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Introduction to NCBI Bioinformatics Resources: dbSNP

A concise introduction to the various bioinformatic data available from NCBI.

dbSNP

dbSNP

dbSNP is a database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants. (from the NCBI web site)

NCBI provides an FAQ on dbSNP at http://www.ncbi.nlm.nih.gov/books/NBK3848/

This guide will show a sample variation viewer using the LCT gene as the source.

First change the database search to SNP and create a search for the gene we are interested in and limit to the organism:

1. Choosing the first LCT variation, click on the "Varview" link:

 

The first page of results includes many variations.  By applying the filter "nonsense", the results now show only the rs121908936 variation, which is what we have asked for above:

The results show that this variation is a substitution of A and T on chromosome 2 at base pair location 135,807,131.

NOTE: Whenever using any data from NCBI it is important to check the Assembly version that this record is built from.  In this case, it is GRCh38.p2.  When we use this variation in the 1000 Genome example, the location of this SNP shows a different location.  This can be seen by clicking on the Variant ID in the above page.  The results are:

 

 

As can be seen, there is an older Assembly, GRCh37.p13.  This is what the data reflects in the 1000 Genome database.  This can be seen from this record by clicking on the magnifying glass icon under the Chr Pos for this chromosome position (136564701):

 

This will discussed in more detail in the 1000 Genome Browser guide.


 

2. Next, view this variation using the Gene viewer. Click the "GeneView" link: