The 1000 Genome Browser is an interactive graphical viewer that allows users to explore variant calls, genotype calls and supporting evidence (such as aligned sequence reads) that have been produced by the 1000 Genomes Project. (from the NCBI web site).
It can be reached directly at http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/. As in most of these resources, there are many ways to find this tool. In the dbSNP Guide there is an example via the Variant ID.
NCBI has provided a tutorial on this tool at http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/help/
Once again this example will continue to use the LCT gene, using variation rs121908936.
From the 1000 Genome Browser page:
There are a few things to notice - At the top of the page there is indication of what genomic assembly was used for this data. This is important because unlike literature databases, the data for bioinformatics is always changing. Also, the default chromosome is 1.
Next we add the variation that we are interested in. In this case it is rs121908936, a SNP that we found in the dbSNP example and click the arrow following the field:
We are now on Chromosome 2 in the Region of LCT, which confirms that we found the correct variation.
This display highlights the region of variation within the 1000 Genome project population. It can be used to determine allele variation percentages within specific groups and across the whole data set.
