{"apiVersion":"v1","directorySlug":"fanta-mcp-1a16e4b2c8","title":"fanta.bio - Functional Genome Annotations Database","description":"fanta.bio provides functional genome annotations with transcriptional activities. Search CREs by gene, SNP, or transcription factor binding across human and mouse genomes.","pageUrl":"https://www.mcpbundles.com/skills/fanta-mcp-1a16e4b2c8","connectPath":"importable","connectAction":"import_server","catalogListing":false,"bundleSlug":null,"listingKind":"remote_mcp","kind":"provider","transportUrl":"https://mcp.fanta.bio/mcp","hostedMcpUrl":null,"toolCount":19,"toolInventoryStatus":"observed","refreshedAt":"2026-11-03T13:26:00.516172+00:00","registryName":"bio.fanta/fanta-mcp-1a16e4b2c8","registryVersion":"2026.11.3","registryEligible":true,"tools":[{"name":"search_genes","description":"Search for genes by name, symbol, or ID using full-text search","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["query"],"properties":{"limit":{"type":"number","default":20,"maximum":100,"minimum":1},"query":{"type":"string"},"organism":{"enum":["any","human","mouse","GRCh38","mm39"],"type":"string","default":"any"}},"additionalProperties":false},"logicalName":"search_genes","displayName":"search_genes","title":"search_genes","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"search_cres","description":"Search for Cis-Regulatory Elements with advanced filters (supports * and ? wildcards)","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","properties":{"limit":{"type":"number","default":20,"maximum":100,"minimum":1},"cre_id":{"type":"string"},"antigen":{"type":"string"},"cre_name":{"type":"string"},"organism":{"enum":["any","human","mouse","GRCh38","mm39"],"type":"string","default":"any"},"external_id":{"type":"string"}},"additionalProperties":false},"logicalName":"search_cres","displayName":"search_cres","title":"search_cres","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"search_snps","description":"Search for SNPs by ID or GWAS trait using full-text search","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["query"],"properties":{"limit":{"type":"number","default":20,"maximum":100,"minimum":1},"query":{"type":"string"},"organism":{"enum":["any","human","mouse","GRCh38","mm39"],"type":"string","default":"any"}},"additionalProperties":false},"logicalName":"search_snps","displayName":"search_snps","title":"search_snps","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_cre_details","description":"Get detailed annotation information about a specific CRE","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["cre_id"],"properties":{"cre_id":{"type":"string"}},"additionalProperties":false},"logicalName":"get_cre_details","displayName":"get_cre_details","title":"get_cre_details","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"find_cres_by_gene","description":"Find CREs associated with a specific gene, sorted by distance from TSS. Accepts gene symbols (e.g., TP53, BRCA1) or Ensembl IDs (e.g., ENSG00000141510.17).","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["gene_id"],"properties":{"limit":{"type":"number","default":50,"maximum":200,"minimum":1},"antigen":{"type":"string"},"gene_id":{"type":"string"}},"additionalProperties":false},"logicalName":"find_cres_by_gene","displayName":"find_cres_by_gene","title":"find_cres_by_gene","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"find_cres_by_snp","description":"Find CREs near a specific SNP, sorted by distance","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["snp_id"],"properties":{"limit":{"type":"number","default":50,"maximum":200,"minimum":1},"snp_id":{"type":"string"}},"additionalProperties":false},"logicalName":"find_cres_by_snp","displayName":"find_cres_by_snp","title":"find_cres_by_snp","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"search_cres_fulltext","description":"Full-text search in CREs using FTS5 with BM25 relevance scoring","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["query"],"properties":{"limit":{"type":"number","default":20,"maximum":100,"minimum":1},"query":{"type":"string"},"organism":{"enum":["any","human","mouse","GRCh38","mm39"],"type":"string","default":"any"}},"additionalProperties":false},"logicalName":"search_cres_fulltext","displayName":"search_cres_fulltext","title":"search_cres_fulltext","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_unique_antigens","description":"Get list of unique antigens/TFs bound to a set of CREs","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["cre_ids"],"properties":{"cre_ids":{"type":"array","items":{"type":"string"},"maxItems":100,"minItems":1}},"additionalProperties":false},"logicalName":"get_unique_antigens","displayName":"get_unique_antigens","title":"get_unique_antigens","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_gene_details","description":"Get full gene information by symbol or Ensembl ID. Returns location, cross-references, and CRE count.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["gene_id"],"properties":{"gene_id":{"type":"string"}},"additionalProperties":false},"logicalName":"get_gene_details","displayName":"get_gene_details","title":"get_gene_details","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_snp_details","description":"Get full SNP information by rs ID. Returns trait, location, and CRE count.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["snp_id"],"properties":{"snp_id":{"type":"string"}},"additionalProperties":false},"logicalName":"get_snp_details","displayName":"get_snp_details","title":"get_snp_details","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_cre_expression","description":"Get expression data for a CRE across all samples. Returns an array of expression values (sparse data expanded to dense array).","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["cre_id"],"properties":{"cre_id":{"type":"string"}},"additionalProperties":false},"logicalName":"get_cre_expression","displayName":"get_cre_expression","title":"get_cre_expression","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_cre_bound_tfs","description":"Get detailed ChIP-Atlas transcription factor binding data for a CRE. Returns TFs with Q-scores and experiment IDs.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["cre_id"],"properties":{"limit":{"type":"number","default":50,"maximum":200,"minimum":1},"cre_id":{"type":"string"}},"additionalProperties":false},"logicalName":"get_cre_bound_tfs","displayName":"get_cre_bound_tfs","title":"get_cre_bound_tfs","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_cres_batch","description":"Batch lookup multiple CREs by ID. Returns full annotation details for each CRE found.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["cre_ids"],"properties":{"cre_ids":{"type":"array","items":{"type":"string"},"maxItems":200,"minItems":1}},"additionalProperties":false},"logicalName":"get_cres_batch","displayName":"get_cres_batch","title":"get_cres_batch","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_gene_expression","description":"Get expression data across all CREs associated with a gene. Accepts gene symbols or Ensembl IDs.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["gene_id"],"properties":{"limit":{"type":"number","default":100,"maximum":200,"minimum":1},"gene_id":{"type":"string"}},"additionalProperties":false},"logicalName":"get_gene_expression","displayName":"get_gene_expression","title":"get_gene_expression","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_gene_antigens","description":"Get unique transcription factors bound to all CREs associated with a gene. Accepts gene symbols or Ensembl IDs.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["gene_id"],"properties":{"gene_id":{"type":"string"}},"additionalProperties":false},"logicalName":"get_gene_antigens","displayName":"get_gene_antigens","title":"get_gene_antigens","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"find_cres_by_region","description":"Find CREs within a genomic coordinate range. Uses an indexed search on chromosome and position.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["chr","start","end"],"properties":{"chr":{"type":"string"},"end":{"type":"integer","minimum":1},"limit":{"type":"number","default":50,"maximum":200,"minimum":1},"start":{"type":"integer","minimum":0},"organism":{"enum":["any","human","mouse","hg38","mm10","GRCh38","mm39"],"type":"string","default":"any"}},"additionalProperties":false},"logicalName":"find_cres_by_region","displayName":"find_cres_by_region","title":"find_cres_by_region","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"find_shared_regulators","description":"Find transcription factors shared across multiple CREs or genes. Identifies common regulatory programs.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","properties":{"cre_ids":{"type":"array","items":{"type":"string"}},"gene_ids":{"type":"array","items":{"type":"string"}},"min_shared":{"type":"integer","default":2,"minimum":1}},"additionalProperties":false},"logicalName":"find_shared_regulators","displayName":"find_shared_regulators","title":"find_shared_regulators","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_gene_regulatory_summary","description":"Get a comprehensive regulatory landscape summary for a gene: gene info, associated CREs with distances, and top transcription factors across all CREs.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["gene_id"],"properties":{"gene_id":{"type":"string"},"cre_limit":{"type":"number","default":50,"maximum":200,"minimum":1}},"additionalProperties":false},"logicalName":"get_gene_regulatory_summary","displayName":"get_gene_regulatory_summary","title":"get_gene_regulatory_summary","annotations":{"untrustedContentHint":true,"readOnlyHint":true}},{"name":"get_snp_regulatory_impact","description":"Analyze the regulatory impact of a SNP: SNP info, affected CREs, and transcription factors bound to those CREs.","inputSchema":{"type":"object","$schema":"http://json-schema.org/draft-07/schema#","required":["snp_id"],"properties":{"snp_id":{"type":"string"},"cre_limit":{"type":"number","default":50,"maximum":200,"minimum":1}},"additionalProperties":false},"logicalName":"get_snp_regulatory_impact","displayName":"get_snp_regulatory_impact","title":"get_snp_regulatory_impact","annotations":{"untrustedContentHint":true,"readOnlyHint":true}}],"toolSource":"directory_preview","agentAction":"both","installLinks":[{"id":"cursor","label":"Cursor","href":"cursor://anysphere.cursor-deeplink/mcp/install?name=fanta-bio---Functional-Genome-Annotations-Database&config=eyJ1cmwiOiAiaHR0cHM6Ly9tY3AuZmFudGEuYmlvL21jcCJ9"},{"id":"vscode","label":"VS Code","href":"vscode:mcp/install?%7B%22name%22%3A%22fanta-bio---Functional-Genome-Annotations-Database%22%2C%22type%22%3A%22http%22%2C%22url%22%3A%22https%3A%2F%2Fmcp.fanta.bio%2Fmcp%22%7D"},{"id":"vscode-insiders","label":"VS Code Insiders","href":"vscode-insiders:mcp/install?%7B%22name%22%3A%22fanta-bio---Functional-Genome-Annotations-Database%22%2C%22type%22%3A%22http%22%2C%22url%22%3A%22https%3A%2F%2Fmcp.fanta.bio%2Fmcp%22%7D"},{"id":"claude-web","label":"Claude.ai","href":"https://claude.ai/customize/connectors?modal=add-custom-connector&connectorName=fanta.bio+-+Functional+Genome+Annotations+Database&connectorUrl=https%3A%2F%2Fmcp.fanta.bio%2Fmcp"},{"id":"codex","label":"Codex","copyText":"codex mcp add \"fanta-bio---Functional-Genome-Annotations-Database\" --url \"https://mcp.fanta.bio/mcp\""},{"id":"chatgpt","label":"ChatGPT","href":"https://www.mcpbundles.com/docs/integrations/chatgpt"}],"catalogUrl":"https://www.mcpbundles.com/api/directory/v1/servers/fanta-mcp-1a16e4b2c8","callUrl":"https://www.mcpbundles.com/api/directory/v1/servers/fanta-mcp-1a16e4b2c8/tools/{tool}","mcpServerUrl":"https://mcp.fanta.bio/mcp","liveCatalogUrl":"https://www.mcpbundles.com/api/directory/v1/servers/fanta-mcp-1a16e4b2c8?live=1"}