Cohort Phenotype Associations and Fine-mapping: parameters and notes

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Find variant–phenotype associations in BioBank Japan

dnakit.databases.bio_bank_japan_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
rsid	string	None	dbSNP rsID, e.g. 'rs7903146'. Auto-resolved to GRCh37 coordinates via Ensembl. Provide this OR 'variant'.
variant	string	None	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	None	Maximum number of phenotype associations to return (sorted by ascending p-value).
max_pval	number | null	None	Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).
verbose	bool	True	Progress flag.

Retrieve FinnGen fine-mapping results for a variant

dnakit.databases.finn_gen_get_variant_finemapping(*, variant, verbose=True)

Parameter	Type	Required / default	Description and constraints
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.
verbose	bool	True	Progress flag.

Query gene burden associations across phenotypes

dnakit.databases.genebass_gene_burden_phewas(*, gene, burden_set=None, limit=None, max_pval=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene	string	Required	Ensembl gene ID (e.g. 'ENSG00000148737') or gene symbol (e.g. 'TCF7L2'). Symbols are auto-resolved via Ensembl.
burden_set	string	None	Variant category aggregated in the burden test. One of: 'pLoF' (default), 'missense|LC', 'synonymous'. Aliases accepted: lof/plof -> pLoF, missense -> missense|LC.
limit	integer	None	Maximum number of phenotype associations to return (sorted by ascending burden p-value).
max_pval	number | null	None	Optional: only return associations with burden p-value <= this threshold (e.g. 2.5e-6 for exome-wide significance).
verbose	bool	True	Progress flag.

Query variant–phenotype associations in TPMI

dnakit.databases.tpmi_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
rsid	string	None	dbSNP rsID, e.g. 'rs7903146'. Auto-resolved to GRCh38 coordinates via Ensembl. Provide this OR 'variant'.
variant	string	None	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	None	Maximum number of phenotype associations to return (sorted by ascending p-value).
max_pval	number | null	None	Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).
verbose	bool	True	Progress flag.

Query variant–phenotype associations in UKB-TOPMed

dnakit.databases.ukbtopmed_phewas_by_variant(*, rsid=None, variant=None, limit=None, max_pval=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
rsid	string	None	dbSNP rsID, e.g. 'rs7903146'. Auto-resolved to GRCh38 coordinates via Ensembl. Provide this OR 'variant'.
variant	string	None	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	None	Maximum number of phenotype associations to return (sorted by ascending p-value).
max_pval	number | null	None	Optional: only return associations with p-value <= this threshold (e.g. 5e-8 for genome-wide significance).
verbose	bool	True	Progress flag.