dbsnp.genes

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('dbsnp.genes')
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	gene_id	gene_symbol	is_pseudogene
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10001	T	A	rs1570391677	100287102	DDX11L1	True
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10001	T	C	rs1570391677	100287102	DDX11L1	True
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10002	A	C	rs1570391692	100287102	DDX11L1	True
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10003	A	C	rs1570391694	100287102	DDX11L1	True
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10007	T	C	rs1639538116	100287102	DDX11L1	True

R

In [1]:

library(bedrockbio)
library(dplyr)

lf <- load_table("dbsnp.genes")
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    | 10001    | T          | A          | rs1570391677
1  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10001    | T          | C          | rs1570391677
2  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10002    | A          | C          | rs1570391692
3  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10003    | A          | C          | rs1570391694
4  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10007    | T          | C          | rs1639538116

Description

Genes overlapping each dbSNP variant, from the dbSNP GENEINFO and PSEUDOGENEINFO annotations.

Gene overlap is annotated per dbSNP record, so alternate alleles at the same site carry the same genes. gene_id is an NCBI Gene ID, not an Ensembl ID.

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.
gene_id	TEXT	NCBI Gene ID (e.g. 348 for APOE). Not an Ensembl ID.
gene_symbol	TEXT	Gene symbol (e.g. APOE).
is_pseudogene	BOOLEAN	Whether the gene is a pseudogene (from PSEUDOGENEINFO rather than GENEINFO).