SIFT retrieving SNPs - HELP

# SIFT SNP Help Page

There are many resources to retrieve SNPs:

### I. From HapMap (human SNPs genotyped in different populations):

1. Go to http://hapmap.ncbi.nlm.nih.gov/
2. On the left hand side, click on HapMart
3. Choose database: Hapmap's latest release
4. Choose dataset: Your population of interest
In the next steps, we want to restrict to nonsynonmyous SNPs only.
5. Click on Filters on left-hand side
6. Check the box " SNPs found in"
7. Set the box to Exons - non-synonymous coding SNPs
8. You can also filter on minor allele frequency, validation, etc.
Now we want to print out the list of rs id's.
9. Click on Attributes on left-hand side panel
10. Under variation, click "marker id"
11. Hit button "Results" in top panel
12. Export all results to get a list of rs id's to enter into the SIFT website

### II. From BioMart (all organisms):

1. Go to http://www.biomart.org/
2. Click on the link for BioMart Central Portal
3. Choose database: Ensembl v.# VARIATION
4. Choose dataset: your organism
In the next steps, we want to restrict to nonsynonmyous SNPs only.
5. Click on Filters on left-hand side
6. Expand Gene associated variation filters
7. Check on the box " Consequence type"
8. Set the box to NON_SYNONYMOUS_CODING
9. You can also filter on regions, genes, etc.
Now we want to print out the list of rs id's.
10. Click on Attributes on left-hand side panel
11. Expand Variation
12. Under variation, click "Variation ID"
13. Hit button "Results" in top panel
14. Export all results to get a list of rs id's to enter into the SIFT website

### III. From dbSNP (all organisms):

1. Open Entrez dbSNP in a new window (right click mouse).
2. 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]
3. Change "Display" button to dbSNP Batch Report and hit "Display"
4. Copy and paste the rs numbers into the SIFT website
[SIFT home page] SIFT help page]

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Last updated: February 2005