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  • Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 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, 600–605 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Umans, B. D., Battle, A. & Gilad, Y. Where are the disease-associated eQTLs? Trends Genet. 37, 109–124 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Gutierrez-Arcelus, M. et al. Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci. Nat. Genet. 52, 247–253 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Davenport, E. E. et al. Discovering in vivo cytokine–eQTL interactions from a lupus clinical trial. Genome Biol. 19, 168 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Strober, B. J. et al. Dynamic genetic regulation of gene expression during cellular differentiation. Science 364, 1287–1290 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cuomo, A. S. E. et al. Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nat. Commun. 11, 810 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhernakova, D. V. et al. Identification of context-dependent expression quantitative trait loci in whole blood. Nat. Genet. 49, 139–145 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Moore, R. et al. A linear mixed-model approach to study multivariate gene-environment interactions. Nat. Genet. 51, 180–186 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Kim-Hellmuth, S. et al. Cell type-specific genetic regulation of gene expression across human tissues. Science 369, eaaz8528 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Raj, T. et al. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science 344, 519–523 (2016).

    ADS 
    Article 
    CAS 

    Google Scholar 

  • Trynka, G. et al. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet. 45, 124–130 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Farh, K. H. et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337–343 (2014).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Wambre, E. et al. A phenotypically and functionally distinct human TH2 cell subpopulation is associated with allergic disorders. Sci. Transl. Med. 9, eaam9171 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Arlehamn, C. L. et al. Transcriptional profile of tuberculosis antigen-specific T cells reveals novel multifunctional features. J. Immunol. 193, 2931–2940 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Eizenberg-Magar, I. et al. Diverse continuum of CD4+ T-cell states is determined by hierarchical additive integration of cytokine signals. Proc. Natl Acad. Sci. USA 114, E6447–E6456 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Annunziato, F., Cosmi, L., Liotta, F., Maggi, E. & Romagnini, S. Defining the human T helper 17 cell phenotype. Trends Immunol. 33, 505–512 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Kiner, E. et al. Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes. Nat. Immunol. 22, 216–228 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • van der Wijst, M. G. P. et al. Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs. Nat. Genet. 50, 493–497 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Jerber, J. et al. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nat. Genet. 53, 304–312 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Neavin, D. et al. Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. Genome Biol. 22, 76 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Randolph, H. E. et al. Genetic ancestry effects on the response to viral infection are pervasive but cell type specific. Science 374, 1127–1133 (2021).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Nathan, A. et al. Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease. Nat. Immunol. 22, 781–793 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Luo, Y. et al. Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians. Nat. Commun. 10, 3765 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Chen, L. et al. Genetic drivers of epigenetic and transcriptional variation in human immune cells. Cell 167, 1398–1414 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 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).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

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

    Article 
    CAS 

    Google Scholar 

  • The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).

    Article 
    CAS 

    Google Scholar 

  • Schmiedel, B. J. et al. Impact of genetic polymorphisms on human immune cell gene expression. Cell 175, 1701–1715 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rothenberg, E. V. & Taghon, T. Molecular genetics of T cell development. Annu. Rev. Immunol. 23, 601–649 (2005).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Townes, F. W., Hicks, S. C., Aryee, M. J. & Irizarry, R. A. Feature selection and dimension reduction for single-cell RNA-seq based on a multinomial model. Genome Biol. 20, 295 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Sarkar, A. & Stephens, M. Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis. Nat. Genet. 53, 770–777 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Dobbyn, A. et al. Landscape of conditional eQTL in dorsolateral prefrontal cortex and co-localization with schizophrenia GWAS. Am. J. Hum. Genet. 102, 1169–1184 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 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–D1012 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Okada, Y. et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376–381 (2014).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Laufer, V. A. et al. Genetic influences on susceptibility to rheumatoid arthritis in African-Americans. Hum. Mol. Genet. 28, 858–874 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 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, 979–986 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Stahl, E. A. et al. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat. Genet. 42, 508–514 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell type-specific gene expression. Nature 459, 108–112 (2009).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hormozdiari, F., Kostem, E., Kang, E. Y., Pasaniuc, B. & Eskin, E. Identifying causal variants at loci with multiple signals of association. Genetics 198, 497–508 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Amariuta, T. et al. IMPACT: genomic annotation of cell-state-specific regulatory elements inferred from the epigenome of bound transcription factors. Am. J. Hum. Genet. 104, 879–895 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zaitlen, N., Pasaniuc, B., Gur, T., Ziv, E. & Halperin, E. Leveraging genetic variability across populations for the identification of causal variants. Am. J. Hum. Genet. 86, 23–33 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Calderon, D. et al. Landscape of stimulation-responsive chromatin across diverse human immune cells. Nat. Genet. 51, 1494–1505 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Smillie, C. S. et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178, 714–730 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Reshef, Y. A. et al. Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics. Nat. Biotechnol. 40, 355–363 (2022).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Burkhardt, D. B. et al. Quantifying the effect of experimental perturbations at single-cell resolution. Nat. Biotechnol. 39, 619–629 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ben-David, E. et al. Whole-organism eQTL mapping at cellular resolution with single-cell sequencing. eLife 10, e65857 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cuomo, A. S. E. et al. Optimizing expression quantitative trait locus mapping workflows for single-cell studies. Genome Biol. 22, 188 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • van der Wijst, M. et al. The single-cell eQTLGen consortium. eLife 9, e52155 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Oelen, R. et al. Single-cell RNA-sequencing reveals widespread personalized, context-specific gene expression regulation in immune cells. Preprint at bioRxiv https://doi.org/10.1101/2021.06.04.447088 (2021).

  • Kotliar, D. et al. Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-seq. eLife 8, e43803 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 



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