Overview

IDAllelesLocationGenome BuildSource
rs2476601A/Gchr1: 11383494638dbsnp146
rs2476601A/G chr1: 114377568 37dbsnp146_grch37
imm_1_114179091A/G chr1: 113834946 38ImmunoChip
imm_1_114179091A/G chr1: 114377568 37ImmunoChip
imm_1_114179091A/G chr1: 114179091 36ImmunoChip

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Historical Ids

Old Marker IDNew Marker IDCurrent Marker IDdbSNP Build
rs117063937rs2476601rs2476601132
rs60104027rs2476601rs2476601130
rs52834763rs2476601rs2476601128

Criteria

rs2476601 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 rs2476601 as derived from dbSNP:
  • in intron
  • has reference
  • has non-synonymous missense
Gene(s) at location of variation:  PTPN22  AP4B1-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 rs2476601, 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.