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)#

Page through all BioBank Japan variant PheWAS associations after stable ascending p-value sorting…

BioBankJapan_phewas_by_variant tool specification

Tool Information:

  • Name: BioBankJapan_phewas_by_variant

  • Type: PheWebPheWASTool

  • Description: Page through all BioBank Japan variant PheWAS associations after stable ascending p-value sorting. Returns true total, returned count, and next offset; accepts an rsID or explicit GRCh37 variant for Japanese-ancestry replication.

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).

  • offset (integer) (optional) Zero-based offset into filtered, p-value-sorted associations.

  • 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)#

Page through all Genebass gene-burden PheWAS associations after stable ascending p-value sorting….

Genebass_gene_burden_phewas tool specification

Tool Information:

  • Name: Genebass_gene_burden_phewas

  • Type: GenebassTool

  • Description: Page through all Genebass gene-burden PheWAS associations after stable ascending p-value sorting. Returns true total, returned count, next offset, and phenotype descriptions for the requested page across ~4,500 UK Biobank phenotypes.

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).

  • offset (integer) (optional) Zero-based offset into filtered, p-value-sorted burden associations.

  • 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)#

Page through all TPMI variant PheWAS associations after stable ascending p-value sorting. Returns…

TPMI_phewas_by_variant tool specification

Tool Information:

  • Name: TPMI_phewas_by_variant

  • Type: PheWebPheWASTool

  • Description: Page through all TPMI variant PheWAS associations after stable ascending p-value sorting. Returns true total, returned count, and next offset; accepts an rsID or explicit GRCh38 variant for Taiwanese-ancestry replication.

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).

  • offset (integer) (optional) Zero-based offset into filtered, p-value-sorted associations.

  • 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)#

Page through all UKB-TOPMed variant PheWAS associations after stable ascending p-value sorting. R…

UKBTOPMed_phewas_by_variant tool specification

Tool Information:

  • Name: UKBTOPMed_phewas_by_variant

  • Type: PheWebPheWASTool

  • Description: Page through all UKB-TOPMed variant PheWAS associations after stable ascending p-value sorting. Returns true total, returned count, and next offset; accepts an rsID or explicit GRCh38 variant for European-ancestry replication.

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).

  • offset (integer) (optional) Zero-based offset into filtered, p-value-sorted associations.

  • 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)