Each variant now can be connected to HalpoReg V2 which rank/annotate variant by ENCODE elements and 1000 genome LD. Click "query" button in the "Genomic Mapping" tab of annotaion panel.
new: 30/04/2013 GWASrap QuickRAP now move to new web site (http://jjwanglab.org/snvrap).
GWASrap QuickRAP now support linkage disequilibrium data of 1000 Genome Project phase 1 release version 2. User can change the LD plot panel between HapMap LD and 1000G LD.
Add a tutorial page showing the usage of GWASrap Web Services, please find the corresponding tab from web services page.
We add as many as 14 statistical values for natural selection signals of query variant using HapMap3 and 1000 genome project data. User can check it in the tab of "Evolution" tab of annotation panel.
Each variant now can connect to RegulomeDB which rank/annotate variant by ENCODE elements. Click "query" button in the "Genomic Mapping" tab of annotaion panel.
Incorporating all of latest GWASdb
SNPs as reference annotation.
Well support NGS data as input file (see the input example for NGS), system can deal with the rare variants. But some effect predication scores are not computed and not mergered into final prioritization score for those variant.
Support GERP++ annotation for constrained elements in multiple alignments by quantifying substitution deficits.
Support the annotation for GENCODE project release 12 including transcript, 2wayconspseudo, polyA, long non-coding RNA and tRNA.
To reduce the surplus or useless annotation, we retrict all our region coverage from 10000bp(up/down) to 1000bp(up/down) of target SNP.
17 top diseaes/traits with latest GWAS information are archived in gallery.
The system provides a help tab to specify detailed manual.