Pheweb Phewas Tools

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

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

Available Tools

BioBankJapan_phewas_by_variant (Type: PheWebPheWASTool)

Phenome-wide association study (PheWAS) lookup for a single variant in BioBank Japan (BBJ), the l…

BioBankJapan_phewas_by_variant tool specification

Tool Information:

  • Name: BioBankJapan_phewas_by_variant

  • Type: PheWebPheWASTool

  • Description: Phenome-wide association study (PheWAS) lookup for a single variant in BioBank Japan (BBJ), the largest Japanese-ancestry biobank. Returns every phenotype associated with the variant (the inverse of a GWAS), sorted by p-value. Accepts an rsID (auto-resolved to GRCh37 via Ensembl) or an explicit chr:pos:ref:alt variant in GRCh37. Use for cross-ancestry replication of a genetic association in an East Asian (Japanese) population.

Parameters:

  • rsid (string) (optional) dbSNP rsID, e.g. ‘rs7903146’. Auto-resolved to GRCh37 coordinates via Ensembl. Provide this OR ‘variant’.

  • variant (string) (optional) Variant in chr:pos:ref:alt or chr-pos-ref-alt format, in GRCh37, e.g. ‘10:114758349:C:T’. Provide this OR ‘rsid’. A bare rsID is also accepted here.

  • limit (integer) (optional) Maximum number of phenotype associations to return (sorted by ascending p-value).

  • max_pval ([‘number’, ‘null’]) (optional) Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).

Example Usage:

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

Genebass_gene_burden_phewas (Type: GenebassTool)

Exome-wide gene-level burden PheWAS from Genebass (UK Biobank ~394K exomes, SAIGE-GENE+). Given o…

Genebass_gene_burden_phewas tool specification

Tool Information:

  • Name: Genebass_gene_burden_phewas

  • Type: GenebassTool

  • Description: Exome-wide gene-level burden PheWAS from Genebass (UK Biobank ~394K exomes, SAIGE-GENE+). Given one gene, returns its rare-variant burden association across ~4,500 phenotypes (GRCh38), sorted by p-value. Aggregates rare coding variants into a single gene-level test, complementing single-variant PheWAS. Accepts an Ensembl gene ID (ENSG…) or a gene symbol (auto-resolved via Ensembl). Choose a burden_set: pLoF (predicted loss-of-function, default), missense|LC, or synonymous.

Parameters:

  • gene (string) (required) Ensembl gene ID (e.g. ‘ENSG00000148737’) or gene symbol (e.g. ‘TCF7L2’). Symbols are auto-resolved via Ensembl.

  • burden_set (string) (optional) Variant category aggregated in the burden test. One of: ‘pLoF’ (default), ‘missense|LC’, ‘synonymous’. Aliases accepted: lof/plof -> pLoF, missense -> missense|LC.

  • limit (integer) (optional) Maximum number of phenotype associations to return (sorted by ascending burden p-value).

  • max_pval ([‘number’, ‘null’]) (optional) Optional: only return associations with burden p-value <= this threshold (e.g. 2.5e-6 for exome-wide significance).

Example Usage:

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

TPMI_phewas_by_variant (Type: PheWebPheWASTool)

Phenome-wide association study (PheWAS) lookup for a single variant in the Taiwan Precision Medic…

TPMI_phewas_by_variant tool specification

Tool Information:

  • Name: TPMI_phewas_by_variant

  • Type: PheWebPheWASTool

  • Description: Phenome-wide association study (PheWAS) lookup for a single variant in the Taiwan Precision Medicine Initiative (TPMI) PheWeb, a large Taiwanese (Han Chinese) biobank. Returns every phenotype associated with the variant, sorted by p-value. Accepts an rsID (auto-resolved to GRCh38 via Ensembl) or an explicit chr:pos:ref:alt variant in GRCh38. Use for cross-ancestry replication in an East Asian (Han Chinese) population.

Parameters:

  • rsid (string) (optional) dbSNP rsID, e.g. ‘rs7903146’. Auto-resolved to GRCh38 coordinates via Ensembl. Provide this OR ‘variant’.

  • variant (string) (optional) Variant in chr:pos:ref:alt or chr-pos-ref-alt format, in GRCh38, e.g. ‘10:112998590:C:T’. Provide this OR ‘rsid’. A bare rsID is also accepted here.

  • limit (integer) (optional) Maximum number of phenotype associations to return (sorted by ascending p-value).

  • max_pval ([‘number’, ‘null’]) (optional) Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).

Example Usage:

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

UKBTOPMed_phewas_by_variant (Type: PheWebPheWASTool)

Phenome-wide association study (PheWAS) lookup for a single variant in the UKB-TOPMed PheWeb (UK …

UKBTOPMed_phewas_by_variant tool specification

Tool Information:

  • Name: UKBTOPMed_phewas_by_variant

  • Type: PheWebPheWASTool

  • Description: Phenome-wide association study (PheWAS) lookup for a single variant in the UKB-TOPMed PheWeb (UK Biobank, ~400K European-ancestry samples, 1,400+ phecode phenotypes). Returns every phenotype associated with the variant, sorted by p-value. Accepts an rsID (auto-resolved to GRCh38 via Ensembl) or an explicit chr:pos:ref:alt variant in GRCh38. Use for variant pleiotropy assessment and replication in a European population.

Parameters:

  • rsid (string) (optional) dbSNP rsID, e.g. ‘rs7903146’. Auto-resolved to GRCh38 coordinates via Ensembl. Provide this OR ‘variant’.

  • variant (string) (optional) Variant in chr:pos:ref:alt or chr-pos-ref-alt format, in GRCh38, e.g. ‘10:112998590:C:T’. Provide this OR ‘rsid’. A bare rsID is also accepted here.

  • limit (integer) (optional) Maximum number of phenotype associations to return (sorted by ascending p-value).

  • max_pval ([‘number’, ‘null’]) (optional) Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).

Example Usage:

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