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We elucidated cell type- and context-specific human leukocyte antigen (HLA) and genome-wide associations with T and B cell receptor repertoires. Colocalization using dynamic genetic regulation provided better understanding of genome-wide association signals. Differential gene and protein expres"],"journal":["Nature genetics"],"pubmed_title":["Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution."],"pmcid":["PMC12339405"],"funding_grant_id":["22gm1810003h0001","22H00476, 24K02697"],"pubmed_authors":["Saito R","Osawa T","Saito Y","Miyazaki Y","Tanino Y","Motooka D","Ihara S","Sonehara K","Watanabe C","Hosoda C","Mashimo S","Ogata T","Takayanagi N","Watanabe H","Isogai S","Watanabe M","Watanabe K","Uchida T","Tsuburai T","Fukuyama S","Uchida S","Kita T","Kashiwada T","Yatomi M","Kuse N","Kanda H","Kagyo J","Nishitsuji M","Morisaki H","Japan COVID-19 Task Force","Saito F","Saito H","Hanada S","Kan-O K","Kishi H","Makino Y","Asano K","Yamasaki M","Sato Y","Makino S","Naito T","Namkoong H","Kimizuka Y","Chubachi S","Hashimoto S","Miyano S","Uchimura Y","Ishikura H","Hashimoto N","Kaneko Y","Ogata H","Ohta S","Kuramochi M","Nanki K","Uwamino Y","Imamura T","Ohta K","Sato T","Sato R","Yamashita T","Sato 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Here, we constructed an immune cell atlas with single-cell transcriptomics of >1.5 million peripheral blood mononuclear cells, host genetics, plasma proteomics and gut metagenomics from 235 Japanese persons, including patients with coronavirus disease 2019 (COVID-19) and healthy individuals. We mapped germline genetic effects on gene expression within immune cell types and across cell states. We elucidated cell type- and context-specific human leukocyte antigen (HLA) and genome-wide associations with T and B cell receptor repertoires. Colocalization using dynamic genetic regulation provided better understanding of genome-wide association signals. Differential gene and protein expres","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Aug","modification":"2026-05-29T16:34:06.001Z","creation":"2026-04-08T05:23:39.044Z"},"accession":"S-EPMC12339405","cross_references":{"pubmed":["40721531"],"doi":["10.1038/s41588-025-02266-3"]}}