ensembl_variation
Analyze genomic variants using VEP consequence prediction, variant lookup, LD analysis, phenotype mapping, and haplotype data. Supports species-specific queries with Variant ID, HGVS notation, or genomic regions.
Instructions
Variant analysis: VEP consequence prediction, variant lookup, LD analysis, phenotype mapping, haplotypes. Covers /variation/, /vep/, /ld/, /phenotype/ endpoints.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| analysis_type | No | Type of variant analysis | |
| consequence_type | No | Filter by consequence type (e.g., 'missense_variant', 'stop_gained', 'splice_donor_variant') | |
| hgvs_notation | No | HGVS notation for VEP analysis (e.g., '17:g.7579472G>C', 'ENST00000288602.6:c.1799T>A', 'NM_007294.3:c.1799T>A') | |
| population | No | Population for LD analysis (e.g., '1000GENOMES:phase_3:EUR', '1000GENOMES:phase_3:AFR', '1000GENOMES:phase_3:ASN') | |
| region | No | Genomic region in format 'chr:start-end' for variant search (e.g., '17:7565096-7590856', 'X:1000000-2000000', '1:100000-200000') | |
| species | No | Species name (e.g., 'homo_sapiens', 'mus_musculus') | homo_sapiens |
| transcript_id | No | Transcript ID for haplotype analysis (e.g., 'ENST00000288602', 'ENST00000350283') | |
| variant_id | No | Variant ID (e.g., 'rs699', 'rs1042779', 'COSM476') or HGVS notation (e.g., '17:g.7579472G>C') |
Input Schema (JSON Schema)
{
"anyOf": [
{
"required": [
"variant_id"
]
},
{
"required": [
"region"
]
},
{
"required": [
"hgvs_notation"
]
}
],
"properties": {
"analysis_type": {
"description": "Type of variant analysis",
"enum": [
"variant_info",
"vep",
"ld",
"phenotype",
"haplotypes"
],
"type": "string"
},
"consequence_type": {
"description": "Filter by consequence type (e.g., 'missense_variant', 'stop_gained', 'splice_donor_variant')",
"type": "string"
},
"hgvs_notation": {
"description": "HGVS notation for VEP analysis (e.g., '17:g.7579472G>C', 'ENST00000288602.6:c.1799T>A', 'NM_007294.3:c.1799T>A')",
"type": "string"
},
"population": {
"description": "Population for LD analysis (e.g., '1000GENOMES:phase_3:EUR', '1000GENOMES:phase_3:AFR', '1000GENOMES:phase_3:ASN')",
"type": "string"
},
"region": {
"description": "Genomic region in format 'chr:start-end' for variant search (e.g., '17:7565096-7590856', 'X:1000000-2000000', '1:100000-200000')",
"type": "string"
},
"species": {
"default": "homo_sapiens",
"description": "Species name (e.g., 'homo_sapiens', 'mus_musculus')",
"type": "string"
},
"transcript_id": {
"description": "Transcript ID for haplotype analysis (e.g., 'ENST00000288602', 'ENST00000350283')",
"type": "string"
},
"variant_id": {
"description": "Variant ID (e.g., 'rs699', 'rs1042779', 'COSM476') or HGVS notation (e.g., '17:g.7579472G>C')",
"type": "string"
}
},
"type": "object"
}