Answers.Body: <p>A few days ago, I was trying to find some GWAS datasets to download. I hope this site for 3000 rice will help: <a href="http://snp-seek.irri.org/" rel="nofollow noreferrer">http://snp-seek.irri.org/</a>. You can click <a href="http://snp-seek.irri.org/_snp.zul" rel="nofollow noreferrer">Genotype</a> in the index page for "Query for SNPs from the 3000 genome project". </p>
  
  <p><strong>UPDATE:</strong> With the help of user manual, I can get IRIS ID from <a href="http://snp-seek.irri.org/_snp.zul" rel="nofollow noreferrer">Genotype</a>. According to this <a href="https://www.ncbi.nlm.nih.gov/pubmed/12855438" rel="nofollow noreferrer">paper</a>, iris id may associate with some phenotype information. But the website of IRIS is under maintenance, I can not get more information about phenotype.  </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-10T15:21:47.400Z
Answers.Text: but it is not linked to phenotype, no? When I checked they just associated it is different populations...
Answers.UserDisplayName: Kamil S Jaron
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Answers.Text: Hi l0o0, thanks for your answer and welcome to Bioinformatics Stack Exchange. I have edited your answer to improve the grammar slightly; if you can provide more information about snp-seek (e.g. whether or not it helps for finding associations with phenotypes), please edit your answer and add that in.
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Answers.LastEditDate: 2017-07-11T06:26:50.940Z
Answers.UserDisplayName: l0o0
Answers.Body: <p>Have you looked at Ensembl? At least for mice, they have pretty rich data for SNPs e.g.
  <a href="http://www.ensembl.org/Mus_musculus/Variation/Explore?db=core;r=2:3225281-3226281;v=rs27096498;vdb=variation;vf=802773" rel="nofollow noreferrer">http://www.ensembl.org/Mus_musculus/Variation/Explore?db=core;r=2:3225281-3226281;v=rs27096498;vdb=variation;vf=802773</a></p>
  
  <p>Assumes you have known dbSNP ids (or 'rs' numbers) for your SNPs. If not you could use their VEP tool to annotate them:
  <a href="http://www.ensembl.org/Homo_sapiens/Tools/VEP?db=core" rel="nofollow noreferrer">http://www.ensembl.org/Homo_sapiens/Tools/VEP?db=core</a></p>
  
  <p>VEP is also available for rice and Arabidopsis:
  <a href="http://plants.ensembl.org/Oryza_sativa/Tools/VEP?db=core" rel="nofollow noreferrer">http://plants.ensembl.org/Oryza_sativa/Tools/VEP?db=core</a></p>
  
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Answers.Text: We also have variation and phenotype data for arabidopsis in Ensembl. The variation data is from the 1001 project and we took the phenotype data from Atwell et al., 2007 (http://europepmc.org/abstract/MED/20336072)
Answers.UserDisplayName: Dan
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Answers.UserDisplayName: ithinkiam
Answers.Body: <p><a href="http://www.mousephenotype.org/" rel="noreferrer">International Mouse Phenotyping Consortium</a> is building a database of phenotypes and knock-outs of mouse. I believe that this database will be fairly complete (20000 knock-outs), but these are knock-outs, not SNPs... There are several mouse GWAS studies, but I am not aware of a database that would pull all the results together.</p>
  
  <p><em>Arabidopsis</em> big GWAS project is called <a href="http://1001genomes.org/tools/" rel="noreferrer">1001 genomes project</a>. A lot more information about <em>Arabidopsis</em> from individual experiments is collected and maintained by <a href="https://www.arabidopsis.org/" rel="noreferrer">The Arabidopsis Information Resource</a>, however this resource is subscription based, therefore what you need might not be available for free.</p>
  
  <p>As mentioned, SNPs of rice were identified and linked to different rice groups in <a href="https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-3-7" rel="noreferrer">The 3,000 rice genomes project</a>. There is also <a href="https://www.ncbi.nlm.nih.gov/pubmed/27322545" rel="noreferrer">GWAS</a> done on 512 individuals, not sure if it is sufficient for reliable conclusions (even they claim that they found supersigificant links).</p>
  
  <p>Is this what you were searching for?</p>
  
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Answers.UserDisplayName: Kamil S Jaron
Body: <p>I have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association. Moreover, for some species, there are not even any functional descriptions. </p>
  
  <p>I need this information for mice, rice, and Arabidopsis Thaliana. Can anyone help me? </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-09T12:59:58.270Z
Comments.Text: What do you start with? Do you have a list of phenotypes you want to match to SNPs or a list of SNPs to match to phenotypes? Or do you have neither and need to find both?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-09T14:07:22.510Z
Comments.Text: @terdon I have both SNPs and phenotypes. I want to know the association between them. However, I don't want to do this with GWAS, because I need to go into wet-lab to verify these findings anyway. I wonder if there is a database with wet-lab verified associations already.
Comments.UserDisplayName: Haohan Wang
Tags: <gene><gwas>
Title: Where can I find a database that has phenotype information together with associated SNPs?
ThreadText: # Where can I find a database that has phenotype information together with associated SNPs?
  
  (Asked by: username_0 on 2017-07-09)
  
  I have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association. Moreover, for some species, there are not even any functional descriptions.
  
  I need this information for mice, rice, and Arabidopsis Thaliana. Can anyone help me?
  
  **Tags:** gene, gwas
  
  > **Comments:**
  > **username_1**: What do you start with? Do you have a list of phenotypes you want to match to SNPs or a list of SNPs to match to phenotypes? Or do you have neither and need to find both?  
  > **username_0**: @username_1 I have both SNPs and phenotypes. I want to know the association between them. However, I don't want to do this with GWAS, because I need to go into wet-lab to verify these findings anyway. I wonder if there is a database with wet-lab verified associations already.  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_3 on 2017-07-10. Score: 8 | Accepted answer
  
  [International Mouse Phenotyping Consortium](http://www.mousephenotype.org/) is building a database of phenotypes and knock-outs of mouse. I believe that this database will be fairly complete (20000 knock-outs), but these are knock-outs, not SNPs... There are several mouse GWAS studies, but I am not aware of a database that would pull all the results together.
  
  *Arabidopsis* big GWAS project is called [1001 genomes project](http://1001genomes.org/tools/). A lot more information about *Arabidopsis* from individual experiments is collected and maintained by [The Arabidopsis Information Resource](https://www.arabidopsis.org/), however this resource is subscription based, therefore what you need might not be available for free.
  
  As mentioned, SNPs of rice were identified and linked to different rice groups in [The 3,000 rice genomes project](https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-3-7). There is also [GWAS](https://www.ncbi.nlm.nih.gov/pubmed/27322545) done on 512 individuals, not sure if it is sufficient for reliable conclusions (even they claim that they found supersigificant links).
  
  Is this what you were searching for?
  
  
  ---
  
  ### Answer by username_2 on 2017-07-10. Score: 4
  
  A few days ago, I was trying to find some GWAS datasets to download. I hope this site for 3000 rice will help: <http://snp-seek.irri.org/>. You can click [Genotype](http://snp-seek.irri.org/_snp.zul) in the index page for "Query for SNPs from the 3000 genome project".
  
  **UPDATE:** With the help of user manual, I can get IRIS ID from [Genotype](http://snp-seek.irri.org/_snp.zul). According to this [paper](https://www.ncbi.nlm.nih.gov/pubmed/12855438), iris id may associate with some phenotype information. But the website of IRIS is under maintenance, I can not get more information about phenotype.
  
  > **Comments:**
  > **username_3**: but it is not linked to phenotype, no? When I checked they just associated it is different populations...  
  > **username_4**: Hi username_2, thanks for your answer and welcome to Bioinformatics Stack Exchange. I have edited your answer to improve the grammar slightly; if you can provide more information about snp-seek (e.g. whether or not it helps for finding associations with phenotypes), please edit your answer and add that in.  
  
  ---
  
  ### Answer by username_5 on 2017-07-11. Score: 1
  
  Have you looked at Ensembl? At least for mice, they have pretty rich data for SNPs e.g.
  <http://www.ensembl.org/Mus_musculus/Variation/Explore?db=core;r=2:3225281-3226281;v=rs27096498;vdb=variation;vf=802773>
  
  Assumes you have known dbSNP ids (or 'rs' numbers) for your SNPs. If not you could use their VEP tool to annotate them:
  <http://www.ensembl.org/Homo_sapiens/Tools/VEP?db=core>
  
  VEP is also available for rice and Arabidopsis:
  <http://plants.ensembl.org/Oryza_sativa/Tools/VEP?db=core>
  
  > **Comments:**
  > **username_6**: We also have variation and phenotype data for arabidopsis in Ensembl. The variation data is from the 1001 project and we took the phenotype data from Atwell et al., 2007 (http://europepmc.org/abstract/MED/20336072)  
  
  ---
  
  