SIFT retrieving SNPs - HELP
SIFT SNP Help Page
There are many resources to retrieve SNPs:
I. From HapMap (human SNPs genotyped in different populations):
- Go to http://hapmap.ncbi.nlm.nih.gov/
- On the left hand side, click on HapMart
- Choose database: Hapmap's latest release
- Choose dataset: Your population of interest
In the next steps, we want to restrict to nonsynonmyous SNPs only.
- Click on Filters on left-hand side
- Check the box " SNPs found in"
- Set the box to Exons - non-synonymous coding SNPs
- You can also filter on minor allele frequency, validation, etc.
Now we want to print out the list of rs id's.
- Click on Attributes on left-hand side panel
- Under variation, click "marker id"
- Hit button "Results" in top panel
- Export all results to get a list of rs id's to enter into the SIFT website
II. From BioMart (all organisms):
- Go to http://www.biomart.org/
- Click on the link for BioMart Central Portal
- Choose database: Ensembl v.# VARIATION
- Choose dataset: your organism
In the next steps, we want to restrict to nonsynonmyous SNPs only.
- Click on Filters on left-hand side
- Expand Gene associated variation filters
- Check on the box " Consequence type"
- Set the box to NON_SYNONYMOUS_CODING
- You can also filter on regions, genes, etc.
Now we want to print out the list of rs id's.
- Click on Attributes on left-hand side panel
- Expand Variation
- Under variation, click "Variation ID"
- Hit button "Results" in top panel
- Export all results to get a list of rs id's to enter into the SIFT website
III. From dbSNP (all organisms):
- Open Entrez dbSNP in a new window (right click mouse).
- Query your gene of interest to find nonsynonymous SNPs.
For example, to get nsSNPs in the human LPL gene, type in "coding nonsynon"[FUNC] AND "human"[ORGN] AND "LPL"[GENE]
- Change "Display" button to dbSNP Batch Report and hit "Display"
- Copy and paste the rs numbers into the SIFT website
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Last updated: February 2005