SNP Detail For rs7521902
1.Mapping Information
Human SNP ID rs7521902
Human chromosome chr1
Human SNP position 22164231
Pig chromosome chr6
Pig SNP position 74185808
2.Annotation Information
PubMed ID20852632
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20852632
StudyA genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.
Disease/TraitOvarian cancer
Initial sample1,768 European ancestry cases, 2,354 European ancestry controls
Replication sample8,709 European ancestry cases, 51,764 European ancestry controls
Region1p36.12
Chromosome idchr1
Chromosome position22164231
Reported geneNR
Mapped geneLOC105376850
Upstream gene id
Downstream gene id
SNP gene ids105376850
Upstream gene distance
Downstream gene distance
SNP risk allelers7521902-?
SNPsrs7521902
Merged0
SNP id current7521902
Contextintergenic_variant
Intergenic0
Allele frequencyNR
P value0.000005
Pvalue mlog5.30102999566398
P value text
Or beta1.12
%95 Ci[1.07-1.18]
PlatformIllumina [2056878] (imputed)
CNVN
Mapped traitovarian carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001075
Study accessionGCST000802
PubMed ID22504420
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22504420
StudyGenome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
Disease/TraitBone mineral density
Initial sampleUp to 32,961 European and East Asian ancestry individuals
Replication sampleUp to 50,933 European and East Asian ancestry individuals
Region1p36.12
Chromosome idchr1
Chromosome position22164231
Reported geneWNT4
Mapped geneLOC105376850
Upstream gene id
Downstream gene id
SNP gene ids105376850
Upstream gene distance
Downstream gene distance
SNP risk allelers7521902-A
SNPsrs7521902
Merged0
SNP id current7521902
Contextintergenic_variant
Intergenic0
Allele frequency0.31
P value0.0000000001
Pvalue mlog10
P value text(LSBMD)
Or beta0.05
%95 Ci[NR] unit decrease
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST001482
PubMed ID23104006
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23104006
StudyGenome-wide association meta-analysis identifies new endometriosis risk loci.
Disease/TraitEndometriosis
Initial sample3,181 European ancestry cases, 8,075 European ancestry controls, 1,423 Japanese ancestry cases, 1,318 Japanese ancestry controls
Replication sample1,044 Japanese ancestry, 4,017 Japanese ancestry controls
Region1p36.12
Chromosome idchr1
Chromosome position22164231
Reported geneWNT4
Mapped geneLOC105376850
Upstream gene id
Downstream gene id
SNP gene ids105376850
Upstream gene distance
Downstream gene distance
SNP risk allelers7521902-A
SNPsrs7521902
Merged0
SNP id current7521902
Contextintergenic_variant
Intergenic0
Allele frequency0.238
P value0.00000000003
Pvalue mlog10.5228787452803
P value text
Or beta1.19
%95 Ci[1.13-1.25]
PlatformIllumina [407632]
CNVN
Mapped traitendometriosis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001065
Study accessionGCST001720
PubMed ID23472165
JournalPLoS One
Linkwww.ncbi.nlm.nih.gov/pubmed/23472165
StudyGenome-wide association study link novel loci to endometriosis.
Disease/TraitEndometriosis
Initial sample1,514 European ancestry casses, 12,660 European ancestry controls
Replication sample505 European ancestry cases, 1,811 European ancestry controls
Region1p36.12
Chromosome idchr1;1;1;1;1
Chromosome position22096228;22164231;22113027;22123994;22159378
Reported geneWNT4
Mapped geneCDC42 - WNT4; LOC105376850; CDC42 - WNT4; WNT4; LOC105376845 - LOC105376850
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers10917151-A; rs7521902-A; rs4654783-T; rs2235529-T; rs16826658-G
SNPsrs10917151; rs7521902; rs4654783; rs2235529; rs16826658
Merged0
SNP id current
Contextupstream_gene_variant; intergenic_variant; downstream_gene_variant; intron_variant; intergenic_variant
Intergenic
Allele frequency0.134
P value0.0000008
Pvalue mlog6.09691001300805
P value text
Or beta1.25
%95 Ci[NR]
PlatformIllumina [580699]
CNVN
Mapped traitendometriosis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001065
Study accessionGCST001894