1. Input data
(Note: The GWAS data uploaded by users will be deleted automatically as soon as the analysis is finished)
1.1 Upload GWAS SNP P-value file (required)
The data should be a text file containing only two columns separated by table and without head line. The first column is SNP ID and the second column is P-value.
Note: Our analysis uses -log10(P-value). If your data has been transformed, please un-tick the option "P-value -> -log10(P-value)".
1.2 Specify the most significant SNPs
The most significant SNPs are defined as SNPs with P-value below certain threshold from the GWAS SNP P-value file. They are utilized to search their
LD neighborhoods with function (e.g. non-synonymous). The default is P-value < 10-5 as utilized by NHGRI GWAS Catalog. Users may define the
threshold to specify the most significant SNPs, or input/upload rs-IDs of the most significant SNPs. The format is as following:
2.1 Options for searching LD neighborhoods of the most significant SNPs
Select a HapMap population to help to search the linkage disequilibrium (LD) neighborhoods of the most significant SNPs. The choices are:
CEU (C): Utah residents with Northern and Western European ancestry from the CEPH collection
ASW (A): African ancestry in Southwest USA
CHB (H): Han Chinese in Beijing, China
CHD (D): Chinese in Metropolitan Denver, Colorado
GIH (G): Gujarati Indians in Houston, Texas
JPT (J): Japanese in Tokyo, Japan
LWK (L): Luhya in Webuye, Kenya
MEX (M): Mexican ancestry in Los Angeles, California
MKK (K): Maasai in Kinyawa, Kenya
TSI (T): Toscans in Italy
YRI (Y): Yoruba in Ibadan, Nigeria (West Africa)
Choose the LD measurement (r2 or D' respectively) cutoff for defining LD neighborhoods.
Distance (up to 200kb)
The maximum distance to search LD neighborhoods.
2.2 Options for pathway based analysis (PBA)
Rules of mapping SNPs to genes
There are several rules of mapping SNPs to genes: "functional SNPs", "within gene", "5 kb upstream and downstream range of gene", "20 kb upstream and downstream range of gene", "100 kb upstream and downstream range of gene" and "500 kb upstream and downstream range of gene".
Pathways/gene set databases
A pathway/gene set represents the genes involved in the same pathway. Pathway-based analysis search a collection of gene sets to identify the pathways associated to traits.