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Your Data - Single
Your Data - Batch
Published - Single
Published - Interactive

LocusZoom - Plot with Your Data


Depending on the size of your data, runs can require 30-60 seconds to generate a plot
Provide
  Details for
    Your Data
Path to Your File
         File will be sent to server and used for plotting (Maximum 2GB) [Help]
P-Value Column Name
    Default is P.value
Set for PLINK data  or   WikiGWA data    
Marker Column Name
    Default is MarkerName
Column Delimiter     Default is tab
Specify
  Region
    to Display


Required:
Fill in
Only ONE
of These
Three
SNP
+/- Kb
SNP Reference Name   Flanking Size
Gene
+/- Kb
Gene Reference Name   Flanking Size Optional Index SNP Default=lowest p-value
Region
Chr:
Mb through Mb
  Starting Chr Position   Ending Chr Position Optional Index SNP Default=lowest p-value
Custom
  Annotation


Optional:
This overrides
Show Annotation
below
Column Name
    Name of annotation column
Category Order
    Order of annotation categories

Optional Controls

Title
  On Plot
    
    Default is name of plot data
Genome Build/
  LD Population
       Please make sure the genome build matches your selected data type!
Legend
  Location
    
Show
  RUG
HapMap

 
Use SNPs
  in Data

    Label for RUG of your SNPs
Maximum Rows
  of Gene
    Names
    
Point Size
  Proportional
    to Sample Size
    
    Specify NOWEIGHT as the column name to disable this
Highlight
  Region
    of Interest
Mb through Mb
Leave blank if no highlighting is needed
Theme     
Show
  Annotation
Built-in annotations disabled (they were far out of date.) You can specify your own annotations using the custom annotation options above.
Y-Axis
Maximum -log 10 pvalue
Y-Axis Label

Other
  Options
Recombination Rate Overlay  
Display Warning for Omitted Genes  

         Typical runs require 20-50 seconds to generate a plot

Frequently Asked Questions
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Report problems via email
Copyright © 2009- University of Michigan, Department of Biostatistics, Center for Statistical Genetics