Genetic Data Resources outside FinnGen

The FinnGen Analysis team incorporates into PheWeb genetic overlaps with published GWAS data in GWAS Catalog and ClinVar. However, there are a number of other places you might use to explore your data.

How to view allele frequencies - gnomAD

For viewing worldwide allele frequencies and looking at measures of severity of a particular variant, gnomAD is the best option. There are different reference genomes available there, but if you search using the variant ID that begins “rs” then you will not have to consider which reference sequence you have (FinnGen genotypes are referenced to the GRCh 38 of the human genome; gnomAD v3.1.1).

Where is the gene expressed in - GTEx

To understand which organ systems your gene is expressed in and if the variant you are interested in causes and gene-specific expression regulation you can find that in GTEx. In GTEx you can explore expression quantitative trait loci (eQTLs, i.e. genetic variants that explain variance in mRNA expression levels). If you are interested in protein-level expression you can visit The Human Protein Atlas.

Public resources - OpenTargets

For a complete view of the public resources about the genetics of a variant or gene, you can visit the OpenTargets (be careful to select "OpenTargets Genetics" as your search engine term, as there have another site which is not as useful).

Publications - PubMed

Of course, when discovering a new association and looking for what biology is known, it is always good to search PubMed. Keep in mind that FinnGen uses the canonical reference name for the gene but genes often have many aliases, especially in older literature. Gene Cards is one easy place you can look up all the aliases for a gene. Often Googling your variant/gene or searching it on Twitter can also provide recent and interesting results.