Overview

IDAllelesLocationGenome BuildSource
rs3749171C/Tchr2: 24063027538dbsnp146
rs3749171C/T chr2: 241569692 37dbsnp146_grch37
1kg_2_241218365T/C chr2: 240630275 38ImmunoChip
1kg_2_241218365T/C chr2: 241569692 37ImmunoChip
1kg_2_241218365T/C chr2: 241218365 36ImmunoChip

Jbrowse

Historical Ids

Old Marker IDNew Marker IDCurrent Marker IDdbSNP Build

Criteria

rs3749171 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 rs3749171 as derived from dbSNP:
  • has reference
  • has non-synonymous missense
Gene(s) at location of variation:  GPR35 

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 rs3749171, 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.