Skip to content

Genetic variant, SNP, gene & locus

Terms
Genetic variant SNP Gene Locus
Definition

These words sit at different scales in the genome: a variant is any sequence difference vs a reference; a SNP is a specific kind of variant (single-nucleotide polymorphism); a gene is a functional unit (annotation); a locus is a position or region (often the interval around a GWAS hit). A paper may report a lead SNP at a locus that contains several genes - the SNP is not "the gene."

Topics
Core genetics GWAS

How they differ

Genetic variant SNP Gene Locus
Scope Umbrella: SNVs, indels, structural changes, etc.—any departure from the chosen reference sequence. One biallelic (typically) single-nucleotide polymorphism at a defined position; GWAS arrays and imputed panels are overwhelmingly SNP-centric. Annotated functional unit (protein-coding or RNA gene) with boundaries, isoforms, regulation. A site or interval on a chromosome—coordinates, a named region, or “the neighborhood” of association.
Typical GWAS role QC, annotation consequence classes, rare vs common variation (depending on study design). Tested marker; rs ID, REF/ALT, strand harmonization across cohorts. Mechanistic interpretation after a hit—nearest gene, gene-based tests, burden. Reporting unit: “locus on chr1” = significant region; fine-mapping narrows candidate variants within the locus.
Relationship SNPs are variants (a subset). A lead SNP tags a locus under LD. Genes lie inside loci; a locus need not be one gene. Spans from a single coordinate to a broad interval before fine-mapping.

Rule of thumb: Variant/SNP = observed DNA change or marker; locus = where the signal maps on the genome; gene = what biology you discuss after mapping (with caution—causal genes are not guaranteed).

Other meanings (optional)

  • SNP vs SNV: Some authors reserve SNV for any single-nucleotide change and SNP for polymorphic (population-frequency) sites; pipelines may not follow this strictly. See SNV.
  • “Gene” in colloquial usage: Phrases like “the gene for X” often mean associated locus; GWAS associations are usually non-coding or tagging—see fine-mapping.

References