Question: Question: Is there a list of human SNPs associated with a disease?

Abhimanyu Singh
202 days ago

Question: Is there a list of human SNPs associated with a disease?

Looking for list of human SNPs associated with a disease? We need to evaluate a large number of human SNPs for their possible association with a disease. So far, the closest I've seen is SNPedia, but a database would be more helpful.

Best Answer
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This is really difficult questions to answer ! As per my knowledge most of the data is not well connected to extract all in one go. Anyway, you can try followings link, if it could help. 

1. SNPs with clinical significance may be searched/viewed/downloaded from ClinVar using following as address
http://www.ncbi.nlm.nih.gov/clinvar?term=human%5Borgn%5D

2. Data sets can be downloaded in VCF format from 
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf.

3. you can look at SNP-phenotype association results using 
http://www.ncbi.nlm.nih.gov/gap/phegeni (there are options for choosing exon/intron… regions)

4. GWAS catalog is the single best source:
http://www.genome.gov/admin/gwascatalog.txt

5. The Broad's SNAP tool is a convenient way to find SNPs that are in high LD. 
http://www.broadinstitute.org/mpg/snap/ldsearch.php

6. HuGE Navigator which is an integrated, searchable knowledge base of genetic associations and human genome epidemiology.
You access it at a web site: http://www.hugenavigator.net/HuGENavigator/home.do

7. Check these valuable sites :
https://www.pharmgkb.org/
https://www.genome.gov/26525384

8. Here is a site listing known SNPs associated with diseases and other traits grouped into categories: http://www.eupedia.com/genetics/medical_dna_test.shtml

 
You might need to do li'l scripting to extract other related information.  

Other Answers
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COSMIC

http://cancer.sanger.ac.uk/cosmic

OMIM (includes gene ans SNP information)

https://www.omim.org/about