CCL21 Gene

HGNC Family	Chemokine ligands (CCL), Endogenous ligands
Name	chemokine (C-C motif) ligand 21
Description	This antimicrobial gene is one of several CC cytokine genes clustered on the p-arm of chromosome 9. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. Similar to other chemokines the protein encoded by this gene inhibits hemopoiesis and stimulates chemotaxis. This protein is chemotactic in vitro for thymocytes and activated T cells, but not for B cells, macrophages, or neutrophils. The cytokine encoded by this gene may also play a role in mediating homing of lymphocytes to secondary lymphoid organs. It is a high affinity functional ligand for chemokine receptor 7 that is expressed on T and B lymphocytes and a known receptor for another member of the cytokine family (small inducible cytokine A19). [provided by RefSeq, Sep 2014]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n CCL21, also known as secondary lymphoid tissue chemokine (SLC), is a homeostatic chemokine that plays a pivotal role in orchestrating immune cell trafficking and organization of lymphoid structures. Genetic studies have identified polymorphisms at the CCL21 locus that are associated with an increased risk of rheumatoid arthritis, suggesting that aberrant lymphocyte recruitment may contribute to disease pathogenesis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In transgenic mouse models, ectopic expression of CCL21 leads to the development of larger and more organized lymphoid infiltrates compared with other homeostatic chemokines, underscoring its superior ability to drive the formation of structured lymphoid tissues that may be important during chronic inflammation and autoimmune responses."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Functionally, CCL21 acts as a key ligand for the chemokine receptor CCR7 and is essential for the migration of various immune cell types. Its expression in lymphoid tissues directs the trafficking of dendritic cells and T cells toward lymph nodes—ensuring the effective priming of adaptive immune responses. For example, the migration of human monocyte‐derived dendritic cells toward lymph node–derived chemokines is critically dependent on CCL21, and CCR7 activation by its ligands governs the intranodal motility of T cells, as well as the migration of positively selected thymocytes from the cortex to the medulla."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Moreover, proper localization of regulatory T cells within lymph nodes—critical for maintaining peripheral tolerance—also relies on CCR7-mediated responses to CCL21. Defects in this pathway can lead to impaired T regulatory cell positioning and consequently perturbed immune homeostasis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In summary, CCL21 is not only central to the development and maintenance of lymphoid tissue architecture but also essential for directing immune cell migration during homeostasis and inflammation. Its role in organizing immune cell infiltrates, coupled with the genetic association with autoimmune conditions, highlights CCL21 as a critical mediator linking immune surveillance, lymphoid neogenesis, and disease susceptibility.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Eli A Stahl, Soumya Raychaudhuri, Elaine F Remmers, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.582"}], "href": "https://doi.org/10.1038/ng.582"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20453842"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20453842"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Soumya Raychaudhuri, Elaine F Remmers, Annette T Lee, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Common variants at CD40 and other loci confer risk of rheumatoid arthritis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.233"}], "href": "https://doi.org/10.1038/ng.233"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18794853"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18794853"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Sanjiv A Luther, Afshin Bidgol, Diana C Hargreaves, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Differing activities of homeostatic chemokines CCL19, CCL21, and CXCL12 in lymphocyte and dendritic cell recruitment and lymphoid neogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Immunol (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.4049/jimmunol.169.1.424"}], "href": "https://doi.org/10.4049/jimmunol.169.1.424"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12077273"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12077273"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Elke Scandella, Ying Men, Silke Gillessen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Prostaglandin E2 is a key factor for CCR7 surface expression and migration of monocyte-derived dendritic cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Blood (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1182/blood-2001-11-0017"}], "href": "https://doi.org/10.1182/blood-2001-11-0017"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12149218"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12149218"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Tomoo Ueno, Fumi Saito, Daniel H D Gray, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CCR7 signals are essential for cortex-medulla migration of developing thymocytes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Exp Med (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1084/jem.20040643"}], "href": "https://doi.org/10.1084/jem.20040643"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15302902"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15302902"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Tim Worbs, Thorsten R Mempel, Jasmin Bölter, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CCR7 ligands stimulate the intranodal motility of T lymphocytes in vivo."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Exp Med (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1084/jem.20061706"}], "href": "https://doi.org/10.1084/jem.20061706"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17325198"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17325198"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Martin A Schneider, Josef G Meingassner, Martin Lipp, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CCR7 is required for the in vivo function of CD4+ CD25+ regulatory T cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Exp Med (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1084/jem.20061405"}], "href": "https://doi.org/10.1084/jem.20061405"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17371928"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17371928"}]}]}]}
Synonyms	TCA4, SCYA21, 6CKINE, ECL, CKB9, SLC
Proteins	CCL21_HUMAN
NCBI Gene ID	6366
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

CCL21 has 6,628 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 111 datasets.

Click the + buttons to view associations for CCL21 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

CCL21 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by CCL21 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CCL21 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of CCL21 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of CCL21 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of CCL21 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CCL21 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of CCL21 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CCL21 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CCL21 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of CCL21 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of CCL21 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of CCL21 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with CCL21 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CCL21 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of CCL21 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of CCL21 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of CCL21 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing CCL21 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with CCL21 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with CCL21 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of CCL21 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with CCL21 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with CCL21 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with CCL21 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with CCL21 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by CCL21 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving CCL21 gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving CCL21 gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with CCL21 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with CCL21 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with CCL21 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with CCL21 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with CCL21 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with CCL21 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at CCL21 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CCL21 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of CCL21 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing CCL21 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with CCL21 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with CCL21 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.