Input View

SNP Selection Section

Search Target:

Choose "A List of SNP IDs" if you have a delimited list reference SNP IDs (rs#) to paste in the "Paste ID List Here" text box.

If you don't have a SNP list, you can choose "Search SNPs", and click on the button "Click Here to Search SNPs" to search for SNPs on various criteria. A pop-up window will appear to let you choose your criteria for SNPs. Once you set your criteria for "Search SNP", clicking on "Query" will return the SNP list automatically to the "Paste ID List Here" text box.

You can also paste a list of UniSTS IDs (currently only numeric IDs are accepted) by choosing "A List of UniSTS IDs".

If you have a text file of delimited SNP or UniSTS IDs, you can upload your file through Upload box below the "Paste ID List Here" text box.

SNP Neighbor Selection:

Option of Genomic Location Neighbor: You can specify the neighborhood size of SNPs to include in your search result. For example, if your input is 100, all SNPs that are located 100bp upstream and downstream of all the SNP in your input list will be included in the final search result.

Option of Gene Neighbor: With this option, you are able to explore all the SNPs within the boundaries of the genes to which your input SNPs are matched. You can also expand your search scope to up to 5kbp upstream of the genes by making the corresponding selection in the drop down list.

Linkage Disequibrilium Criteria Section

LD Score Selection (Optional):

You can specify D', r2, or LOD score filter by selecting the desired item in the drop down list, and fill in the corresponding range values. All the SNPs within the LD range will be returned.

Haplotype Block Selection (Optional):

You can also include all the SNPs in the haplotype blocks to which your selected SNPs belong. Four populations and two haplotype block calculation methods are provided.

Result View

Right Frame

Functionality

The right panel are the annotations for all the SNPs that satisfy user selection. The annotations are categorized into 6 levels. The annotations for each level will be displayed upon click on the corresponding tab on the top.

If the annotation is 'Y', that means the corresponding SNP is matched to the particular annotation. You can click on 'Y' to look at the detailed annotation. Or you can click on ">>" (if available) below the annotation title to view the details of all the matched SNPs to that annotation.

Filter Function: You can click on the checkboxes below the annotation titles to filter the SNP list that only have matches to the corresponding annotations. For example, checking on the checkboxes below Splice Site and Conserved Element and clicking on "Filter" button will show only SNPs that are located in Splice Site AND Conserved Element. To remove the filter, simply click on "Remove All Filters" button.

Annotations

SNP Disease Prediction:

This annotation is contributed by Richard J Dobson at Queen Mary University of London. In Disease State column, 1 indicates nsSNP prone to disease, and 0 means neutral. Disease Score column shows the confidence score of such prediction. For information about the prediction method, please refer to the author's publication Predicting deleterious nsSNPs: an analysis of sequence and structural attributes" BMC Bioinformatics. 2006; 7: 217.

Left Frame

The left panel provides a tree view of all functional/structural categories from Gene Ontology, KEGG, Biocarta, Neurobiology, GenMAPP and cytogenetic band. You can look at the matches of the SNPs to these categories  by going to the "Pathway" level, and clicking on the "C" icon next to the individual SNP.

Each category has a set of corresponding UniGene, Entrez Gene, Gene Symbol, as well as the category's description and original link, which is embedded in the italicized number. Clicking it would direct you to the concept's original web link

Black nodes represent pathways that are near root and are more general.

Blue nodes are pathway that is near leaf and is quite specific. Red color nodes mean there are hits between SNP web service and the pathway's corresponding gene set.

When you click any black nodes, a little icon 'D' would appear, clicking it would allow user customize the download format and download all information of the node and all nodes underneath it. Also you can download data formats for either GenePattern or our FunctionGroup package for function category-based data analysis.

When you click blue nodes, two more icon 'S' and 'G' swould appear. 'S' is for SNP portal web service, which can be used to retrieve all SNPs related to the corresponding category based on user-defined criteria. 'G' is for viewing those corresponding Gene information on-line.