Human SNP ID | rs4430796 |
---|---|
Human chromosome | chr17 |
Human SNP position | 37738049 |
Pig chromosome | chr12 |
Pig SNP position | 40839984 |
PubMed ID | 17603485 |
---|---|
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/17603485 |
Study | Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. |
Disease/Trait | Prostate cancer |
Initial sample | 1,501 European ancestry cases, 11,290 European ancestry controls |
Replication sample | 1,992 European ancestry cases, 3,058 European ancestry controls |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | TCF2 |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-A |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.49 |
P value | 0.00000000001 |
Pvalue mlog | 11 |
P value text | |
Or beta | 1.22 |
%95 Ci | [1.15-1.30] |
Platform | Illumina [310520] |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST000050 |
PubMed ID | 18264096 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/18264096 |
Study | Multiple loci identified in a genome-wide association study of prostate cancer. |
Disease/Trait | Prostate cancer |
Initial sample | 1,172 European ancestry cases, 1,157 European ancestry controls |
Replication sample | 3,941 European ancestry cases, 3,964 European ancestry controls |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | HNF1B |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-A |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.54 |
P value | 0.000000001 |
Pvalue mlog | 9 |
P value text | |
Or beta | 1.18 |
%95 Ci | [1.04-1.32] |
Platform | Illumina [527869] |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST000154 |
PubMed ID | 19767754 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/19767754 |
Study | Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. |
Disease/Trait | Prostate cancer |
Initial sample | Up to 1,968 European ancestry cases, 35,382 European ancestry controls |
Replication sample | Up to 11,806 European ancestry cases, 12,387 European ancestry controls |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | intergenic |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-A |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.52 |
P value | 0.000008 |
Pvalue mlog | 5.09691001300805 |
P value text | |
Or beta | 1.19 |
%95 Ci | [1.10-1.28] |
Platform | Illumina [310520] |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST000489 |
PubMed ID | 20581827 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/20581827 |
Study | Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. |
Disease/Trait | Type 2 diabetes |
Initial sample | 8,130 European ancestry cases, 38,987 European ancestry controls |
Replication sample | Up to 34,412 European ancestry cases, 59,925 European ancestry controls |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | HNF1B, TCF2 |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-G |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | |
P value | 0.000002 |
Pvalue mlog | 5.69897000433601 |
P value text | |
Or beta | 1.14 |
%95 Ci | [1.08-1.20] |
Platform | Affymetrix, Illumina [2426886] (imputed) |
CNV | N |
Mapped trait | type II diabetes mellitus |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001360 |
Study accession | GCST000712 |
PubMed ID | 21160077 |
Journal | Sci Transl Med |
Link | www.ncbi.nlm.nih.gov/pubmed/21160077 |
Study | Genetic correction of PSA values using sequence variants associated with PSA levels. |
Disease/Trait | Serum prostate-specific antigen levels |
Initial sample | 7,538 European ancestry individuals |
Replication sample | 2,373 European ancestry individuals |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | HNF1B |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-A |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.52 |
P value | 0.00000000006 |
Pvalue mlog | 10.2218487496163 |
P value text | |
Or beta | 9.4 |
%95 Ci | [NR] % increase |
Platform | Illumina [304070] |
CNV | N |
Mapped trait | prostate specific antigen measurement |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004624 |
Study accession | GCST000919 |
PubMed ID | 21499250 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/21499250 |
Study | Genome-wide association study identifies a common variant associated with risk of endometrial cancer. |
Disease/Trait | Endometrial cancer |
Initial sample | 1,265 European ancestry cases, 5,190 European ancestry controls |
Replication sample | 3,957 European ancestry cases, 6,886 European ancestry controls |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | HNF1B |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-A |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.52 |
P value | 0.0000000007 |
Pvalue mlog | 9.15490195998574 |
P value text | |
Or beta | 1.19 |
%95 Ci | [1.12-1.27] |
Platform | Illumina [519655] |
CNV | N |
Mapped trait | endometrial neoplasm |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004230 |
Study accession | GCST001040 |
PubMed ID | 22961080 |
Journal | Diabetes |
Link | www.ncbi.nlm.nih.gov/pubmed/22961080 |
Study | A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans. |
Disease/Trait | Type 2 diabetes |
Initial sample | 1,839 Han Chinese ancestry cases, 1,873 Han Chinese ancestry controls |
Replication sample | 15,979 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 |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | HNF1B |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-G |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.276 |
P value | 0.00000000002 |
Pvalue mlog | 10.698970004336 |
P value text | |
Or beta | 1.19 |
%95 Ci | [1.13-1.25] |
Platform | Illumina [2234194] (imputed) |
CNV | N |
Mapped trait | type II diabetes mellitus |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001360 |
Study accession | GCST001666 |
PubMed ID | 23945395 |
Journal | Hum Mol Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/23945395 |
Study | Genome-wide association study identifies three novel loci for type 2 diabetes. |
Disease/Trait | Type 2 diabetes |
Initial sample | 5,976 Japanese ancestry cases, 20,829 Japanese ancestry controls |
Replication sample | 24,416 East Asian ancestry cases, 13,985 East Asian ancestry controls |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | HNF1B |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-G |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.37 |
P value | 0.000004 |
Pvalue mlog | 5.39794000867203 |
P value text | |
Or beta | 1.11 |
%95 Ci | [1.06-1.16] |
Platform | Illumina [6209637] (imputed) |
CNV | N |
Mapped trait | type II diabetes mellitus |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001360 |
Study accession | GCST002128 |
PubMed ID | 24509480 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/24509480 |
Study | Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. |
Disease/Trait | Type 2 diabetes |
Initial sample | 12,171 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 sample | 21,491 European ancestry cases, 55,647 European ancestry controls |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | HNF1B |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-G |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | 0.53 |
P value | 0.0000000009 |
Pvalue mlog | 9.04575749056067 |
P value text | |
Or beta | 1.13 |
%95 Ci | [1.07-1.09] |
Platform | Affymetrix, Illumina [2500000] (imputed) |
CNV | N |
Mapped trait | type II diabetes mellitus |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001360 |
Study accession | GCST002352 |
PubMed ID | 26443449 |
Journal | Nat Commun |
Link | www.ncbi.nlm.nih.gov/pubmed/26443449 |
Study | Large-scale association analysis in Asians identifies new susceptibility loci for prostate cancer. |
Disease/Trait | Prostate cancer |
Initial sample | 3,000 East Asian ancestry cases, 4,394 East Asian ancestry controls |
Replication sample | 3,605 East Asian ancestry cases, 3,919 East Asian ancestry controls |
Region | 17q12 |
Chromosome id | chr17 |
Chromosome position | 37738049 |
Reported gene | HNF1B |
Mapped gene | HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | 6928 |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4430796-A |
SNPs | rs4430796 |
Merged | 0 |
SNP id current | 4430796 |
Context | intron_variant |
Intergenic | 0 |
Allele frequency | NR |
P value | 0.00000006 |
Pvalue mlog | 7.22184874961635 |
P value text | |
Or beta | 1.2345679 |
%95 Ci | [NR] |
Platform | Illumina [4550396] (imputed) |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST003148 |
PubMed ID | 22219177 |
Journal | Carcinogenesis |
Link | www.ncbi.nlm.nih.gov/pubmed/22219177 |
Study | A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. |
Disease/Trait | Prostate cancer (gene x gene interaction) |
Initial sample | 4,723 European ancestry cases, 4,792 European ancestry controls |
Replication sample | NA |
Region | 1p34.3 x 17q12 |
Chromosome id | chr1 x 17 |
Chromosome position | 37731169 x 37738049 |
Reported gene | EPHA10 x HNF1B |
Mapped gene | EPHA10 x HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs731174-? x rs4430796-? |
SNPs | rs731174 x rs4430796 |
Merged | 0 |
SNP id current | |
Context | intron_variant x intron_variant |
Intergenic | |
Allele frequency | NR |
P value | 0.000005 |
Pvalue mlog | 5.30102999566398 |
P value text | |
Or beta | 1.27 |
%95 Ci | [1.15-1.40] |
Platform | Affymetrix, Illumina [1117531] (imputed) |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST001370 |
PubMed ID | 22219177 |
Journal | Carcinogenesis |
Link | www.ncbi.nlm.nih.gov/pubmed/22219177 |
Study | A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. |
Disease/Trait | Prostate cancer (gene x gene interaction) |
Initial sample | 4,723 European ancestry cases, 4,792 European ancestry controls |
Replication sample | NA |
Region | 12q13.11 x 17q12 |
Chromosome id | chr12 x 17 |
Chromosome position | 48417317 x 37738049 |
Reported gene | ANP32D x HNF1B |
Mapped gene | LOC105369754 - C12orf54 x HNF1B |
Upstream gene id | |
Downstream gene id | |
SNP gene ids | |
Upstream gene distance | |
Downstream gene distance | |
SNP risk allele | rs4489787-? x rs4430796-? |
SNPs | rs4489787 x rs4430796 |
Merged | 0 |
SNP id current | |
Context | non_coding_transcript_exon_variant x intron_variant |
Intergenic | |
Allele frequency | NR |
P value | 0.000001 |
Pvalue mlog | 6 |
P value text | |
Or beta | 1.47 |
%95 Ci | [1.25-1.72] |
Platform | Affymetrix, Illumina [1117531] (imputed) |
CNV | N |
Mapped trait | prostate carcinoma |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001663 |
Study accession | GCST001370 |