dbsnp.clinvar_disease_xrefs

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('dbsnp.clinvar_disease_xrefs')
rel = rel.filter("assembly_accession = 'GCF_000001405.25' AND chromosome = '1'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

Out[1]:

	sources	build	assembly_accession	assembly_name	chromosome	position	ref_allele	alt_allele	rsid	clinvar_accession	xref_source	xref_id
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248059312	C	T	rs189993261	RCV000203259.3	MedGen	C3661900
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248059367	C	T	rs986202655	RCV002943576.2	MedGen	C3661900
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248059739	T	G	rs2103350294	RCV002038468.3	MedGen	C3661900
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248059809	G	A	rs774936311	RCV002976130.2	MedGen	C3661900
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248129337	G	A	rs371051095	RCV004503896.1	MedGen	CN169374

R

In [1]:

library(bedrockbio)
library(dplyr)

lf <- load_table("dbsnp.clinvar_disease_xrefs")
df <- filter(lf, assembly_accession == "GCF_000001405.25", chromosome == "1") |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 12 columns)
   assembly_accession | chromosome | build | assembly_name | position  | ref_allele | alt_allele | rsid
   ------------------ | ---------- | ----- | ------------- | --------- | ---------- | ---------- | ------------
0  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248059312 | C          | T          | rs189993261
1  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248059367 | C          | T          | rs986202655
2  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248059739 | T          | G          | rs2103350294
3  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248059809 | G          | A          | rs774936311
4  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248129337 | G          | A          | rs371051095

Description

External condition identifiers associated with ClinVar records.

Identifiers are pooled across a record’s conditions, so dbSNP does not link one identifier to one condition name.

OMIM values are disease MIM numbers, distinct from the allelic variant numbers in clinvar_variant_xrefs.

Partitions

• assembly_accession
  • 'GCF_000001405.25'
  • 'GCF_000001405.40'
• chromosome
  • '1'
  • '10'
  • '11'
  • '12'
  • '13'
  • '14'
  • '15'
  • '16'
  • '17'
  • '18'
  • '19'
  • '2'
  • '20'
  • '21'
  • '22'
  • '3'
  • '4'
  • '5'
  • '6'
  • '7'
  • '8'
  • '9'
  • 'MT'
  • 'X'
  • 'Y'

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Source provenance for the row.
build	TEXT	dbSNP build version (e.g. b157).
assembly_accession	TEXT	Partition column. Versioned RefSeq assembly accession (GCF) for the variant coordinates.
assembly_name	TEXT	Exact NCBI assembly name, including its patch release (for example, GRCh38.p14).
chromosome	TEXT	Partition column. Chromosome on which the variant is located (1-22, X, Y, MT).
position	INT	Variant position within the chromosome (1-based).
ref_allele	TEXT	Reference allele.
alt_allele	TEXT	Alternate allele.
rsid	TEXT	NCBI RefSNP identifier.
clinvar_accession	TEXT	ClinVar RCV accession with version.
xref_source	TEXT	Database or organization that maintains the condition identifier.
xref_id	TEXT	Condition identifier in xref_source.