If you’re interested in a specific gene (or set of genes) of the human genome, one of the important question you might consider is what (and what kind of and how many) variants are usually found in that particular genomic region.

So here’s a list of online resources, to help you with this task. Feel free to add additional resources in the comments!

Kaviar

This is an online query tool that uses several variant databases and individual genomes and allows you to list variants for a list genomic locations.

NCBI variant related resources

• dbSNP: NCBI database of short variants. It has human variants and variants for several other species as well. (VCF formatted files can be downloaded from here.)
• dbVar: NCBI database for structural variants.
• ClinVar: NCBI clinical variant database.
• GeneReview: information about diagnostically relevant variations.
• dbGaP: information about genotype and phenotype interaction.

EBI variant related resources

• DGVarchive: EBI database for structural variants.
• EGA: European Genome-phenome Archive.

1000 Genomes project

VCF formatted files containing all variants for all sequenced individuals can be downloaded via the NCBI or EBI ftp sites. Note that 1000 Genomes variants are submitted to dbSNP and DGVa, but it can take a few month for new variants to get processed and show up in these databases.

Database of Genomic Variants

Curated structural variant database.

HGVS

The Human Genome Variaton Society provides several collections of databases organised by different criteria.