A Manhattan Plot  is created in GWAS studies to visualize where SNP positions and there logarithmic p-values.
Can somebody please with the help of a simple numerical example for 2 or 3 chromosome show how this plot is made?


**Update**:

Actually I am confused how data is processed so that each SNP has different p-values  . Take for the sake of argument that I have following scenario

    Chromosomes=23
    Controls=500
    Subjects=800
    SNP=20000/SNP  that is each chromosome has 20000 SNPs

Now my confusion is that how those dots are made . I mean how is it possible that on horizontal axis that is representing a particular SNP on a specific chromosome how could we have multiple dots going up or down? that is my confusion?


regards
You seem have some issues reading what is said.

 - Each chromosome has multiple SNPs
 - For each SNP you perform one statistical test
 - Each SNP has one position and one p-value
 - Each SNP has only one dot in a Manhattan plot
 - It looks like they're lots of dots stacked on each other, but that's just because you are testing many many SNPs.