GWAS information

FeatureValue

SNPs plots

Manhattan plot

For plotting, overlapping data points are not drawn (filtering was performed only for SNPs with P-value ≥ 1e-5, see documentation for more details of filtering).
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Q-Q plot

For plotting purposes, overlapping data points are not drawn (filtering was performed only for SNPs with P-value ≥ 1e-5, see documentation for details of filtering).
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Top SNPs

Top SNPs are defined as the most significant SNP in a genomic risk locus. See documentation for details of definition of the genomic risk loci.

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CHR POS rsID P

MAGMA plots (gene-based test)

Manhattan plot

Label top genes.
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Q-Q plot

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Gene set analysis

MAGMA gene-set analysis is performed for curated gene sets and GO terms obtained from MsigDB (total of 10894 gene sets).
The table displays either significant gene sets with Pbon < 0.05 or the top 10 gene sets sorted by P-value.

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Gene SetN genesBetaBeta STDSEPPbon

Genetic Correlations

GWAS selection

GWAS with sample size > 5,000, the number of SNPs > 450,000, SNP h2 Z-score > 2, EUR popultaion and non-sex specific trait are available.

Exclude traits with the same name (if there is any).
Select GWAS with the maximum sample size per trait.
P-value threshold:
Pbon threshold:
Display top correlated phenotypes.
Manually select GWAS.
Selected trait (0) Clear


GC plot

The number of tested traits are based on after filtering of 'Exclude traits with the same name', 'Select GWAS with the maximum sample size per trail' and the manual selection if any of them is selected, but before the filtering of P-value or Bonferroni corrected P-value.
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GC table

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IDTraitrgsezPP-bon