The SNP Dossier presents a concise table view of a SNP or a list of SNPs emphasizing T1D-specific data.
Operating Instructions:
To operate the program, specify one or more SNPs and click the "Create
Dossier" button. SNPs can be input via the text box either by hand,using the LD tool, or
by uploading a file of identifiers, with each identifier appearing on a separate line.
The most reliable SNP identifiers are dbSNP identifiers(rs#).
The LD tool allows queries to be constructed to include all markers that are in a region
of LD with the target marker. Just add the SNP identifier into the target marker text box, select
thresholds and the dataset to use and click 'Go'. If this operation is successful then the text box
above should contain a list of variants, and the SNP Dossier can be queried by using the 'Create Dossier'
button.
The LD calculation service contains a few canned QC steps that might filter out a SNP and lead
to unexpected results. As it stands variants with call rate of less than 90%,
minor allele frequency of less than 0.05 and Hardy Weinberg z-score2 greater than 25 are
excluded.
Results page:
Note that if a SNP identifier is not found in our database it will be listed in the Identifiers not found section.
Currently this tool has the following assays:
- Imputed: Shows if a SNP overlaps an imputed genome wide association study. Headings are by disease. See key for further details on colour coding and symbols.
- GWAS: Shows if a SNP overlaps a genome wide association study. Headings are by disease. See key for further details on colour coding and symbols.
- ImmunoChip: Shows if a SNP overlaps a study carried out on the ImmunoChip.Headings are by disease. See key for further details on colour coding and symbols.
- Genotyping Platform: Shows if a particular platform has an assay for SNP. See key for further details on colour coding and symbols.
- Function:Shows any functional information associated with SNP. Note that where multiple functions exist we show these in order of import Non Synonymous > Synonymous > UTR > Intronic > Gene Region. See key for further details.
- Gene:Shows any genes that overlap SNP based on refseq annotation.
To find out more about the source of data within a column, rollover the 
icon. By default the key is hidden, to toggle visibility click the / ![[-]](/images/collapse.jpg)
marked Key.
For entries or lists with over 10 entries extra search and pagination capabilities are enabled.
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