SNP Detail For rs6903608
1.Mapping Information
Human SNP ID rs6903608
Human chromosome chr6
Human SNP position 32460508
Pig chromosome chr7
Pig SNP position 29063118
2.Annotation Information
PubMed ID21037568
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21037568
StudyA genome-wide association study of Hodgkin__s lymphoma identifies new susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3).
Disease/TraitHodgkin__s lymphoma
Initial sample589 European ancestry cases, 5,199 European ancestry controls
Replication sample2,057 European ancestry cases, 3,416 European ancestry controls
Region6p21.32
Chromosome idchr6
Chromosome position32460508
Reported geneHLA-DRA
Mapped geneHLA-DRA - HLA-DRB5
Upstream gene id3122
Downstream gene id3127
SNP gene ids
Upstream gene distance15462
Downstream gene distance56866
SNP risk allelers6903608-G
SNPsrs6903608
Merged0
SNP id current6903608
Contextintron_variant
Intergenic1
Allele frequency0.27
P value3E-50
Pvalue mlog49.5228787452803
P value text
Or beta1.7
%95 Ci[1.58-1.82]
PlatformIllumina [504374]
CNVN
Mapped traitHodgkins lymphoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000183
Study accessionGCST000851
PubMed ID24920014
JournalNat Commun
Linkwww.ncbi.nlm.nih.gov/pubmed/24920014
StudyA meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus.
Disease/TraitHodgkin__s lymphoma
Initial sample1,816 European ancestry cases, 7,877 European ancestry controls
Replication sample1,281 European ancestry cases, 3,218 European ancestry controls
Region6p21.32
Chromosome idchr6
Chromosome position32460508
Reported geneHLA class II, HLA class I
Mapped geneHLA-DRA - HLA-DRB5
Upstream gene id3122
Downstream gene id3127
SNP gene ids
Upstream gene distance15462
Downstream gene distance56866
SNP risk allelers6903608-C
SNPsrs6903608
Merged0
SNP id current6903608
Contextintron_variant
Intergenic1
Allele frequency0.3
P value7E-31
Pvalue mlog30.1549019599857
P value text
Or beta1.64
%95 Ci[1.51鈥?.78]
PlatformAffymetrix, Illumina [1004829] (imputed)
CNVN
Mapped traitHodgkins lymphoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000183
Study accessionGCST002480
PubMed ID24149102
JournalNat Commun
Linkwww.ncbi.nlm.nih.gov/pubmed/24149102
StudyVariation at 3p24.1 and 6q23.3 influences the risk of Hodgkin__s lymphoma.
Disease/TraitHodgkin__s lymphoma
Initial sample1,465 European ancestry cases, 6,417 European ancestry controls
Replication sample1,071 European ancestry cases, 953 cases, 1,853 controls
Region6p21.32
Chromosome idchr6
Chromosome position32460508
Reported geneNR
Mapped geneHLA-DRA - HLA-DRB5
Upstream gene id3122
Downstream gene id3127
SNP gene ids
Upstream gene distance15462
Downstream gene distance56866
SNP risk allelers6903608-G
SNPsrs6903608
Merged0
SNP id current6903608
Contextintron_variant
Intergenic1
Allele frequency0.27
P value5E-27
Pvalue mlog26.3010299956639
P value text
Or beta1.62
%95 Ci[NR]
PlatformIllumina [296129]
CNVN
Mapped traitHodgkins lymphoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000183
Study accessionGCST002237
PubMed ID22086417
JournalBlood
Linkwww.ncbi.nlm.nih.gov/pubmed/22086417
StudyA genome-wide meta-analysis of nodular sclerosing Hodgkin lymphoma identifies risk loci at 6p21.32.
Disease/TraitNodular sclerosis Hodgkin lymphoma
Initial sample393 European ancestry cases, 3,315 European ancestry controls
Replication sample113 European ancestry cases, 214 European ancestry controls
Region6p21.32
Chromosome idchr6;6;6;6;6
Chromosome position32460508;32604474;32142202;32415331;32416944
Reported geneHLA-DQB1, HLA-DRB1
Mapped geneHLA-DRA - HLA-DRB5; HLA-DRB1 - HLA-DQA1; FKBPL - PRRT1; BTNL2 - HLA-DRA; BTNL2 - HLA-DRA
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers6903608-T; rs2858870-C; rs204999-G; rs9268528-A; rs9268542-A
SNPsrs6903608; rs2858870; rs204999; rs9268528; rs9268542
Merged0
SNP id current
Contextintron_variant; intron_variant; intergenic_variant; intergenic_variant; intergenic_variant
Intergenic
Allele frequencyNR
P value0.000000000000000008
Pvalue mlog17.096910013008
P value text
Or beta2.5
%95 Ci[NR]
PlatformIllumina [705591]
CNVN
Mapped traitnodular sclerosis Hodgkin lymphoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004708
Study accessionGCST001323
PubMed ID22086417
JournalBlood
Linkwww.ncbi.nlm.nih.gov/pubmed/22086417
StudyA genome-wide meta-analysis of nodular sclerosing Hodgkin lymphoma identifies risk loci at 6p21.32.
Disease/TraitNodular sclerosis Hodgkin lymphoma
Initial sample393 European ancestry cases, 3,315 European ancestry controls
Replication sample113 European ancestry cases, 214 European ancestry controls
Region6p21.32
Chromosome idchr6;6;6;6;6
Chromosome position32460508;32604474;32142202;32415331;32416944
Reported geneHLA-DQB1, HLA-DRB1
Mapped geneHLA-DRA - HLA-DRB5; HLA-DRB1 - HLA-DQA1; FKBPL - PRRT1; BTNL2 - HLA-DRA; BTNL2 - HLA-DRA
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers6903608-C; rs2858870-T; rs204999-A; rs9268528-G; rs9268542-G
SNPsrs6903608; rs2858870; rs204999; rs9268528; rs9268542
Merged0
SNP id current
Contextintron_variant; intron_variant; intergenic_variant; intergenic_variant; intergenic_variant
Intergenic
Allele frequencyNR
P value0.0000002
Pvalue mlog6.69897000433601
P value text
Or beta1.7
%95 Ci[NR]
PlatformIllumina [705591]
CNVN
Mapped traitnodular sclerosis Hodgkin lymphoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004708
Study accessionGCST001323