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EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure
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Variant mapping query #1397

Open Santhi1901 opened 1 month ago

Santhi1901 commented 1 month ago

A user wanted an explanation of how the variants are mapped.

They are particularly interested in this variant, rs6011066, which is mapped to gene ZGPAT in UI. But the link to Ensembl shows the variant is in a gene-dense region that includes all of these genes (ZGPAT, LIME1, SLC2A4RG).

sajo-ebi commented 1 month ago

@Santhi1901 based on my investigation the mapped Gene is computed as the below -:

  1. We check the overlapping gene , if any matching vaues are found mapped gene is assigned
  2. if no overlapping gene exists then 2 closest genes are found , 1 upstream & 1 downstream.

In this case ZGPAT came out to be the overlapping gene for 'rs6011066'

sajo-ebi commented 1 week ago

@Santhi1901 kindly confirm if this can be closed

Santhi1901 commented 1 week ago

this can be closed