If you were genotyped by 23andMe, deCODEme, or FamilyTreeDNA, you can upload the raw genotype data downloaded from your DTC test provider. The data will then be openly available for the world to see and download. We also parse these SNPs and annotate them.
For annotation, we include the manually curated SNPedia and find open-access primary publications appearing in the journals of The Public Library of Science (PLoS), an open-access publishing group. Additionally, we screen Mendeley, a crowd-sourced repository of scientific publications.
You can also publish some of your phenotypes so, someday, it might be possible to associate some SNPs with phenotypes (because of this we really would like to encourage you to do so; helping science generates this warm, fuzzy feeling inside of you).
And, of course, you can also share your knowledge about SNPs and phenotypes with other users and can socialize.
The site is hosted and was coded by Bastian, Helge and Philipp. We are not working full time on this project, this is more of a hobby. Please give us some time to answer your questions, fix bugs and stuff like this as we are doing this in our free time besides our studies and day jobs. You can find some more details on our About Us page.
openSNP is a non-profit, open-source project that is about sharing genetic and phenotypic information. The idea for this project came to Bastian after he was genotyped by 23andMe in May 2011 and started playing around with his data. During his research he became frustrated, because it was not that easy to find more data. He started working on openSNP to fix this. To be clear: This project is not about making money, selling data or to quote Google: “We don’t wanna be evil”. We are just interested in making science more open and accessible.
This heavily depends on how many other users are in the queue, waiting for their data to be parsed. Right now openSNP runs on a small scale server so it may take 2-3 days until all your variations can be found on the site. But you can start using openSNP right away and others can download your raw-data right from the start. The parsing only affects the "other users sharing this SNP" and the "my genotype"-views.
23andMe has a limited exome sequencing offer. If you've have had your exome sequenced through 23andMe you can now upload the VCF (Variant Call Format, see the filetypes-FAQ) version of your exome as well. But there are some limitations: While users will be able to download your complete VCF-file we currently don't have the computing power to parse all of your variation. So currently we will only parse the already known SNPs out of your file. For the same reasons we currently can't offer uploads of the raw sequence data.
The feature is still in an early beta stage, so please notify us if something goes wrong.
We are always interested in adding more data. If your company is missing up to now it is because we did not have an example-file to optimize our parser on it. But if you contact us at email@example.com and send us your file we can fix this, so that all customers of the DTC company of your choice can participate.
Completely open: Everyone can see everything you enter or upload (except your private messages and your password, of course). We warn every user twice about this: Once during the user-creation and once before the genotyping-file-upload. You can find more information about the risks of publishing the data by reading the disclaimer
You can easily add this phenotype as long as you are logged in. Just visit the page for phenotype creation and enter a name and a description that enables other users to understand what you are interested in.
# More Comments up here # More information on reference human assembly build 36: # http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606&build=36 # # rsid chromosome position genotype rs4477212 1 72017 AA rs3094315 1 742429 AA rs3131972 1 742584 GG rs12124819 1 766409 AG rs11240777 1 788822 AG rs6681049 1 789870 CC rs4970383 1 828418 CC rs4475691 1 836671 CC rs7537756 1 844113 AA
Name,Variation,Chromosome,Position,Strand,YourCode rs4477212,A/G,1,72017,+,AA rs2185539,C/T,1,556738,+,CC rs6681105,C/T,1,581938,+,TT rs11240767,C/T,1,718814,+,CC rs3094315,C/T,1,742429,-,TT rs3131972,C/T,1,742584,-,CC rs3131969,C/T,1,744045,-,CC rs1048488,C/T,1,750775,+,TT rs2905046,A/G,1,752518,-,GG
RSID,CHROMOSOME,POSITION,RESULT "rs3094315","1","742429","AG" "rs3131972","1","742584","AG" "rs12562034","1","758311","GG" "rs12124819","1","766409","AA" "rs11240777","1","788822","GG" "rs6681049","1","789870","CC" "rs4970383","1","828418","CC" "rs4475691","1","836671","CC" "rs7537756","1","844113","AA"
We are always interested in adding more data. If your company is missing up to now it is, because we did not have an example-file to optimize our parser on it. But if you contact us at firstname.lastname@example.org and send us your file we can fix this, so that all customers of the DTC company of your choice can participate.