SNP Detail For rs4430796
1.Mapping Information
Human SNP ID rs4430796
Human chromosome chr17
Human SNP position 37738049
Pig chromosome chr12
Pig SNP position 40839984
2.Annotation Information
PubMed ID17603485
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/17603485
StudyTwo variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes.
Disease/TraitProstate cancer
Initial sample1,501 European ancestry cases, 11,290 European ancestry controls
Replication sample1,992 European ancestry cases, 3,058 European ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneTCF2
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-A
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency0.49
P value0.00000000001
Pvalue mlog11
P value text
Or beta1.22
%95 Ci[1.15-1.30]
PlatformIllumina [310520]
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST000050
PubMed ID18264096
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/18264096
StudyMultiple loci identified in a genome-wide association study of prostate cancer.
Disease/TraitProstate cancer
Initial sample1,172 European ancestry cases, 1,157 European ancestry controls
Replication sample3,941 European ancestry cases, 3,964 European ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneHNF1B
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-A
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency0.54
P value0.000000001
Pvalue mlog9
P value text
Or beta1.18
%95 Ci[1.04-1.32]
PlatformIllumina [527869]
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST000154
PubMed ID19767754
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19767754
StudyGenome-wide association and replication studies identify four variants associated with prostate cancer susceptibility.
Disease/TraitProstate cancer
Initial sampleUp to 1,968 European ancestry cases, 35,382 European ancestry controls
Replication sampleUp to 11,806 European ancestry cases, 12,387 European ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneintergenic
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-A
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency0.52
P value0.000008
Pvalue mlog5.09691001300805
P value text
Or beta1.19
%95 Ci[1.10-1.28]
PlatformIllumina [310520]
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST000489
PubMed ID20581827
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20581827
StudyTwelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
Disease/TraitType 2 diabetes
Initial sample8,130 European ancestry cases, 38,987 European ancestry controls
Replication sampleUp to 34,412 European ancestry cases, 59,925 European ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneHNF1B, TCF2
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-G
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency
P value0.000002
Pvalue mlog5.69897000433601
P value text
Or beta1.14
%95 Ci[1.08-1.20]
PlatformAffymetrix, Illumina [2426886] (imputed)
CNVN
Mapped traittype II diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001360
Study accessionGCST000712
PubMed ID21160077
JournalSci Transl Med
Linkwww.ncbi.nlm.nih.gov/pubmed/21160077
StudyGenetic correction of PSA values using sequence variants associated with PSA levels.
Disease/TraitSerum prostate-specific antigen levels
Initial sample7,538 European ancestry individuals
Replication sample2,373 European ancestry individuals
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneHNF1B
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-A
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency0.52
P value0.00000000006
Pvalue mlog10.2218487496163
P value text
Or beta9.4
%95 Ci[NR] % increase
PlatformIllumina [304070]
CNVN
Mapped traitprostate specific antigen measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004624
Study accessionGCST000919
PubMed ID21499250
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21499250
StudyGenome-wide association study identifies a common variant associated with risk of endometrial cancer.
Disease/TraitEndometrial cancer
Initial sample1,265 European ancestry cases, 5,190 European ancestry controls
Replication sample3,957 European ancestry cases, 6,886 European ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneHNF1B
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-A
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency0.52
P value0.0000000007
Pvalue mlog9.15490195998574
P value text
Or beta1.19
%95 Ci[1.12-1.27]
PlatformIllumina [519655]
CNVN
Mapped traitendometrial neoplasm
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004230
Study accessionGCST001040
PubMed ID22961080
JournalDiabetes
Linkwww.ncbi.nlm.nih.gov/pubmed/22961080
StudyA genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.
Disease/TraitType 2 diabetes
Initial sample1,839 Han Chinese ancestry cases, 1,873 Han Chinese ancestry controls
Replication sample15,979 East Asian ancestry cases, 19,360 East Asian ancestry controls, 794 Malay ancestry cases, 1,240 Malay ancestry controls, 159 Filipino ancestry cases, 1,624 Filipino ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneHNF1B
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-G
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency0.276
P value0.00000000002
Pvalue mlog10.698970004336
P value text
Or beta1.19
%95 Ci[1.13-1.25]
PlatformIllumina [2234194] (imputed)
CNVN
Mapped traittype II diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001360
Study accessionGCST001666
PubMed ID23945395
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23945395
StudyGenome-wide association study identifies three novel loci for type 2 diabetes.
Disease/TraitType 2 diabetes
Initial sample5,976 Japanese ancestry cases, 20,829 Japanese ancestry controls
Replication sample24,416 East Asian ancestry cases, 13,985 East Asian ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneHNF1B
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-G
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency0.37
P value0.000004
Pvalue mlog5.39794000867203
P value text
Or beta1.11
%95 Ci[1.06-1.16]
PlatformIllumina [6209637] (imputed)
CNVN
Mapped traittype II diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001360
Study accessionGCST002128
PubMed ID24509480
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24509480
StudyGenome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
Disease/TraitType 2 diabetes
Initial sample12,171 European ancestry cases, 56,862 European ancestry controls, 6,952 East Asian ancestry cases, 11,865 East Asian ancestry controls, 5,561 South Asian ancestry cases, 14,458 South Asian ancestry controls, 1,804 Mexican ancestry cases, 779 Mexican ance
Replication sample21,491 European ancestry cases, 55,647 European ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneHNF1B
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-G
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequency0.53
P value0.0000000009
Pvalue mlog9.04575749056067
P value text
Or beta1.13
%95 Ci[1.07-1.09]
PlatformAffymetrix, Illumina [2500000] (imputed)
CNVN
Mapped traittype II diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001360
Study accessionGCST002352
PubMed ID26443449
JournalNat Commun
Linkwww.ncbi.nlm.nih.gov/pubmed/26443449
StudyLarge-scale association analysis in Asians identifies new susceptibility loci for prostate cancer.
Disease/TraitProstate cancer
Initial sample3,000 East Asian ancestry cases, 4,394 East Asian ancestry controls
Replication sample3,605 East Asian ancestry cases, 3,919 East Asian ancestry controls
Region17q12
Chromosome idchr17
Chromosome position37738049
Reported geneHNF1B
Mapped geneHNF1B
Upstream gene id
Downstream gene id
SNP gene ids6928
Upstream gene distance
Downstream gene distance
SNP risk allelers4430796-A
SNPsrs4430796
Merged0
SNP id current4430796
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.00000006
Pvalue mlog7.22184874961635
P value text
Or beta1.2345679
%95 Ci[NR]
PlatformIllumina [4550396] (imputed)
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST003148
PubMed ID22219177
JournalCarcinogenesis
Linkwww.ncbi.nlm.nih.gov/pubmed/22219177
StudyA genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
Disease/TraitProstate cancer (gene x gene interaction)
Initial sample4,723 European ancestry cases, 4,792 European ancestry controls
Replication sampleNA
Region1p34.3 x 17q12
Chromosome idchr1 x 17
Chromosome position37731169 x 37738049
Reported geneEPHA10 x HNF1B
Mapped geneEPHA10 x HNF1B
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers731174-? x rs4430796-?
SNPsrs731174 x rs4430796
Merged0
SNP id current
Contextintron_variant x intron_variant
Intergenic
Allele frequencyNR
P value0.000005
Pvalue mlog5.30102999566398
P value text
Or beta1.27
%95 Ci[1.15-1.40]
PlatformAffymetrix, Illumina [1117531] (imputed)
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST001370
PubMed ID22219177
JournalCarcinogenesis
Linkwww.ncbi.nlm.nih.gov/pubmed/22219177
StudyA genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
Disease/TraitProstate cancer (gene x gene interaction)
Initial sample4,723 European ancestry cases, 4,792 European ancestry controls
Replication sampleNA
Region12q13.11 x 17q12
Chromosome idchr12 x 17
Chromosome position48417317 x 37738049
Reported geneANP32D x HNF1B
Mapped geneLOC105369754 - C12orf54 x HNF1B
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers4489787-? x rs4430796-?
SNPsrs4489787 x rs4430796
Merged0
SNP id current
Contextnon_coding_transcript_exon_variant x intron_variant
Intergenic
Allele frequencyNR
P value0.000001
Pvalue mlog6
P value text
Or beta1.47
%95 Ci[1.25-1.72]
PlatformAffymetrix, Illumina [1117531] (imputed)
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST001370