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bedrock.bio

open_targets.variant

import bedrock_bio as bb

rel = bb.load_table('open_targets.variant')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
variantId chromosome position referenceAllele alternateAllele variantEffect mostSevereConsequenceId transcriptConsequences rsIds hgvsId alleleFrequencies dbXrefs variantDescription version
0 1_17005_A_G 1 17005 A G [{'method': 'VEP', 'assessment': 'non_coding_t... SO_0001792 [{'variantFunctionalConsequenceIds': ['SO_0001... [rs201833382] 1:g.17005A>G [{'populationName': 'sas_adj', 'alleleFrequenc... [{'id': 'rs201833382', 'source': 'ensembl_vari... Non coding transcript exon variant overlapping... 26.09
1 1_51427_T_G 1 51427 T G [{'method': 'VEP', 'assessment': 'upstream_gen... SO_0001631 [{'variantFunctionalConsequenceIds': ['SO_0001... [rs551041711] 1:g.51427T>G [{'populationName': 'sas_adj', 'alleleFrequenc... [{'id': 'rs551041711', 'source': 'ensembl_vari... Upstream gene variant 464 basepair away from E... 26.09
2 1_61743_G_C 1 61743 G C [{'method': 'VEP', 'assessment': 'intron_varia... SO_0001627 [{'variantFunctionalConsequenceIds': ['SO_0001... [rs184286948] 1:g.61743G>C [{'populationName': 'sas_adj', 'alleleFrequenc... [{'id': 'rs184286948', 'source': 'ensembl_vari... Intron variant overlapping with ENSG0000029082... 26.09
3 1_62716_C_T 1 62716 C T [{'method': 'VEP', 'assessment': 'intron_varia... SO_0001627 [{'variantFunctionalConsequenceIds': ['SO_0001... [rs557590765] 1:g.62716C>T [{'populationName': 'sas_adj', 'alleleFrequenc... [{'id': 'rs557590765', 'source': 'ensembl_vari... Intron variant overlapping with ENSG0000029082... 26.09
4 1_62738_T_C 1 62738 T C [{'method': 'VEP', 'assessment': 'intron_varia... SO_0001627 [{'variantFunctionalConsequenceIds': ['SO_0001... [rs11810446] 1:g.62738T>C [{'populationName': 'sas_adj', 'alleleFrequenc... [{'id': 'rs11810446', 'source': 'ensembl_varia... Intron variant overlapping with ENSG0000029082... 26.09

Description

Section titled “Description”

Core variant information for all variants in the Platform.

Variants are included if any phenotypic information is available for the variant, including GWAS or molQTL credible sets, ClinVar, Uniprot or ClinPGx.

The dataset includes variant metadata as well as variant effects derived from Ensembl VEP [Genetics]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
variantId TEXT Unique identifier for the variant following schema: {chromosome}-{position}-{referenceAllele}-{alternateAllele}
chromosome TEXT Chromosome on which the variant is located
position INT Variant’s position on the chromosome
referenceAllele TEXT Reference allele for the variant
alternateAllele TEXT Alternate allele for the variant
variantEffect STRUCT(method TEXT, assessment TEXT, score FLOAT, assessmentFlag TEXT, targetId TEXT, normalisedScore DOUBLE)[] Predicted or measured effect of the variant based on various methods
mostSevereConsequenceId TEXT Sequence ontology identifier of the most severe consequence of the variant based on Ensembl VEP [bioregistry:so]
transcriptConsequences STRUCT(variantFunctionalConsequenceIds TEXT[], aminoAcidChange TEXT, uniprotAccessions TEXT[], isEnsemblCanonical BOOLEAN, codons TEXT, distanceFromFootprint BIGINT, distanceFromTss BIGINT, appris TEXT, maneSelect TEXT, targetId TEXT, impact TEXT, lofteePrediction TEXT, siftPrediction FLOAT, polyphenPrediction FLOAT, consequenceScore FLOAT, transcriptIndex INT, approvedSymbol TEXT, biotype TEXT, transcriptId TEXT)[] Predicted consequences on transcript context
rsIds TEXT[] RsIds for the variant
hgvsId TEXT HGVS identifier of the variant
alleleFrequencies STRUCT(populationName TEXT, alleleFrequency DOUBLE)[] Allele frequencies of the variant in different populations
dbXrefs STRUCT(id TEXT, source TEXT)[] Cross-references for the variant in different databases
variantDescription TEXT Short summary of the variant effect
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.