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NCBI Resources: dbSNP

Contains information about the NCBI databases to be used as a teaching tool.

dbSNP Unique Identifiers

  • rsXXXX - reference SNP, generated by compiling multiple submittions
  • ssXXXX - submitted SNP, submitted from one experiment
  • HGVS - human genome variant society; a standardized way to represent changes to a nucleotide or protein sequence. Not actually a unique identifier, as there are several way to describe the same SNP in the genome, but it can be useful for searching.

Boolean Operators

Boolean operators allow you to combine search terms: 

  • AND: Finds documents that contain both terms.
  • OR: Finds documents that contain either term. 
  • NOT: Finds documents that contain the term on the left but not the term on the right.

Advanced Search

By default, Entrez searches your text in "All fields", which looks for the text anywhere in the entry. So if you're getting irrelevant results, try limiting your text to a particular field.

Don't know what fields you can search for? Use the Advanced search

1. Click on advanced beneath the search bar. 

2. Click the drop down menu under Builder to see what fields are stored in gene records.

This is a comprehensive list of all fields you can search for. Fields will vary by database. Example shown here is for the Gene database. 

Need help? Ask Wlad

Searching dbSNP

In dbSNP, you can search by

These fields can be combined using Boolean operators to create refined search strategies for SNPs.

Search Results

After submitting your search, a list of results will appear with gene records that match your query. The results page is divided into 3 columns:

  1. Filters: more ways to limit your search by things like genome location
  2. Results: a list of the Gene records that match your query with basic information
  3. Discovery Column: links to other databases and Search details

You can use the filters to limit by factors like a particular organism, SNPs that cause disease (pathogenic), and the type of SNP (eg, missense)

The results show the unique identifier for the SNP, the SNP in context of surrounding sequence, the chromosomal location, the gene the SNP lies in (if available), functional consequences, and links to external databases. 

To access a specific record, click on the rs number.

dbSNP records

The results page for an individual SNP contains:

  • SNP (organism, molecule type, link to PubMed
  • Allele (Variation class, RefSNP allele, Allele origin, Links to variation viewer and OMIM, Clinical Significance, MAF)
  • Integrated maps (links to SNP on Chromosome, Variation viewer, contigs, etc) 
  • GeneView (links to gene-centric information)
  • Submitter records (links to individual data that contributed to RefSNP record)
  • FASTA sequence
  • Links to other NCBI resources
  • Population diversity (allele frequencies)

See the following link for an example

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1799945