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Download result file            Parameters
Job Name untitled Email
Most significant SNPs specify SNP by P-value < 1.0E-5 GWAS SNP P-value file example data
P-value -> -log10(P-value) true Population CEU
LD CutOff r2 :0.8 Distance 200kb
Rule of mapping SNPs to genes within gene FDR cutoff for PBA 0.05
Pathway/Gene Set size(min) 5 Pathway/Gene Set size(max) 100
Pathway/Gene Set KEGG,BioCarta,GO biological process,GO molecular function


Hypothesis

rs2476601(non_synonymous_coding(deleterious)) PTPN22 PROTEIN_TYROSINE_PHOSPHATASE_ACTIVITY
rs2230926(non_synonymous_coding) TNFAIP3 cd40Pathway

Candidate causal SNPs

Candidate causal SNP Functional class Gene Candidate causal pathwaya -log10(P)b In LD with r2 D' -log10(P)c
rs2476601 dbSNP Ensembl SNPedia non_synonymous_coding(deleterious) PTPN22 GeneCards Ensembl 1 - rs6679677 dbSNP Ensembl SNPedia 1.0 1.0 25.4918744639168
rs2230926 dbSNP Ensembl SNPedia non_synonymous_coding TNFAIP3 GeneCards Ensembl 2 - rs5029939 dbSNP Ensembl SNPedia 1.0 1.0 5.50003813440381
a The number indicates the index of pathways, which are ranked by their statistical significance (FDR).
b -log10(P) for candidate causal SNP in original GWAS. '-' denotes that this SNP is not represented in the original GWAS.
c -log10(P) for the SNP (which candidate causal SNP is in LD with) in original GWAS.

Candidate causal pathways

Index  Candidate causal pathway Description Nominal P FDR
1 PROTEIN_TYROSINE_PHOSPHATASE_ACTIVITY
Genes and SNPs in the pathway
Genes annotated by the GO term GO:0004725. Catalysis of the...... Genes annotated by the GO term GO:0004725. Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate. More... 0.0040 0.041
2 cd40Pathway
Genes and SNPs in the pathway
CD40L Signaling Pathway CD40L Signaling Pathway 0.01 0.0416

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