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. 10.1093/nar/gkq1237 for more information.