How to: View all SNPs associated with a gene

Starting with...

A GENE NAME

  1. Search the Gene database with the gene name. If you know the gene symbol and species, enter them as follows: tpo[sym] AND human[orgn]
  2. Click on the desired gene.
  3. In the list of Links on the right, click "GeneView in dbSNP". If the link is not present, no SNPs are currently linked to this gene.
  4. For human genes, another option is to go to the variation section (Click on Variation in the table of contents in the upper right), and follow links to Variation Viewer for either the GRCh37/hg19 or GRCh39/h38 assemblies, to the 1000 Genomes Browser, ClinVar and more.

A NUCLEOTIDE OR PROTEIN ACCESSION NUMBER (e.g. NM_001126)

  1. Search the Nucleotide or Protein database with the accession number.
  2. In the Links menu in the upper right, click on "GeneView in dbSNP". If the link is not present, click on the "Gene" link in the same menu and continue at step 3 above under "a gene name".

A NUCLEOTIDE SEQUENCE

  1. Go to the BLAST home page and click "nucleotide blast" under Basic BLAST.
  2. Paste the sequence in the query box.
  3. Enter the name of the organism of interest in the "Organism" box. Click the BLAST button.
  4. Click on the desired sequence from the results.
  5. Continue at step 2 under "a nucleotide or protein accession number" above.

A PROTEIN SEQUENCE

  1. Go to the BLAST home page and click "protein blast" under Basic BLAST.
  2. Paste the sequence in the query box.
  3. Enter the name of the organism of interest in the "Organism" box. Click the BLAST button.
  4. Click on the desired sequence from the results.
  5. Continue at step 2 under "a nucleotide or protein accession number" above.

Variation Viewer (human only)

  1. Go to Variation Viewer
  2. Go to the search section in the left section and enter a gene symbol in the query box.
  3. Filter results in the Variation Data table by making selections Filter by section.
  4. Download your results
  5. More on YouTube

1000 GENOMES BROWSER  (human only)

  1. Go to the 1000 Genomes Browser.
  2. Go to the search section in the left section and enter a gene symbol in the query box.
  3. Select the populations for which you want to review allele frequences or genotype counts per SNP.
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