BOSTON UNIVERSITY SCHOOL OF MEDICINEdepartment of genetics & genomicsGMED
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Create a plot
Index SNP dbSNP ID:
 
bases down:
 
bases up:
 
HapMap populations to include:
CEU
YRI
JPT + CHB
 
 
 
 
 
Modify weighted clustering parameter
weighting bin size:
 

The weighting bin size determines the number of SNPs that are included in each group for the decaying weight clustering. Equal weight is assigned to the SNPs in each group, and groups closer to the index SNP are weighted more heavily than those further away. To have each SNP be weighted independently, choose bin size 1. To decrease the effect of weighting, choose a larger bin size.

Introduction to the Chromoplotter

Chromoplotter visualizes haplotypes from the HapMap population samples you select in the region around the index SNP you enter.

The haplotypes are organized via a decaying-weight hierarchical clustering scheme that places the most importance on the alleles of the index SNP and SNPs immediately adjacent to the index SNP. The purpose of this decaying weight is to ensure that the organization of haplotypes is determined most strongly by the genotypes of your index SNP and immediately adjacent SNPs.

The output is either a resolution-free PDF document or low-resolution screen image that includes several components. The main component is the phased chromosome alignment of the region for each of the populations selected. Genotypes are color-coded according to the minor and major alleles of each SNP across all user-selected populations. This uniform coding of the SNP alleles across populations facilitates inspection of haplotype differences across populations. Due to the large quantity of information that can be displayed using Chromoplotter, the PDF document may be more useful for detailed analysis.

To the left of the plot, SNP functional information is displayed using a yellow to blue color scale. The names and extents of any genes in the region (as identified in Entrez Gene) are also shown. Annotation information about the SNPs that are included in the visualization can be accessed via the link below the image. This annotation information is also included in the PDF document.

More information about Chromoplotter can be found here.

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