97","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1038\/s41588-023-01384-0","volume":"55","author":"Z Liu","year":"2023","unstructured":"Liu, Z. et al. Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries. Nat. Genet. 55, 796\u2013806 (2023).","journal-title":"Nat. Genet."},{"key":"10721_CR98","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/s41588-023-01422-x","volume":"55","author":"K Kiryluk","year":"2023","unstructured":"Kiryluk, K. et al. Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy. Nat. Genet. 55, 1091\u20131105 (2023).","journal-title":"Nat. Genet."},{"key":"10721_CR99","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1038\/ng.3892","volume":"49","author":"JD McKay","year":"2017","unstructured":"McKay, J. D. et al. Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes. Nat. Genet. 49, 1126\u20131132 (2017).","journal-title":"Nat. Genet."},{"key":"10721_CR100","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1038\/ng.2770","volume":"45","author":"International Multiple Sclerosis Genetics Consortium (IMSGC) et al.","year":"2013","unstructured":"International Multiple Sclerosis Genetics Consortium (IMSGC) et al. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat. Genet. 45, 1353\u20131360 (2013).","journal-title":"Nat. Genet."},{"key":"10721_CR101","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1016\/S1474-4422(19)30320-5","volume":"18","author":"MA Nalls","year":"2019","unstructured":"Nalls, M. A. et al. Identification of novel risk loci, causal insights, and heritable risk for Parkinson\u2019s disease: a meta-analysis of genome-wide association studies. Lancet Neurol. 18, 1091\u20131102 (2019).","journal-title":"Lancet Neurol."},{"key":"10721_CR102","doi-asserted-by":"publisher","first-page":"2065","DOI":"10.1038\/s41588-023-01534-4","volume":"55","author":"A Wang","year":"2023","unstructured":"Wang, A. et al. Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants. Nat. Genet. 55, 2065\u20132074 (2023).","journal-title":"Nat. Genet."},{"key":"10721_CR103","doi-asserted-by":"publisher","first-page":"1640","DOI":"10.1038\/s41588-022-01213-w","volume":"54","author":"K Ishigaki","year":"2022","unstructured":"Ishigaki, K. et al. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nat. Genet. 54, 1640\u20131651 (2022).","journal-title":"Nat. Genet."},{"key":"10721_CR104","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.1038\/ng.3434","volume":"47","author":"J Bentham","year":"2015","unstructured":"Bentham, J. et al. Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nat. Genet. 47, 1457\u20131464 (2015).","journal-title":"Nat. Genet."},{"key":"10721_CR105","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1038\/s41586-021-03552-w","volume":"594","author":"J Chiou","year":"2021","unstructured":"Chiou, J. et al. Interpreting type 1 diabetes risk with genetics and single-cell epigenomics. Nature 594, 398\u2013402 (2021).","journal-title":"Nature"},{"key":"10721_CR106","doi-asserted-by":"publisher","unstructured":"Abnar, S. & Zuidema, W. Quantifying attention flow in transformers. Preprint at\u00a0https:\/\/doi.org\/10.48550\/arXiv.2005.00928 (2020).","DOI":"10.48550\/arXiv.2005.00928"},{"key":"10721_CR107","doi-asserted-by":"crossref","unstructured":"Bates, D., M\u00e4chler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models Usinglme4. J. Stat. Softw. 67, (2015).","DOI":"10.18637\/jss.v067.i01"},{"key":"10721_CR108","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289\u20131296 (2019).","journal-title":"Nat. Methods"},{"key":"10721_CR109","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/s41587-021-01066-4","volume":"40","author":"YA Reshef","year":"2022","unstructured":"Reshef, Y. A. et al. Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics. Nat. Biotechnol. 40, 355\u2013363 (2022).","journal-title":"Nat. Biotechnol."},{"key":"10721_CR110","doi-asserted-by":"publisher","unstructured":"Korotkevich, G. et al. Fast gene set enrichment analysis. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/060012 (2016).","DOI":"10.1101\/060012"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-10721-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-10721-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-10721-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T10:00:00Z","timestamp":1794477600000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-10721-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,28]]},"references-count":110,"journal-issue":{"issue":"8140","published-print":{"date-parts":[[2026,11,12]]}},"alternative-id":["10721"],"URL":"https:\/\/doi.org\/10.1038\/s41586-026-10721-2","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,28]]},"assertion":[{"value":"21 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 October 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"E.B.-D., L.C. and K.K.-H.F. are employed at Illumina Inc. D.G.M. is a paid advisor to Insitro and GSK, and receives research funding from Google and Microsoft, unrelated to the work described in this paper. G.A.F. reports grants from the NHMRC (Australia), grants from Abbott Diagnostic, Sanofi, Janssen Pharmaceuticals and NSW Health. G.A.F. reports honorarium from CSL, CPC Clinical Research, Sanofi, Boehringer-Ingelheim, Heart Foundation and Abbott. G.A.F. serves as Board Director for the Australian Cardiovascular Alliance (past President), Executive Committee Member for CPC Clinical Research, Founding Director and CMO for Prokardia and Kardiomics, and Executive Committee member for the CAD Frontiers A2D2 Consortium. In addition, G.A.F. serves as CMO for the non-profit, CAD Frontiers, with industry partners including, Novartis, Amgen, Siemens Healthineers, ELUCID, Foresite Labs LLC, HeartFlow, Canon, Cleerly, Caristo, Genentech, Artyra and Bitterroot Bio, Novo Nordisk and Allelica. In addition, G.A.F. has the following patents: \u2018Patent Biomarkers and Oxidative Stress\u2019 awarded USA May 2017 (US9638699B2) issued to Northern Sydney Local Health District, \u2018Use of P2X7R antagonists in cardiovascular disease\u2019 PCT\/AU2018\/050905 licensed to Prokardia, \u2018Methods for treatment and prevention of vascular disease\u2019 PCT\/AU2015\/000548 issued to The University of Sydney\/Northern Sydney Local Health District, \u2018Methods for predicting coronary artery disease\u2019 AU202290266 issued to The University of Sydney, and the patent \u2018Novel P2X7 Receptor Antagonists\u2019 PCT\/AU2022\/051400 (23 November 2022), International Application No. WO\/2023\/092175 (1 June 2023), issued to The University of Sydney. The other authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}