Cohort Phenotype Associations and Fine-mapping¶

See the FAQ for dependencies and return conventions.

1) Find variant–phenotype associations in BioBank Japan¶

Purpose: Find variant–phenotype associations in BioBank Japan.
Method: Use PheWebPheWAS to query or submit the supplied input and parse the response.
API： dnakit.databases.bio_bank_japan_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a mapping with variant, rsids, nearest_genes, associations and related fields.
Example code:

import dnakit

result = dnakit.databases.bio_bank_japan_phewas_by_variant(
    rsid='rs7903146',
    max_pval=5e-08,
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "variant": "<string>",
  "rsids": "<string>",
  "nearest_genes": "<string>",
  "associations": [
    {
      "phenocode": "<string>",
      "phenostring": "<string>",
      "category": "<string>",
      "pval": "<number>",
      "beta": "<number>",
      "sebeta": "<number>",
      "af": "<number>",
      "num_cases": "<number>"
    }
  ]
}

Full parameters and usage notes

2) Retrieve FinnGen fine-mapping results for a variant¶

Purpose: Retrieve FinnGen fine-mapping results for a variant.
Method: Use FinnGen to query or submit the supplied input and parse the response.
API： dnakit.databases.finn_gen_get_variant_finemapping(*, variant, verbose=True)
Input: Provide variant.
Output: Returns a list of records; each record includes phenocode, chromosome, start, end and related fields.
Example code:

import dnakit

result = dnakit.databases.finn_gen_get_variant_finemapping(
    variant='19:44908684:T:C',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "phenocode": "<string>",
    "chromosome": "<integer>",
    "start": "<integer>",
    "end": "<integer>",
    "type": "<string>"
  }
]

Full parameters and usage notes

3) Query gene burden associations across phenotypes¶

Purpose: Query gene burden associations across phenotypes.
Method: Use Genebass to query or submit the supplied input and parse the response.
API： dnakit.databases.genebass_gene_burden_phewas(*, gene, burden_set=None, limit=None, max_pval=None, verbose=True)
Input: Provide gene.
Output: Returns a mapping with gene_id, gene_symbol, burden_set, associations and related fields.
Example code:

import dnakit

result = dnakit.databases.genebass_gene_burden_phewas(
    gene='TCF7L2',
    burden_set='pLoF',
    limit=10,
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "gene_id": "<string>",
  "gene_symbol": "<string>",
  "burden_set": "<string>",
  "associations": [
    {
      "phenocode": "<string>",
      "description": "<string>",
      "trait_type": "<string>",
      "pval": "<number>",
      "pval_skat": "<number>",
      "beta": "<number>",
      "total_variants": "<number>"
    }
  ]
}

Full parameters and usage notes

4) Query variant–phenotype associations in TPMI¶

Purpose: Query variant–phenotype associations in TPMI.
Method: Use PheWebPheWAS to query or submit the supplied input and parse the response.
API： dnakit.databases.tpmi_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a mapping with variant, rsids, nearest_genes, associations and related fields.
Example code:

import dnakit

result = dnakit.databases.tpmi_phewas_by_variant(
    rsid='rs7903146',
    limit=10,
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "variant": "<string>",
  "rsids": "<string>",
  "nearest_genes": "<string>",
  "associations": [
    {
      "phenocode": "<string>",
      "phenostring": "<string>",
      "category": "<string>",
      "pval": "<number>",
      "beta": "<number>",
      "sebeta": "<number>",
      "af": "<number>",
      "num_cases": "<number>"
    }
  ]
}

Full parameters and usage notes

5) Query variant–phenotype associations in UKB-TOPMed¶

Purpose: Query variant–phenotype associations in UKB-TOPMed.
Method: Use PheWebPheWAS to query or submit the supplied input and parse the response.
API： dnakit.databases.ukbtopmed_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a mapping with variant, rsids, nearest_genes, associations and related fields.
Example code:

import dnakit

result = dnakit.databases.ukbtopmed_phewas_by_variant(
    rsid='rs7903146',
    max_pval=5e-08,
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "variant": "<string>",
  "rsids": "<string>",
  "nearest_genes": "<string>",
  "associations": [
    {
      "phenocode": "<string>",
      "phenostring": "<string>",
      "category": "<string>",
      "pval": "<number>",
      "beta": "<number>",
      "sebeta": "<number>",
      "af": "<number>",
      "num_cases": "<number>"
    }
  ]
}

Full parameters and usage notes