SNPStats

Your web tool for SNP analysis

SNPStats is a simple, ready-to-use software which has been designed to analyze genetic-epidemiology studies of association using SNPs.

You can upload your data and, for each selected SNP, you will receive:

• Allele and genotype frequencies
• Test for Hardy-Weinberg equilibrium
• Analysis of association with a response variable based on linear or logistic regression
• Multiple inheritance models: co-dominant, dominant, recessive, over-dominant and additive
• Analysis of interactions (gene-gene or gene-environment)

If multiple SNPs are selected:

• Linkage disequilibrium statistics
• Haplotype frequency estimation
• Analysis of association of haplotypes with the response
• Analysis of interactions (haplotypes-covariate)

Paper SNPStats: a web tool for the analysis of association studies
Xavier Sole, Elisabet Guino, Joan Valls, Raquel Iniesta, and Victor Moreno
Bioinformatics 2006 22: 1928-1929.

Tutorial with details of the computations and interpretation guide is available [tutorial]

Source code for local installation is available [download]

Disclaimer: We are aware that the complete analysis may fail with some datasets, specially when analysing interactions with SNPs that have low allele frequencies. We are trying to detect this problems and provide nice output. If the results page does not show the return button at the end, something has failed during the computations. Please report any problem and suggestions for improvement.