LeadSNPFinder

LeadSNPFinder obtains a list of significantly-independent SNPs that are associated with one or multiple phenotypes of interest. Start by affording your own GWAS summary data, then setting the threshold of significance P-value and LD R².

Input

Or load file from disk

Database

Maximum P-value of index variant

R² threshold for independent SNPs

SP2 column P-value threshold

Second R² threshold for lead SNPs

Clump kb radius

Run

Input

SNP P
 2:4250379 2.14e-05
 2:4260493 7.09e-06
 2:4267368 3.27e-05
 2:4363973 1.31e-05
 5:40813158 6.78e-06
 5:40836021 5.58e-05
 5:40934088 2.56e-05
 5:40974254 1.03e-06
 8:7577565 2.91e-05
 8:7595767 7.71e-05
 8:7596194 7.85e-05
 16:29578794 3.47e-05
 16:29621120 2.17e-05
 16:31838543 6.08e-05
 16:32445623 0.000101
 16:32588581 5.88e-12
 16:32603434 1.39e-09
 16:32629442 5.56e-11
 16:32637581 3.28e-17
 16:32644453 8.38e-07
 16:32651304 1.43e-07
 16:32698542 1.17e-07
 16:32725297 8.66e-13
 16:32734593 6.3e-13
 16:32763342 2.59e-07
 16:32764135 2.21e-16
 16:32777894 1.9e-07
 16:32796708 2.23e-07
 16:32838190 1.03e-21
 16:32840492 1.84e-25
 16:32847923 1.62e-16
 16:33018083 4.79e-35
 16:33038110 9.18e-09
 16:33119116 3.52e-07
 16:33167192 2.12e-16
 16:33182780 3.17e-18
 16:33318274 1.12e-19
 16:33351218 1.44e-15
 16:33362755 8.01e-14
 16:33415484 1.35e-06
 16:33663403 2.01e-05
 16:33679375 3.39e-05
 16:33715054 1.3e-07
 16:36552189 6.89e-05
 16:37153578 1.37e-05
 16:37157790 2.03e-05
 16:37381270 2.85e-05
 17:37284864 5.18e-07
 17:37452896 5.25e-06

Demo Result

GWAS summary text or GWAS summary file

Reference Panel

Optional Parameters

Email Address

Demo

Data Processing Pipeline