fanta.bio Web API

The fanta.bio REST API gives programmatic access to the same functional genome annotations powering the website — CREs, genes, SNPs, expression data, and ChIP-Atlas transcription factor binding. It is the foundation for tools, notebooks, and the MCP server.

Base URL

https://api.fanta.bio

What’s available

The API exposes four resource families plus a unified search endpoint:

Resource	Purpose	Example
CREs	Cis-regulatory elements with coordinates, expression, and TF binding	`/v0/cres/FCHS_1`
Genes	Gene records resolved by Ensembl ID, symbol, or synonym	`/v0/genes/TP53`
SNPs	GWAS-associated variants with trait annotations	`/v0/snps/rs10001548`
Analysis	Cross-database aggregations (shared regulators, regulatory summaries)	`POST /v0/analysis/shared-regulators`
Unified search	One query fans out to genes + SNPs + CREs in parallel	`POST /v0/search`

For the full endpoint list and request/response shapes, browse the interactive docs at api.fanta.bio/docs.

Quick examples

Search for a gene

curl "https://api.fanta.bio/v0/genes?query=TP53"

The gene resolver accepts Ensembl IDs (ENSG00000141510.20), official symbols (TP53), or synonyms (p53) — all three resolve to the same canonical record.

Find CREs near a SNP

curl "https://api.fanta.bio/v0/snps/rs10001548/cres"

Unified cross-entity search

curl -X POST "https://api.fanta.bio/v0/search" \
  -H "Content-Type: application/json" \
  -d '{"query": "TP53", "limit": 10}'

The endpoint auto-detects entity-shaped queries: rs10001548 → SNPs only, ENSG00000141510.20 → genes only, free text → all three in parallel.

Cross-database analysis

curl -X POST "https://api.fanta.bio/v0/analysis/gene-regulatory-summary" \
  -H "Content-Type: application/json" \
  -d '{"gene_id": "TP53", "cre_limit": 50}'

Returns the gene record, associated CREs sorted by distance from TSS, and the dominant transcription factors binding those CREs — in a single request.

Response format

All responses follow the same envelope:

{
  "success": true,
  "data": [...],
  "meta": {
    "version": "v0",
    "count": 20,
    "limit": 20,
    "offset": 0,
    "hasMore": true
  }
}

Errors return {success: false, error: {code, message, details?}} with HTTP status codes that match the error class (404, 400, 429, etc.).

Features at a glance

FTS5 full-text search with weighted BM25 and exact-match boost — TP53 ranks ahead of TP53TG3
Synonym resolution — p53, IFI15, official symbols, and Ensembl IDs all work
Wildcard filters — * (any chars), ? (single char) on CRE filter endpoints
Rate limiting with per-endpoint hourly limits (returns RATE_LIMIT_EXCEEDED with retryAfter)
Response caching for idempotent reads
OpenAPI 3.1 for type-safe client generation in any language