SIFT retrieving SNPs - HELP
 SIFT SNP Help Page
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 interestIn 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 organismIn 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