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

This string will extract all data available (~62000 SNPs) which can be filtered using left-panel filters on the page.

Also, datasets can be downloaded in VCF format from

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf.

In addition, 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)

PheGenI integrates published results provided in GWAS catalog and results from dbGaP GWAS studies.

You could make your own if you like the content of SNPedia: http://snpedia.com/index.php/Bulk

You could try the GWAS catalog and filter for disease traits

You can use Uniprot's annotation of OMIM disease mutations:

http://www.uniprot.org/docs/humsavar

Look at this one

http://www.ncbi.nlm.nih.gov/pubmed/

on the left side, there is a menu including SNPs.

You probably want to look at ClinVar and/or OMIM

http://www.ncbi.nlm.nih.gov/clinvar/

http://www.ncbi.nlm.nih.gov/omim

Thanks Bora. That UniProt table is very good. But I should precise that we need to consider SNPs in non-coding regions.

You are welcome. For non-coding mutations, it might be useful to look at the COSMIC database (catalog of somatic mutations in cancer). There are both coding and non-coding mutations in this resource. However, not all mutations are drivers. Some of them may be passengers.

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

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

This string will extract all data available (~62000 SNPs) which can be filtered using left-panel filters on the page.

Also, datasets can be downloaded in VCF format from

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf.

In addition, 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)

PheGenI integrates published results provided in GWAS catalog and results from dbGaP GWAS studies.

Miguel, you can try to look at The Genetic Association Database which is an archive of human genetic association studies of complex diseases and disorders:

http://geneticassociationdb.nih.gov/

Human mutation database http://www.hgmd.org/ is good for diseases causing mutations

Miguel - I think it depends on whether you're looking for disease *causing* mutations or simply SNPs *associated* with disease.

For the latter, the GWAS catalog is the single best source:

http://www.genome.gov/admin/gwascatalog.txt

The difficulty of course is that GWAS-identified SNPs are best interpreted as identifying a region, not a particular causal or functional variant.

To make best use of the GWAS SNPs, you'll need to also use LD information. 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

Note that you'll want to make sure you use a reference population (ethnicity) that is as close as possible to the population in your study.

If you have a SNP in high LD with a GWAS SNP, it's reasonable to conclude that your SNP is also associated with the disease.

We have far less information on disease *causing* mutations, and the vast majority of these are amino-acid changing variants. As mentioned above, hgmd, omim and uniprot are all good options for these.

My question was not precise. Definitively, disease causing. Thanks Eric.

Miguel, I think that one of the best databases you can use to answer your question is 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

Good luck!

Alexey

SNPs with clinical significance may be searched/viewed/downloaded from Invar using following as address:

http://www.ncbi.nlm.nih.gov/clinvar?term=human%5Borgn%5D

Hopefully this link will be helpful for your studies...!!!

https://www.researchgate.net/publication/257498467_Single_nucleotide_polymorphism_in_genome-wide_association_of_human_population_A_tool_for_broad_spectrum_service

Article Single nucleotide polymorphism in genome-wide association of...

Check these valuable sites :

https://www.pharmgkb.org/

https://www.genome.gov/26525384

What a useful comments, thank you all :)

Hi Miguel,

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

From what I understand, having a particular SNP is not a definite cause for the disease but rather a chance developing a particular disease. Hope, it is useful. Elena

check this too

http://www.disgenet.org

The premise that the association of disease with Single Nucleotide Plymorphisms in the Genome Wide Association Studies has revealed taht genetic components usually explain a little number of cases,  and it  was a reductionist view of genotype-phenotype correlation,  because de mayority diseases are a complex traits.