An S4 class to represent a set of GWAS Catalog variants

The variants object consists of four slots, each a table (tibble), that combined form a relational database of a subset of GWAS Catalog variants. Each variant is an observation (row) in the variants table --- main table. All tables have the column variant_id as primary key.

Slots

variants

A tibble listing variants. Columns:

variant_id: Variant identifier, e.g., 'rs1333048'.
merged: Whether this SNP has been merged with another SNP in a newer genome build.
functional_class: Class according to Ensembl's predicted consequences that each variant allele may have on transcripts. See Ensembl Variation - Calculated variant consequences.
chromosome_name: Chromosome name.
chromosome_position: Chromosome position.
chromosome_region: Cytogenetic location.
last_update_date: Last time this variant was updated.

genomic_contexts

A tibble listing genomic contexts associated with each variant. Columns:

variant_id: Variant identifier.
gene_name: Gene symbol according to HUGO Gene Nomenclature (HGNC).
chromosome_name: Chromosome name.
chromosome_position: Chromosome position.
distance: Genomic distance between the variant and the gene (in base pairs).
is_mapped_gene: Whether this is a mapped gene to this variant. A mapped gene is either an overlapping gene with the variant or the two closest genes upstream and downstream of the variant. Moreover, only genes whose mapping source is 'Ensembl' are considered.
is_closest_gene: Whether this is the closest gene to this variant.
is_intergenic: Whether this variant is intergenic, i.e, if there is no gene up or downstream within 100kb.
is_upstream: Whether this variant is upstream of this gene.
is_downstream: Whether this variant is downstream of this gene.
source: Gene mapping source, either Ensembl or NCBI.
mapping_method: Gene mapping method.

ensembl_ids

A tibble listing gene Ensembl identifiers associated with each genomic context. Columns:

variant_id: Variant identifier.
gene_name: Gene symbol according to HUGO Gene Nomenclature (HGNC).
ensembl_id: The Ensembl identifier of an Ensembl gene, see Section Gene annotation in Ensembl for more information.

entrez_ids

A tibble listing gene Entrez identifiers associated with each genomic context. Columns:

variant_id: Variant identifier.
gene_name: Gene symbol according to HUGO Gene Nomenclature (HGNC).
entrez_id: The Entrez identifier of a gene, see ref. doi:10.1093/nar/gkq1237 for more information.