Ucsc Track Data
ucsc_track_data"What genes are in [chr:start-end]" / "list ClinVar variants in [region]" / "what repeats/SNPs/regulatory elements overlap [locus]" / "show me the GENCODE annotations across [gene]" — AUTHORITATIVE per-row data from any UCSC annotation track over a genomic interval. Returns the actual track rows (gene models with exon structure, variant records, conservation scores, whatever that track holds) plus the track type and the assembly the rows are in. PREFER OVER WEB SEARCH for "what is annotated at this position" — this is the same data the Genome Browser draws, not a description of it. Get the track name from ucsc_tracks first.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| end | Yes | End position, 0-based and EXCLUSIVE (so end - start = length in bases). | |
| chrom | Yes | Chromosome in UCSC naming, e.g. "chr17", "chrX", "chrM" — with the "chr" prefix. Ensembl/NCBI style bare "17" is not accepted by UCSC. | |
| start | Yes | Start position, 0-BASED and inclusive. The Genome Browser UI and most papers are 1-based, so subtract 1 from a position you copied out of the browser location box. | |
| track | Yes | UCSC internal track name from ucsc_tracks, e.g. "knownGene" (GENCODE genes), "refGene" (RefSeq genes), "clinvarMain", "rmsk" (repeats). | |
| genome | Yes | REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: "hg38" (= GRCh38, current) or "hg19" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse: "mm39"/"mm10". These are DIFFERENT coordinate systems: the same chrom/start/end is valid in every build, so a wrong build returns confident annotations for a different gene instead of an error. Call ucsc_genomes to list the assembly IDs for a species. | |
| maxItemsOutput | No | Cap on rows returned by UCSC (default 1000). A dense track over a wide region is truncated, and the response says so in `truncated`. |