Overview

IDAllelesLocationGenome BuildSource
rs653178C/Tchr12: 11156995238dbsnp146
rs653178C/T chr12: 112007756 37dbsnp146_grch37
imm_12_110492139T/C chr12: 111569952 38ImmunoChip
imm_12_110492139T/C chr12: 112007756 37ImmunoChip
imm_12_110492139T/C chr12: 110492139 36ImmunoChip

Jbrowse

Historical Ids

Old Marker IDNew Marker IDCurrent Marker IDdbSNP Build
rs60407737rs653178rs653178130
rs386603326rs653178rs653178142

Criteria

rs653178 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 rs653178 as derived from dbSNP:
  • in intron
Gene(s) at location of variation:  ATXN2 

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 rs653178, 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.