How to know which dot is which SNP in Locus zoom

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6.7 years ago

khn ▴ 130

Hello,

Can anybody please teach me how to figure out which dot is which SNP? A dot that I want to know the name of SNP is r2 of 0.8, and which is located far from the SNP that I used to generate the figure. The p-value of the SNP to generate the figure is 5E-8, but the p-value of the dot that I want to know SNP is 5E-2. And the other dots near the dot that I want to know SNP are all r2 of 0.4.

Thank you in advance!

SNP genome snp • 1.6k views

ADD COMMENT • link updated 6.7 years ago by WouterDeCoster 47k • written 6.7 years ago by khn ▴ 130

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Why don't you label the SNPs and/or just look at the results values, i.e. outside the plot? You should have the position and you have already implied that the r2 of the SNP of interest is ~double that of surrounding SNPs.

To label, look here:

https://genome.sph.umich.edu/wiki/LocusZoom_Standalone#Labeling_multiple_SNPs

ADD REPLY • link 6.7 years ago by Kevin Blighe 88k

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