Welcome To Ricopili

Ricopili is a tool for visualizing regions of interest in select GWAS data sets.

The following data sets are currently available for free access:
_{(click on the consortium name for more information and on the journal for a direct link to the publication)}

Schizophrenia, PGC - Psychiatric Genetics Consortium (Nature, 2022)
Bipolar disorder, PGC - Psychiatric Genetics Consortium (Nature Genetics, 2011)
Major depressive disorder, PGC - Psychiatric Genetics Consortium (Molecular Psychiatry, 2012)
ADHD, PGC - Psychiatric Genetics Consortium (JAACAP, 2010)
Psychiatric Cross Disorder Analysis PGC - Psychiatric Genetics Consortium (The Lancet, 2013)
--
Inflammatory Bowel Disease:, International IBD Genetics Consortium (Nature, 2012)
Host control of HIV-1, International HIV Controllers Study (Science, 2010)
GWAS, Tobacco and Genetics (TAG) Consortium (Nature Genetics, 2010)
GWAS, rheumatoid arthritis risk: public download (Nature Genetics, 2010)
--
Antidepressant Efficacy in Major Depressive Disorder (here called Pharmacogenetics - PhaCoGe): (The American Journal of Psychiatry, 2013)

You can find many more as whole genome downloads here: PGC - public downloads

How it works

Choose a data set and enter a genomic location or a gene name in the form below. A .pdf plot will be generated, as well as a text file with single SNP results. You can also specify the following options:

Clumping: Independent regions will be colored differently, to highlight LD. If you request more than one clump, be sure to have at least one SNP passing the specified p-value-threshold (for performance reasons.)
SNP: SNPs in the region are colored by LD to this index SNP.
Anonymity: Frequency information is from HapMap to protect anonymity.
NHGRI results: Results from the NHGRI GWAS catalog will be included in the plot.

Finally, please note that this tool is in development (it was released on September 19th, 2011) and should be considered "beta". In particular, our development server is not equipped for high traffic. If the server fails to respond to your request, please try again at a later time.

Please contact us if you encounter any problems, or if you have any suggestions.

Basic info

Your email address:

Plot title:

Result data set:

Click here to log in and view more data sets.

Gene and window

Gene (e.g. NOD2):

Window (in kb, default 200):

Genomic coordinates

Chromosome (integer, e.g. 4):

Start Position (in Mb, e.g. 10.5):

End Position (in Mb, 10.9):

Plot Modifiers

Index SNP (if different than best SNP, rs-name, e.g. rs12345):

Y-Axis, upper limit (-log10-scale, e.g. 13):

Clumping Options

Max number of clumps

P value threshold

r2 threshold (between 0 and 1, such as .05)

NHGRI gwas catalog (May 4th 2013)

Include catalog results

Submit

Ricopili is sponsored jointly by the Analytic and Translational Genetics Unit at Mass General Hospital and the Broad Institute. Ricopili is the work of Stephan Ripke (sripke (at) broadinstitute (dot) org) and Brett Thomas.