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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?

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  • $\begingroup$ 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? $\endgroup$ – terdon Jul 9 '17 at 12:59
  • $\begingroup$ @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. $\endgroup$ – Haohan Wang Jul 9 '17 at 14:07
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International Mouse Phenotyping Consortium 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. A lot more information about Arabidopsis from individual experiments is collected and maintained by The Arabidopsis Information Resource, 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. There is also GWAS 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?

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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 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. According to this paper, iris id may associate with some phenotype information. But the website of IRIS is under maintenance, I can not get more information about phenotype.

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  • $\begingroup$ but it is not linked to phenotype, no? When I checked they just associated it is different populations... $\endgroup$ – Kamil S Jaron Jul 10 '17 at 15:21
  • $\begingroup$ 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. $\endgroup$ – gringer Jul 10 '17 at 19:56
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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

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    $\begingroup$ 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 (europepmc.org/abstract/MED/20336072) $\endgroup$ – Dan Jul 11 '17 at 15:20

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