{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T12:12:17Z","timestamp":1792843937203,"version":"4.5.0"},"reference-count":81,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI122220"],"award-info":[{"award-number":["R01 AI122220"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000890","name":"National Multiple Sclerosis Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000890","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["5R35GM127131"],"award-info":[{"award-number":["5R35GM127131"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"U.S. Department of Health & Human Services | NIH | National Institute of Mental Health","doi-asserted-by":"publisher","award":["2R01MH101244"],"award-info":[{"award-number":["2R01MH101244"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute","doi-asserted-by":"publisher","award":["5U01HG012009"],"award-info":[{"award-number":["5U01HG012009"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Genet"],"published-print":{"date-parts":[[2024,5]]},"DOI":"10.1038\/s41588-024-01732-8","type":"journal-article","created":{"date-parts":[[2024,5,13]],"date-time":"2024-05-13T10:01:39Z","timestamp":1715594499000},"page":"838-845","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["Genetic mapping across autoimmune diseases reveals shared associations and mechanisms"],"prefix":"10.1038","volume":"56","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2962-6253","authenticated-orcid":false,"given":"Matthew R.","family":"Lincoln","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noah","family":"Connally","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre-Paul","family":"Axisa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0524-6005","authenticated-orcid":false,"given":"Christiane","family":"Gasperi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitja","family":"Mitrovic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0637-2265","authenticated-orcid":false,"given":"David","family":"van Heel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cisca","family":"Wijmenga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7704-3437","authenticated-orcid":false,"given":"Sebo","family":"Withoff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2304-7939","authenticated-orcid":false,"given":"Iris H.","family":"Jonkers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2950-5670","authenticated-orcid":false,"given":"Leonid","family":"Padyukov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"International Multiple Sclerosis Genetics Consortium","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley H.","family":"Beecham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikolaos A.","family":"Patsopoulos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Cotsapas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Booth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An","family":"Goris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annette","family":"Oturai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janna","family":"Saarela","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Betrand","family":"Fontaine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bertrand","family":"Hemmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Claes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frauke","family":"Zipp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"D\u2019Alfonso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filippo","family":"Martinelli-Boneschi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanne F.","family":"Harbo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingrid","family":"Kockum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Hillert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomas","family":"Olsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge R.","family":"Oksenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rogier","family":"Hintzen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa F.","family":"Barcellos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"Alfredsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Esposito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roland","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan L.","family":"Haines","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret A.","family":"Pericak-Vance","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian J.","family":"Ivinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graeme","family":"Stewart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Hafler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen L.","family":"Hauser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alastair","family":"Compston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gil","family":"McVean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"De Jager","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J.","family":"Sawcer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jakob L.","family":"McCauley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3872-7793","authenticated-orcid":false,"given":"Stephen S.","family":"Rich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7151-4277","authenticated-orcid":false,"given":"Robert R.","family":"Graham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick M.","family":"Gaffney","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4266-6949","authenticated-orcid":false,"given":"Carl D.","family":"Langefeld","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Vyse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4664-535X","authenticated-orcid":false,"given":"David A.","family":"Hafler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3440-1913","authenticated-orcid":false,"given":"Sung","family":"Chun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5715-5677","authenticated-orcid":false,"given":"Shamil R.","family":"Sunyaev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7772-5910","authenticated-orcid":false,"given":"Chris","family":"Cotsapas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,13]]},"reference":[{"key":"1732_CR1","doi-asserted-by":"publisher","first-page":"2228","DOI":"10.1172\/JCI78088","volume":"125","author":"MD Rosenblum","year":"2015","unstructured":"Rosenblum, M. D., Remedios, K. A. & Abbas, A. K. Mechanisms of human autoimmunity. J. Clin. Invest. 125, 2228\u20132233 (2015).","journal-title":"J. Clin. Invest."},{"key":"1732_CR2","unstructured":"International Multiple Sclerosis Genetics Consortium. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science 365, eaav7188 (2019)."},{"key":"1732_CR3","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1038\/ng.3760","volume":"49","author":"KM de Lange","year":"2017","unstructured":"de Lange, K. M. et al. Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nat. Genet. 49, 256\u2013261 (2017).","journal-title":"Nat. Genet."},{"key":"1732_CR4","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1126\/science.1222794","volume":"337","author":"MT Maurano","year":"2012","unstructured":"Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190\u20131195 (2012).","journal-title":"Science"},{"key":"1732_CR5","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.ajhg.2014.10.004","volume":"95","author":"A Gusev","year":"2014","unstructured":"Gusev, A. et al. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Am. J. Hum. Genet. 95, 535\u2013552 (2014).","journal-title":"Am. J. Hum. Genet."},{"key":"1732_CR6","doi-asserted-by":"publisher","first-page":"1228","DOI":"10.1038\/ng.3404","volume":"47","author":"HK Finucane","year":"2015","unstructured":"Finucane, H. K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228\u20131235 (2015).","journal-title":"Nat. Genet."},{"key":"1732_CR7","doi-asserted-by":"publisher","first-page":"2845","DOI":"10.1002\/art.24749","volume":"60","author":"K Hemminki","year":"2009","unstructured":"Hemminki, K., Li, X., Sundquist, K. & Sundquist, J. Shared familial aggregation of susceptibility to autoimmune diseases. Arthritis Rheum. 60, 2845\u20132847 (2009).","journal-title":"Arthritis Rheum."},{"key":"1732_CR8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jaut.2007.05.002","volume":"29","author":"WW Eaton","year":"2007","unstructured":"Eaton, W. W., Rose, N. R., Kalaydjian, A., Pedersen, M. G. & Mortensen, P. B. Epidemiology of autoimmune diseases in Denmark. J. Autoimmun. 29, 1\u20139 (2007).","journal-title":"J. Autoimmun."},{"key":"1732_CR9","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1001\/jamainternmed.2015.3528","volume":"175","author":"C-F Kuo","year":"2015","unstructured":"Kuo, C.-F. et al. Familial aggregation of systemic lupus erythematosus and coaggregation of autoimmune diseases in affected families. JAMA Intern. Med. 175, 1518\u20131526 (2015).","journal-title":"JAMA Intern. Med."},{"key":"1732_CR10","doi-asserted-by":"publisher","first-page":"e1002254","DOI":"10.1371\/journal.pgen.1002254","volume":"7","author":"C Cotsapas","year":"2011","unstructured":"Cotsapas, C. et al. Pervasive sharing of genetic effects in autoimmune disease. PLoS Genet. 7, e1002254 (2011).","journal-title":"PLoS Genet."},{"key":"1732_CR11","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/ng.3528","volume":"48","author":"D Ellinghaus","year":"2016","unstructured":"Ellinghaus, D. et al. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nat. Genet. 48, 510\u2013518 (2016).","journal-title":"Nat. Genet."},{"key":"1732_CR12","doi-asserted-by":"publisher","first-page":"e1000792","DOI":"10.1371\/journal.pgen.1000792","volume":"5","author":"M Sirota","year":"2009","unstructured":"Sirota, M., Schaub, M. A., Batzoglou, S., Robinson, W. H. & Butte, A. J. Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet. 5, e1000792 (2009).","journal-title":"PLoS Genet."},{"key":"1732_CR13","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1136\/annrheumdis-2022-222460","volume":"81","author":"Y Shirai","year":"2022","unstructured":"Shirai, Y. et al. Multi-trait and cross-population genome-wide association studies across autoimmune and allergic diseases identify shared and distinct genetic component. Ann. Rheum. Dis. 81, 1301\u20131312 (2022).","journal-title":"Ann. Rheum. Dis."},{"key":"1732_CR14","doi-asserted-by":"publisher","first-page":"3498","DOI":"10.1093\/hmg\/ddz145","volume":"28","author":"JG Pouget","year":"2019","unstructured":"Pouget, J. G. et al. Cross-disorder analysis of schizophrenia and 19 immune-mediated diseases identifies shared genetic risk. Hum. Mol. Genet. 28, 3498\u20133513 (2019).","journal-title":"Hum. Mol. Genet."},{"key":"1732_CR15","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1038\/ng.3330","volume":"47","author":"MD Fortune","year":"2015","unstructured":"Fortune, M. D. et al. Statistical colocalization of genetic risk variants for related autoimmune diseases in the context of common controls. Nat. Genet. 47, 839\u2013846 (2015).","journal-title":"Nat. Genet."},{"key":"1732_CR16","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/nrg3502","volume":"14","author":"M Parkes","year":"2013","unstructured":"Parkes, M., Cortes, A., van Heel, D. A. & Brown, M. A. Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat. Rev. Genet. 14, 661\u2013673 (2013).","journal-title":"Nat. Rev. Genet."},{"key":"1732_CR17","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-020-00797-4","volume":"12","author":"OS Burren","year":"2020","unstructured":"Burren, O. S. et al. Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases. Genome Med. 12, 106 (2020).","journal-title":"Genome Med."},{"key":"1732_CR18","doi-asserted-by":"publisher","first-page":"e1005535","DOI":"10.1371\/journal.pgen.1005535","volume":"11","author":"M van de Bunt","year":"2015","unstructured":"van de Bunt, M. et al. Evaluating the performance of fine-mapping strategies at common variant GWAS loci. PLoS Genet. 11, e1005535 (2015).","journal-title":"PLoS Genet."},{"key":"1732_CR19","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1038\/s41588-017-0009-4","volume":"50","author":"P Turley","year":"2018","unstructured":"Turley, P. et al. Multi-trait analysis of genome-wide association summary statistics using MTAG. Nat. Genet. 50, 229\u2013237 (2018).","journal-title":"Nat. Genet."},{"key":"1732_CR20","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1038\/ng.3211","volume":"47","author":"BK Bulik-Sullivan","year":"2015","unstructured":"Bulik-Sullivan, B. K. et al. LD score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291\u2013295 (2015).","journal-title":"Nat. Genet."},{"key":"1732_CR21","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1038\/ng.3406","volume":"47","author":"B Bulik-Sullivan","year":"2015","unstructured":"Bulik-Sullivan, B. et al. An atlas of genetic correlations across human diseases and traits. Nat. Genet. 47, 1236\u20131241 (2015).","journal-title":"Nat. Genet."},{"key":"1732_CR22","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/nrendo.2013.161","volume":"9","author":"A Zhernakova","year":"2013","unstructured":"Zhernakova, A., Withoff, S. & Wijmenga, C. Clinical implications of shared genetics and pathogenesis in autoimmune diseases. Nat. Rev. Endocrinol. 9, 646\u2013659 (2013).","journal-title":"Nat. Rev. Endocrinol."},{"key":"1732_CR23","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1207-1","volume":"18","author":"V Matzaraki","year":"2017","unstructured":"Matzaraki, V., Kumar, V., Wijmenga, C. & Zhernakova, A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol. 18, 76 (2017).","journal-title":"Genome Biol."},{"key":"1732_CR24","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1186\/ar3204","volume":"13","author":"A Cortes","year":"2011","unstructured":"Cortes, A. & Brown, M. A. Promise and pitfalls of the ImmunoChip. Arthritis Res. Ther. 13, 101 (2011).","journal-title":"Arthritis Res. Ther."},{"key":"1732_CR25","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.ajhg.2010.11.011","volume":"88","author":"J Yang","year":"2011","unstructured":"Yang, J., Lee, S. H., Goddard, M. E. & Visscher, P. M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76\u201382 (2011).","journal-title":"Am. J. Hum. Genet."},{"key":"1732_CR26","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1093\/bioinformatics\/btw018","volume":"32","author":"C Benner","year":"2016","unstructured":"Benner, C. et al. FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics 32, 1493\u20131501 (2016).","journal-title":"Bioinformatics"},{"key":"1732_CR27","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1126\/science.aan0814","volume":"359","author":"V Mohanan","year":"2018","unstructured":"Mohanan, V. et al. C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions. Science 359, 1161\u20131166 (2018).","journal-title":"Science"},{"key":"1732_CR28","doi-asserted-by":"publisher","first-page":"1066","DOI":"10.1038\/ng.952","volume":"43","author":"MA Rivas","year":"2011","unstructured":"Rivas, M. A. et al. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat. Genet. 43, 1066\u20131073 (2011).","journal-title":"Nat. Genet."},{"key":"1732_CR29","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/nature13835","volume":"518","author":"KK-H Farh","year":"2015","unstructured":"Farh, K. K.-H. et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337\u2013343 (2015).","journal-title":"Nature"},{"key":"1732_CR30","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1038\/ng.2504","volume":"45","author":"G Trynka","year":"2013","unstructured":"Trynka, G. et al. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat. Genet. 45, 124\u2013130 (2013).","journal-title":"Nat. Genet."},{"key":"1732_CR31","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1038\/ng.3795","volume":"49","author":"S Chun","year":"2017","unstructured":"Chun, S. et al. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Nat. Genet. 49, 600\u2013605 (2017).","journal-title":"Nat. Genet."},{"key":"1732_CR32","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.e24 (2016).","journal-title":"Cell"},{"key":"1732_CR33","doi-asserted-by":"publisher","first-page":"eabb8786","DOI":"10.1126\/sciimmunol.abb8786","volume":"5","author":"JL Pappalardo","year":"2020","unstructured":"Pappalardo, J. L. et al. Transcriptomic and clonal characterization of T cells in the human central nervous system. Sci. Immunol. 5, eabb8786 (2020).","journal-title":"Sci. Immunol."},{"key":"1732_CR34","doi-asserted-by":"publisher","first-page":"D139","DOI":"10.1093\/nar\/gkw1064","volume":"45","author":"S Kumar","year":"2017","unstructured":"Kumar, S., Ambrosini, G. & Bucher, P. SNP2TFBS\u2014a database of regulatory SNPs affecting predicted transcription factor binding site affinity. Nucleic Acids Res. 45, D139\u2013D144 (2017).","journal-title":"Nucleic Acids Res."},{"key":"1732_CR35","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/s41588-022-01025-y","volume":"54","author":"K Kundu","year":"2022","unstructured":"Kundu, K. et al. Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases. Nat. Genet. 54, 251\u2013262 (2022).","journal-title":"Nat. Genet."},{"key":"1732_CR36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20885-8","volume":"12","author":"CN Foley","year":"2021","unstructured":"Foley, C. N. et al. A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits. Nat. Commun. 12, 764 (2021).","journal-title":"Nat. Commun."},{"key":"1732_CR37","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26364-y","volume":"12","author":"N Hern\u00e1ndez","year":"2021","unstructured":"Hern\u00e1ndez, N. et al. The flashfm approach for fine-mapping multiple quantitative traits. Nat. Commun. 12, 6147 (2021).","journal-title":"Nat. Commun."},{"key":"1732_CR38","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? Trends Genet. 37, 109\u2013124 (2021).","journal-title":"Trends Genet."},{"key":"1732_CR39","doi-asserted-by":"crossref","unstructured":"The Lenercept Multiple Sclerosis Study Group & The University of British Columbia MS\/MRI Analysis Group. TNF neutralization in MS: results of a randomized, placebo-controlled multicenter study. Neurology 53, 457\u2013465 (1999).","DOI":"10.1212\/WNL.53.3.457"},{"key":"1732_CR40","doi-asserted-by":"publisher","first-page":"508","DOI":"10.1038\/nature11307","volume":"488","author":"AP Gregory","year":"2012","unstructured":"Gregory, A. P. et al. TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis. Nature 488, 508\u2013511 (2012).","journal-title":"Nature"},{"key":"1732_CR41","doi-asserted-by":"publisher","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","volume":"47","author":"A Buniello","year":"2019","unstructured":"Buniello, A. et al. The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47, D1005\u2013D1012 (2019).","journal-title":"Nucleic Acids Res."},{"key":"1732_CR42","doi-asserted-by":"publisher","first-page":"1449","DOI":"10.1038\/ng.3424","volume":"47","author":"L Paternoster","year":"2015","unstructured":"Paternoster, L. et al. Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis. Nat. Genet. 47, 1449\u20131456 (2015).","journal-title":"Nat. Genet."},{"key":"1732_CR43","doi-asserted-by":"publisher","first-page":"1752","DOI":"10.1038\/ng.3985","volume":"49","author":"MA Ferreira","year":"2017","unstructured":"Ferreira, M. A. et al. Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology. Nat. Genet. 49, 1752\u20131757 (2017).","journal-title":"Nat. Genet."},{"key":"1732_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15649-3","volume":"11","author":"Y Han","year":"2020","unstructured":"Han, Y. et al. Genome-wide analysis highlights contribution of immune system pathways to the genetic architecture of asthma. Nat. Commun. 11, 1776 (2020).","journal-title":"Nat. Commun."},{"key":"1732_CR45","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1038\/ng.543","volume":"42","author":"PCA Dubois","year":"2010","unstructured":"Dubois, P. C. A. et al. Multiple common variants for celiac disease influencing immune gene expression. Nat. Genet. 42, 295\u2013302 (2010).","journal-title":"Nat. Genet."},{"key":"1732_CR46","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12515-9","volume":"10","author":"PA Lyons","year":"2019","unstructured":"Lyons, P. A. et al. Genome-wide association study of eosinophilic granulomatosis with polyangiitis reveals genomic loci stratified by ANCA status. Nat. Commun. 10, 5120 (2019).","journal-title":"Nat. Commun."},{"key":"1732_CR47","doi-asserted-by":"publisher","first-page":"1425","DOI":"10.1038\/ng.3675","volume":"48","author":"PG Bronson","year":"2016","unstructured":"Bronson, P. G. et al. Common variants at PVT1, ATG13\u2013AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency. Nat. Genet. 48, 1425\u20131429 (2016).","journal-title":"Nat. Genet."},{"key":"1732_CR48","doi-asserted-by":"publisher","first-page":"2396","DOI":"10.2337\/dc18-1032","volume":"41","author":"DL Cousminer","year":"2018","unstructured":"Cousminer, D. L. et al. First genome-wide association study of latent autoimmune diabetes in adults reveals novel insights linking immune and metabolic diabetes. Diabetes Care 41, 2396\u20132403 (2018).","journal-title":"Diabetes Care"},{"key":"1732_CR49","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms9019","volume":"6","author":"HJ Cordell","year":"2015","unstructured":"Cordell, H. J. et al. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways. Nat. Commun. 6, 8019 (2015).","journal-title":"Nat. Commun."},{"key":"1732_CR50","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1038\/ng.3745","volume":"49","author":"S-G Ji","year":"2017","unstructured":"Ji, S.-G. et al. Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease. Nat. Genet. 49, 269\u2013273 (2017).","journal-title":"Nat. Genet."},{"key":"1732_CR51","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1136\/annrheumdis-2018-214158","volume":"78","author":"A Aterido","year":"2019","unstructured":"Aterido, A. et al. Genetic variation at the glycosaminoglycan metabolism pathway contributes to the risk of psoriatic arthritis but not psoriasis. Ann. Rheum. Dis. 78, 355\u2013364 (2019).","journal-title":"Ann. Rheum. Dis."},{"key":"1732_CR52","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":"1732_CR53","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12760-y","volume":"10","author":"E L\u00f3pez-Isac","year":"2019","unstructured":"L\u00f3pez-Isac, E. et al. GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways. Nat. Commun. 10, 4955 (2019).","journal-title":"Nat. Commun."},{"key":"1732_CR54","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.1038\/ng.3680","volume":"48","author":"Y Jin","year":"2016","unstructured":"Jin, Y. et al. Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants. Nat. Genet. 48, 1418\u20131424 (2016).","journal-title":"Nat. Genet."},{"key":"1732_CR55","doi-asserted-by":"publisher","first-page":"e1000606","DOI":"10.1371\/journal.pgen.1000606","volume":"5","author":"B-J Feng","year":"2009","unstructured":"Feng, B.-J. et al. Multiple loci within the major histocompatibility complex confer risk of psoriasis. PLoS Genet. 5, e1000606 (2009).","journal-title":"PLoS Genet."},{"key":"1732_CR56","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature12873","volume":"506","author":"Y Okada","year":"2014","unstructured":"Okada, Y. et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376\u2013381 (2014).","journal-title":"Nature"},{"key":"1732_CR57","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature15393","volume":"526","author":"The 1000 Genomes Project Consortium.","year":"2015","unstructured":"The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68\u201374 (2015).","journal-title":"Nature"},{"key":"1732_CR58","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1038\/nature09298","volume":"467","author":"International HapMap 3 Consortium","year":"2010","unstructured":"International HapMap 3 Consortium et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52\u201358 (2010).","journal-title":"Nature"},{"key":"1732_CR59","doi-asserted-by":"publisher","first-page":"1193","DOI":"10.1038\/ng.998","volume":"43","author":"G Trynka","year":"2011","unstructured":"Trynka, G. et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat. Genet. 43, 1193\u20131201 (2011).","journal-title":"Nat. Genet."},{"key":"1732_CR60","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1038\/ng.3359","volume":"47","author":"JZ Liu","year":"2015","unstructured":"Liu, J. Z. et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat. Genet. 47, 979\u2013986 (2015).","journal-title":"Nat. Genet."},{"key":"1732_CR61","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1038\/ng.2770","volume":"45","author":"International Multiple Sclerosis Genetics Consortium (IMSGC","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":"1732_CR62","doi-asserted-by":"publisher","first-page":"1336","DOI":"10.1038\/ng.2462","volume":"44","author":"S Eyre","year":"2012","unstructured":"Eyre, S. et al. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat. Genet. 44, 1336\u20131340 (2012).","journal-title":"Nat. Genet."},{"key":"1732_CR63","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms16021","volume":"8","author":"CD Langefeld","year":"2017","unstructured":"Langefeld, C. D. et al. Transancestral mapping and genetic load in systemic lupus erythematosus. Nat. Commun. 8, 16021 (2017).","journal-title":"Nat. Commun."},{"key":"1732_CR64","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1038\/ng.3782","volume":"49","author":"J Zhao","year":"2017","unstructured":"Zhao, J. et al. A missense variant in NCF1 is associated with susceptibility to multiple autoimmune diseases. Nat. Genet. 49, 433\u2013437 (2017).","journal-title":"Nat. Genet."},{"key":"1732_CR65","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/ng.3245","volume":"47","author":"S Onengut-Gumuscu","year":"2015","unstructured":"Onengut-Gumuscu, S. et al. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat. Genet. 47, 381\u2013386 (2015).","journal-title":"Nat. Genet."},{"key":"1732_CR66","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1093\/rheumatology\/keq302","volume":"50","author":"A Rasmussen","year":"2011","unstructured":"Rasmussen, A. et al. The lupus family registry and repository. Rheumatology 50, 47\u201359 (2011).","journal-title":"Rheumatology"},{"key":"1732_CR67","doi-asserted-by":"publisher","DOI":"10.1186\/s13742-015-0047-8","volume":"4","author":"CC Chang","year":"2015","unstructured":"Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4, 7 (2015).","journal-title":"GigaScience"},{"key":"1732_CR68","doi-asserted-by":"publisher","first-page":"289","DOI":"10.32614\/RJ-2016-021","volume":"8","author":"L Scrucca","year":"2016","unstructured":"Scrucca, L., Fop, M., Murphy, T. B. & Raftery, A. E. mclust 5: clustering, classification and density estimation using Gaussian finite mixture models. R J. 8, 289\u2013317 (2016).","journal-title":"R J."},{"key":"1732_CR69","doi-asserted-by":"publisher","first-page":"e93766","DOI":"10.1371\/journal.pone.0093766","volume":"9","author":"G Abraham","year":"2014","unstructured":"Abraham, G. & Inouye, M. Fast principal component analysis of large-scale genome-wide data. PLoS ONE 9, e93766 (2014).","journal-title":"PLoS ONE"},{"key":"1732_CR70","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1038\/nmeth.2307","volume":"10","author":"O Delaneau","year":"2013","unstructured":"Delaneau, O., Zagury, J.-F. & Marchini, J. Improved whole-chromosome phasing for disease and population genetic studies. Nat. Methods 10, 5\u20136 (2013).","journal-title":"Nat. Methods"},{"key":"1732_CR71","doi-asserted-by":"publisher","first-page":"e1000529","DOI":"10.1371\/journal.pgen.1000529","volume":"5","author":"BN Howie","year":"2009","unstructured":"Howie, B. N., Donnelly, P. & Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529 (2009).","journal-title":"PLoS Genet."},{"key":"1732_CR72","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1038\/ng2088","volume":"39","author":"J Marchini","year":"2007","unstructured":"Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906\u2013913 (2007).","journal-title":"Nat. Genet."},{"key":"1732_CR73","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v036.i03","volume":"36","author":"W Viechtbauer","year":"2010","unstructured":"Viechtbauer, W. Conducting meta-analyses in R with the metafor package. J. Stat. Softw. 36, 1\u201348 (2010).","journal-title":"J. Stat. Softw."},{"key":"1732_CR74","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":"1732_CR75","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2009","unstructured":"Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2009).","journal-title":"Bioinformatics"},{"key":"1732_CR76","doi-asserted-by":"publisher","first-page":"e1000770","DOI":"10.1371\/journal.pcbi.1000770","volume":"6","author":"O Stegle","year":"2010","unstructured":"Stegle, O., Parts, L., Durbin, R. & Winn, J. A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput. Biol. 6, e1000770 (2010).","journal-title":"PLoS Comput. Biol."},{"key":"1732_CR77","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888\u20131902.e21 (2019).","journal-title":"Cell"},{"key":"1732_CR78","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":"1732_CR79","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"1732_CR80","unstructured":"cotsapaslab \/ CrossDiseaseImmunochip. GitHub https:\/\/github.com\/cotsapaslab\/CrossDiseaseImmunochip (2021)."},{"key":"1732_CR81","doi-asserted-by":"publisher","unstructured":"Lincold, M. R. matthewlincoln\/xd-release: release. Zenodo https:\/\/doi.org\/10.5281\/zenodo.8371032 (2023).","DOI":"10.5281\/zenodo.8371032"}],"container-title":["Nature Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01732-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01732-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01732-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T13:06:21Z","timestamp":1715778381000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01732-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5]]},"references-count":81,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2024,5]]}},"alternative-id":["1732"],"URL":"https:\/\/doi.org\/10.1038\/s41588-024-01732-8","relation":{},"ISSN":["1061-4036","1546-1718"],"issn-type":[{"value":"1061-4036","type":"print"},{"value":"1546-1718","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5]]},"assertion":[{"value":"29 September 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 March 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}