upstream_gene_variant [SO_0001631]

A sequence variant located 5’ of a gene.

upstream_gene_variant

ID: SO_0001631

Class

A sequence variant located 5' of a gene.

Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.

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Classification

intergenic_variant

Alternative Names

Synonym	Scope	Reference
ANNOVAR:upstream	related synonym	//www.openbioinformatics.org/annovar/annovar_download.html, VAR
Jannovar:upstream_gene_variant	exact synonym	//doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html
upstream gene variant	exact synonym
VEP:upstream_gene_variant	exact synonym	VAR
snpEff:UPSTREAM	exact synonym	VAR

References

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lay:flex;"> "types": [ "Entity", "Individual", "pub" ], "short_form": "Unattributed", "label": "" }, "FlyBase": "", "PubMed": "", "DOI": "" } }, { "synonym": { "scope": "has_exact_synonym", "label": "upstream gene variant", "type": "" }, "pub": { "core": { "symbol": "", "iri": "http://flybase.org/reports/Unattributed", "types": [ "Entity", "Individual", "pub" ], "short_form": "Unattributed", "label": "" }, "FlyBase": "", "PubMed": "", "DOI": "" } }, { "synonym": { "scope": "has_exact_synonym", "label": "snpEff:UPSTREAM", "type": "" }, "pub": { "core": { "symbol": "", "iri": "http://flybase.org/reports/Unattributed", "types": [ "Entity", "Individual", "pub" ], "short_form": "Unattributed", "label": "" }, "FlyBase": "", "PubMed": "", "DOI": "" } }, { "synonym": { "scope": "has_related_synonym", "label": "ANNOVAR:upstream", "type": "http://purl.obolibrary.org/obo/so#VAR" }, "pub": { "core": { "symbol": "", "iri": "http://flybase.org/reports/Unattributed", "types": [ "Entity", "Individual", "pub" ], "short_form": "Unattributed", "label": "" }, "FlyBase": "", "PubMed": "", "DOI": "" } } ], "def_pubs": [] }

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