ensembl_query_region
ActiveTool of io.github.cyanheads/ensembl-mcp-server
Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name. Useful for "what's in this locus?" and for seeding follow-up lookups. Region format is chr:start-end (e.g. 13:32315086-32400268 for the BRCA2 locus). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. The feature parameter defaults to gene only to prevent overwhelming returns — requesting variation in an 85 kb region returns 44,000+ entries. Explicitly include variation, regulatory, transcript, or exon only when needed. Exon rows carry the parent transcript ID, so the same exon appears once per transcript it belongs to.
Parameters schema
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"required": [
"species",
"region"
],
"properties": {
"region": {
"type": "string",
"description": "Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."
},
"biotype": {
"type": "string",
"description": "Optional biotype filter (e.g. protein_coding, lncRNA, SNV). Applied server-side by Ensembl. Not all feature types support biotype filtering."
},
"feature": {
"type": "array",
"items": {
"enum": [
"gene",
"transcript",
"variation",
"regulatory",
"exon"
],
"type": "string",
"description": "A feature type to retrieve: gene, transcript, variation, regulatory, or exon."
},
"default": [
"gene"
],
"description": "Feature types to retrieve. Default is gene only. Requesting variation in a large region can return tens of thousands of features. Include variation only for targeted small regions (single gene loci or smaller)."
},
"species": {
"type": "string",
"description": "Species in Ensembl internal format (e.g. homo_sapiens, mus_musculus). Use ensembl_list_species to discover valid values."
}
}
}Parent server
io.github.cyanheads/ensembl-mcp-server
https://github.com/cyanheads/ensembl-mcp-server
1/7 registries