How to know which dot is which SNP in Locus zoom
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!
• 1,935 views
•
link
updated
by
WouterDeCoster
•
written
by
khn
•
written
by
khn
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Meta analysis using METAL
written by khn
-
Adjust Y axis scale in ggplot2
written by santiagoboccardo31 •
-
FINEMAP - output files
written by khn
-
Adding dosage for a SNP as a covariate to a phenotype file
written by khn
-
Population stratification analysis for a small candidate gene case control study
written by khn
-
Dot plots for biomarkers
written by Nate •
-
How to define the LD interval where a SNP locates?
written by Tao
-
Duplicate ID in bed file
written by janhuang.cn
-
Binary to DNA sequence
written by khn
-
CYP2D6 haplotype reconstruction
written by khn
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