Overview

SNPMap is a web application that deciphers the implication of SNPs based on their keywords, which are obtained through the related biomedical literature of the SNPs.

Search

Information about SNPs and their keywords could be queried through the search bar.

The search bar can be found at the top of each page, while also appearing at the front page.

Legitimate queries

Legitimate queries include:

  • Keywords and key terms that are referenced in any SNP. Keyword suggestions would appear as a drop-down menu.
  • SNPs, when referenced through their RSIDs.

If your query does not fit into the two groups above, it will return an error page.

SNP Pages

Basic Information

The basic information card at the top of the page includes the following contents:

  • The HGVS name of the SNP
  • The gene where the SNP is located
  • The chromosome where the SNP is located
  • The position of the SNP on its chromosome
  • The timing when the SNP data was last updated

The basic information card also provides the following external links:

  • The dbSNP page of the SNP
  • The SNPedia page of the SNP

Keyword Map

The keyword maps contains a visualized representation of the concepts related to the SNP. Each dot represents a concept related to the SNP, and each line represents a connection between two concepts. The bigger the dot, or the wider the line, the stronger the relation/connection. After clicking on a certain dot, the user will be redirected to a web page dedicated to the concept under the SNP.

The keyword maps can be displayed as a keywords network or a circular map depending on the tab selected at the top of the graph.

The slider at the top of the graph can be used to adjust the quantities of keywords displayed inside the graphs, while the legend at the top of the graph can be used to limit the words displayed inside the graphs to the categories of diseases, chemicals, or genes.

Keyword List

The keyword list is a form that lists all the concepts related to an SNP (or an concept under an SNP). The keywords can be sorted by alphabetical order or significance value.

Population Map

The population map is a graph that display the difference in variant frequencies among different ethnic groups.

  • African Others: Individuals with African ancestry
  • African American: African American
  • African: African Others and African American combined
  • European: European
  • Latin American 1: Latin American individiuals with Afro-Caribbean ancestry
  • Latin American 2: Latin American individiuals with mostly European and Native American Ancestry
  • South Asian: South Asian
  • East Asian: East Asian
  • Asian: East Asian and Other Asian combined (excluding South Asian)
  • Other Asian: Asian individuals excluding South or East Asian

GWAS

GWAS information related to the SNP is included in the table under the "GWAS" tab, which listed GWAS studies and their p-values, beta-values, traits.

Articles related to the SNP are listed in the table under the "Related articles" tab, including their PMID, year of publishing, title, and keywords.

Keyword Pages

Most keywords that are mentioned in any SNP have their own keyword pages as well. These pages are created to demonstrate the relations of each keyword to other keywords or SNPs.

When two keywords are mentioned inside the same article in SNPMap, the significancce of their connection is added by one. After all calculations, the keywords with the highest significance are rendered on the graph with their sizes positively correlated with their significance values. The keywords are also listed in a table beside the graph and sorted by their significance values.

SNPs are listed in a table and sorted by their significance values of their connections to the keyword. The RSID, value, and top keywords are listed for each SNP. The significance value is calculated through two factors:

  • The frequency ratio of the keyword among all keywords under each SNP.
  • The total value of frequencies among all keywords under each SNP.