Finngen Tools

Configuration File: finngen_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the finngen_tools.json configuration file.

Available Tools

FinnGen_get_phenotype (Type: FinnGenTool)

Get detailed information about a specific FinnGen disease endpoint (phenotype). Returns case/cont…

FinnGen_get_phenotype tool specification

Tool Information:

  • Name: FinnGen_get_phenotype

  • Type: FinnGenTool

  • Description: Get detailed information about a specific FinnGen disease endpoint (phenotype). Returns case/control counts, genomic control lambda values, and genome-wide significant loci count for a given phenocode. Use phenocodes from FinnGen_list_phenotypes (e.g., ‘T2D’ for type 2 diabetes, ‘I9_CHD’ for coronary heart disease, ‘C3_BREAST’ for breast cancer).

Parameters:

  • phenocode (string) (required) FinnGen phenotype code (e.g., ‘T2D’, ‘I9_CHD’, ‘C3_BREAST’, ‘J10_ASTHMA’). Get valid codes from FinnGen_list_phenotypes.

Example Usage:

query = {
    "name": "FinnGen_get_phenotype",
    "arguments": {
        "phenocode": "example_value"
    }
}
result = tu.run(query)

FinnGen_get_region_associations (Type: FinnGenTool)

Get regional association and fine-mapping credible set data for a FinnGen phenotype in a specific…

FinnGen_get_region_associations tool specification

Tool Information:

  • Name: FinnGen_get_region_associations

  • Type: FinnGenTool

  • Description: Get regional association and fine-mapping credible set data for a FinnGen phenotype in a specific genomic region. Returns credible sets with lead variants, posterior probabilities, and minor allele frequencies. Use to examine GWAS signals at a specific locus for a Finnish population disease endpoint.

Parameters:

  • phenocode (string) (required) FinnGen phenotype code (e.g., ‘T2D’, ‘I9_CHD’). Get codes from FinnGen_list_phenotypes.

  • region (string) (required) Genomic region in chr:start-end format (GRCh38). Example: ‘9:22000000-22200000’ for the CDKN2A/B locus on chromosome 9.

Example Usage:

query = {
    "name": "FinnGen_get_region_associations",
    "arguments": {
        "phenocode": "example_value",
        "region": "example_value"
    }
}
result = tu.run(query)

FinnGen_get_variant_finemapping (Type: FinnGenTool)

Get fine-mapping regions associated with a genomic variant in FinnGen. Returns phenotypes where t…

FinnGen_get_variant_finemapping tool specification

Tool Information:

  • Name: FinnGen_get_variant_finemapping

  • Type: FinnGenTool

  • Description: Get fine-mapping regions associated with a genomic variant in FinnGen. Returns phenotypes where this variant appears in a credible set from statistical fine-mapping. Input variant in chr:pos:ref:alt format (GRCh38). Useful for understanding which disease associations a variant contributes to in the Finnish population.

Parameters:

  • variant (string) (required) Genomic variant in chr:pos:ref:alt format (GRCh38). Examples: ‘19:44908684:T:C’ (APOE rs429358), ‘10:112998590:C:T’ (TCF7L2 rs7903146). Also accepts chr-pos-ref-alt format.

Example Usage:

query = {
    "name": "FinnGen_get_variant_finemapping",
    "arguments": {
        "variant": "example_value"
    }
}
result = tu.run(query)

FinnGen_list_phenotypes (Type: FinnGenTool)

Search and list FinnGen disease endpoints (phenotypes). FinnGen is a Finnish population genomics …

FinnGen_list_phenotypes tool specification

Tool Information:

  • Name: FinnGen_list_phenotypes

  • Type: FinnGenTool

  • Description: Search and list FinnGen disease endpoints (phenotypes). FinnGen is a Finnish population genomics study with 486,367 participants and 2,470 phenotypes. Search by keyword (e.g., ‘diabetes’, ‘asthma’, ‘cancer’) or browse by category. Returns phenotype codes, case/control counts, and number of genome-wide significant loci. Use phenocode values from results with FinnGen_get_phenotype and FinnGen_get_region_associations.

Parameters:

  • query ([‘string’, ‘null’]) (optional) Search query to filter phenotypes by code, name, or category (e.g., ‘diabetes’, ‘breast cancer’, ‘asthma’). Case-insensitive.

  • category ([‘string’, ‘null’]) (optional) Filter by disease category (e.g., ‘Diabetes’, ‘circulatory’, ‘Neoplasms’). Case-insensitive substring match.

  • min_cases ([‘integer’, ‘null’]) (optional) Minimum number of cases required. Use to filter for well-powered phenotypes (e.g., 1000).

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default 50).

Example Usage:

query = {
    "name": "FinnGen_list_phenotypes",
    "arguments": {
    }
}
result = tu.run(query)