Overview

IDAllelesLocationGenome BuildSource
rs6476839A/Tchr9: 429082338dbsnp146
rs6476839A/T chr9: 4290823 37dbsnp146_grch37
imm_9_4280823A/T chr9: 4290823 38ImmunoChip
imm_9_4280823A/T chr9: 4290823 37ImmunoChip
imm_9_4280823A/T chr9: 4280823 36ImmunoChip

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Historical Ids

Old Marker IDNew Marker IDCurrent Marker IDdbSNP Build
rs59283472rs6476839rs6476839130
rs17717174rs6476839rs6476839123

Criteria

rs6476839 meets the following criteria:

Criteria Name
Details
Disease Tags
Marker is GW-Significant in a Study 
Marker is in r2>0.8 with an index SNP 
Marker is an index SNP in a Region 

Functional Information

Gene function properties for rs6476839 as derived from dbSNP:
  • in intron
Gene(s) at location of variation:  GLIS3 

Study

Studies containing regions of association that span this marker are shown below. Please note that when making comparisons across studies, that they may vary in terms of size, genotyping platform, and exclusion criteria. If the 'Odds Ratio' is less than 1 then the region is protective (alleles are marked as blue) otherwise it is susceptible (alleles marked as red).

StudyPublicationDiseaseRegionMarkerAllelesP-valueORMAFGene(s)

Populations

Populations data from Ensembl 1000 Genome data release May 2013:

Linkage Disequilibrium Statistics

LD Search Options

Linkage disequilibrium (LD) statistics are calculated for rs6476839, using the 1000 genomes data release May 2013. Calculations are performed with the snpStats R library, covering 1Mb either side of the marker; and with the following filters applied: MAF > 0.01, call rate < 0.9, and chi-squared test for deviation from HWE > 25.