Overview

IDAllelesLocationGenome BuildSource
rs2366643T/Cchr3: 16001869838dbsnp146
rs2366643T/C chr3: 159736485 37dbsnp146_grch37
imm_3_161219179A/G chr3: 160018698 38ImmunoChip
imm_3_161219179A/G chr3: 159736485 37ImmunoChip
imm_3_161219179A/G chr3: 161219179 36ImmunoChip

Jbrowse

Historical Ids

Old Marker IDNew Marker IDCurrent Marker IDdbSNP Build
rs2561283rs2366643rs2366643103

Criteria

rs2366643 meets the following criteria:

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

Functional Information

Gene function properties for rs2366643 as derived from dbSNP:
  • in 5prime gene region
  • in intron
Gene(s) at location of variation:  LINC01100  IL12A-AS1 

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 rs2366643, 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.