T1DBase Variants

Variant data on T1DBase is from dbSNP135.

Variants can be searched for by rs id (e.g. rs3087243) or by common aliases (e.g. CT60) by entering your search term in the box at the top right of every page.

Furthermore, more complex variant-based querying of the website can be undertaken below, or through the Batch Query Tool.

Advanced Searches
What Variants are in LD with my Variant?

Linkage disequilibrium (LD) statistics have been calculated with respect to this marker, using the HapMap CEU Founders dataset. The calculations were performed with the snpMatrix R library, covering 1Mb either side of the marker; and with the following filters applied: MAF > 0.05, call rate > 0.9, and chi-squared test for deviation from HWE < 25.

Enter your SNP of interest in the search box and alter the R2, D′ or LOD filters as you wish.

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What Studies has my Variant been typed in?

Data from various Genome Wide Assocaition Studies (GWAS) have been incorporated into T1DBase.

Enter your snp of interest (rs id) into the search box and view p-values from all available studies.
An empty box or N/A shows the SNP was typed in a study, but excluded or no p-value returned for some reason (see marker page for reasons). If the study doesn't appear, the SNP wasn't typed in that study.

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