SNP Detail For rs6920220
1.Mapping Information
Human SNP ID rs6920220
Human chromosome chr6
Human SNP position 137685367
Pig chromosome chr1
Pig SNP position 30012057
2.Annotation Information
PubMed ID17982456
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/17982456
StudyTwo independent alleles at 6q23 associated with risk of rheumatoid arthritis.
Disease/TraitRheumatoid arthritis
Initial sample397 European ancestry cases, 1,211 controls
Replication sample1,408 cases, 2,426 controls, 875 European ancestry cases, 832 European ancestry controls
Region6q23.3
Chromosome idchr6
Chromosome position137685367
Reported geneTNFAIP3, OLIG3
Mapped geneLOC102723649 - LOC442263
Upstream gene id102723649
Downstream gene id442263
SNP gene ids
Upstream gene distance10813
Downstream gene distance20456
SNP risk allelers6920220-?
SNPsrs6920220
Merged0
SNP id current6920220
Contextintron_variant
Intergenic1
Allele frequency0.2
P value0.0000001
Pvalue mlog7
P value text
Or beta1.22
%95 Ci[NR]
PlatformAffymetrix [79853]
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST000122
PubMed ID18794853
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/18794853
StudyCommon variants at CD40 and other loci confer risk of rheumatoid arthritis.
Disease/TraitRheumatoid arthritis
Initial sample3,393 European ancestry cases, 12,460 European ancestry controls
Replication sample3,929 European ancestry cases, 5,807 European ancestry controls
Region6q23.3
Chromosome idchr6
Chromosome position137685367
Reported geneTNFIP3, OLIG3
Mapped geneLOC102723649 - LOC442263
Upstream gene id102723649
Downstream gene id442263
SNP gene ids
Upstream gene distance10813
Downstream gene distance20456
SNP risk allelers6920220-?
SNPsrs6920220
Merged0
SNP id current6920220
Contextintron_variant
Intergenic1
Allele frequency0.22
P value0.000000002
Pvalue mlog8.69897000433601
P value text
Or beta1.24
%95 Ci[1.16-1.32]
PlatformAffymetrix, Illumina [at least 315971] (imputed)
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST000232
PubMed ID21297633
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21297633
StudyMeta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Disease/TraitUlcerative colitis
Initial sample6,687 European ancestry cases, 19,718 European ancestry controls
Replication sample9,628 European ancestry cases, 12,917 European ancestry controls
Region6q23.3
Chromosome idchr6
Chromosome position137685367
Reported geneintergenic
Mapped geneLOC102723649 - LOC442263
Upstream gene id102723649
Downstream gene id442263
SNP gene ids
Upstream gene distance10813
Downstream gene distance20456
SNP risk allelers6920220-A
SNPsrs6920220
Merged0
SNP id current6920220
Contextintron_variant
Intergenic1
Allele frequency0.21
P value0.00000000000000008
Pvalue mlog16.096910013008
P value text
Or beta1.14
%95 Ci[1.09-1.20]
PlatformAffymetrix, Illumina [~ 1100000] (imputed)
CNVN
Mapped traitulcerative colitis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000729
Study accessionGCST000964
PubMed ID20453842
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20453842
StudyGenome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
Disease/TraitRheumatoid arthritis
Initial sample5,539 European ancestry cases, 20,169 European ancestry controls
Replication sample6,768 European ancestry cases, 8,806 European ancestry controls
Region6q23.3
Chromosome idchr6
Chromosome position137685367
Reported geneTNFAIP3
Mapped geneLOC102723649 - LOC442263
Upstream gene id102723649
Downstream gene id442263
SNP gene ids
Upstream gene distance10813
Downstream gene distance20456
SNP risk allelers6920220-A
SNPsrs6920220
Merged0
SNP id current6920220
Contextintron_variant
Intergenic1
Allele frequency0.22
P value0.0000000000009
Pvalue mlog12.0457574905606
P value text
Or beta1.22
%95 Ci[1.16-1.29]
PlatformAffymetrix, Illumina [~ 2716259] (imputed)
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST000679
PubMed ID24449572
JournalArthritis Rheumatol
Linkwww.ncbi.nlm.nih.gov/pubmed/24449572
StudyNovel rheumatoid arthritis susceptibility locus at 22q12 identified in an extended UK genome-wide association study.
Disease/TraitRheumatoid arthritis
Initial sample3,034 European ancestry cases, 5,271 European ancestry controls
Replication sample4,726 European ancestry cases, 2,625 European ancestry controls
Region6q23.3
Chromosome idchr6
Chromosome position137685367
Reported geneTNFAIP3
Mapped geneLOC102723649 - LOC442263
Upstream gene id102723649
Downstream gene id442263
SNP gene ids
Upstream gene distance10813
Downstream gene distance20456
SNP risk allelers6920220-?
SNPsrs6920220
Merged0
SNP id current6920220
Contextintron_variant
Intergenic1
Allele frequency
P value0.00000003
Pvalue mlog7.52287874528033
P value text
Or beta1.23
%95 Ci[1.14-1.32]
PlatformAffymetrix, Illumina [1831729] (imputed)
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST002323
PubMed ID23128233
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/23128233
StudyHost-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Disease/TraitInflammatory bowel disease
Initial sample12,924 European ancestry cases, 21,442 European ancestry controls
Replication sample25,683 European ancestry cases, 17,015 European ancestry controls
Region6q23.3
Chromosome idchr6
Chromosome position137685367
Reported geneTNFAIP3
Mapped geneLOC102723649 - LOC442263
Upstream gene id102723649
Downstream gene id442263
SNP gene ids
Upstream gene distance10813
Downstream gene distance20456
SNP risk allelers6920220-A
SNPsrs6920220
Merged0
SNP id current6920220
Contextintron_variant
Intergenic1
Allele frequency0.206
P value1E-21
Pvalue mlog21
P value text
Or beta1.102
%95 Ci[1.064-1.141]
PlatformAffymetrix, Illumina [1230000] (imputed)
CNVN
Mapped traitinflammatory bowel disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003767
Study accessionGCST001725
PubMed ID26192919
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26192919
StudyAssociation analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.
Disease/TraitUlcerative colitis
Initial sample6,968 European ancestry cases, 20,464 European ancestry controls
Replication sample10,679 European ancestry cases, 26,715 European ancestry controls, 397 Iranian ancestry cases, 342 Iranian ancestry controls, 1,239 Indian ancestry cases, 990 Indian ancestry controls, 1,134 East Asian ancestry cases, 3,719 East Asian ancestry controls
Region6q23.3
Chromosome idchr6
Chromosome position137685367
Reported geneNR
Mapped geneLOC102723649 - LOC442263
Upstream gene id102723649
Downstream gene id442263
SNP gene ids
Upstream gene distance10813
Downstream gene distance20456
SNP risk allelers6920220-A
SNPsrs6920220
Merged0
SNP id current6920220
Contextintron_variant
Intergenic1
Allele frequency0.2086
P value5E-22
Pvalue mlog21.3010299956639
P value text(EA)
Or beta1.1582799
%95 Ci[1.13-1.19]
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitulcerative colitis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000729
Study accessionGCST003045
PubMed ID26192919
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26192919
StudyAssociation analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.
Disease/TraitInflammatory bowel disease
Initial sample12,882 European ancestry cases, 21,770 European ancestry controls
Replication sample25,273 European ancestry cases, 26,715 European ancestry controls, 548 Iranian ancestry cases, 342 Iranian ancestry control, 1,423 Indian ancestry cases, 990 Indian ancestry controls, 2,824 East Asian ancestry cases, 3,719 East Asian ancestry controls
Region6q23.3
Chromosome idchr6
Chromosome position137685367
Reported geneNR
Mapped geneLOC102723649 - LOC442263
Upstream gene id102723649
Downstream gene id442263
SNP gene ids
Upstream gene distance10813
Downstream gene distance20456
SNP risk allelers6920220-A
SNPsrs6920220
Merged0
SNP id current6920220
Contextintron_variant
Intergenic1
Allele frequency0.2086
P value0.00000000000001
Pvalue mlog14
P value text(EA)
Or beta1.0993968
%95 Ci[1.08-1.12]
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitinflammatory bowel disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003767
Study accessionGCST003043