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SNP Detail For rs7524102
1.Mapping Information
| Human SNP ID | rs7524102 |
|---|---|
| Human chromosome | chr1 |
| Human SNP position | 22371954 |
| Pig chromosome | chr6 |
| Pig SNP position | 74371120 |
2.Annotation Information
| PubMed ID | 18445777 |
|---|---|
| Journal | N Engl J Med |
| Link | www.ncbi.nlm.nih.gov/pubmed/18445777 |
| Study | Multiple genetic loci for bone mineral density and fractures. |
| Disease/Trait | Bone mineral density (spine) |
| Initial sample | 5,861 European ancestry individuals |
| Replication sample | 7,925 European ancestry individuals |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | ZBTB40 |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-A |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.82 |
| P value | 0.000000009 |
| Pvalue mlog | 8.04575749056067 |
| P value text | |
| Or beta | 0.11 |
| %95 Ci | [0.07-0.15] s.d. decrease |
| Platform | Illumina [301019] |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST000180 |
| PubMed ID | 18445777 |
| Journal | N Engl J Med |
| Link | www.ncbi.nlm.nih.gov/pubmed/18445777 |
| Study | Multiple genetic loci for bone mineral density and fractures. |
| Disease/Trait | Bone mineral density (hip) |
| Initial sample | 5,861 European ancestry individuals |
| Replication sample | 7,925 European ancestry individuals |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | ZBTB40 |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-A |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.82 |
| P value | 0.0000000000000005 |
| Pvalue mlog | 15.3010299956639 |
| P value text | |
| Or beta | 0.15 |
| %95 Ci | [0.11-0.19] s.d. decrease |
| Platform | Illumina [301019] |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST000181 |
| PubMed ID | 19079262 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19079262 |
| Study | New sequence variants associated with bone mineral density. |
| Disease/Trait | Bone mineral density (hip) |
| Initial sample | 6,865 European ancestry individuals |
| Replication sample | 8,510 European ancestry individuals |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | intergenic |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-A |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.82 |
| P value | 0.0000000000000001 |
| Pvalue mlog | 16 |
| P value text | |
| Or beta | 0.15 |
| %95 Ci | [0.11-0.18] s.d. decrease |
| Platform | Illumina [305051] |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST000297 |
| PubMed ID | 19801982 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19801982 |
| Study | Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. |
| Disease/Trait | Bone mineral density (spine) |
| Initial sample | 19,195 European ancestry individuals |
| Replication sample | NA |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | ZBTB40 |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-G |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.17 |
| P value | 0.0000000003 |
| Pvalue mlog | 9.52287874528033 |
| P value text | |
| Or beta | 0.09 |
| %95 Ci | [0.06-0.12] s.d. increase |
| Platform | Affymetrix, Illumina [2543686] (imputed) |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST000494 |
| PubMed ID | 21297633 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21297633 |
| Study | Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. |
| Disease/Trait | Ulcerative colitis |
| Initial sample | 6,687 European ancestry cases, 19,718 European ancestry controls |
| Replication sample | 9,628 European ancestry cases, 12,917 European ancestry controls |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | intergenic |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-A |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.83 |
| P value | 0.0000000000002 |
| Pvalue mlog | 12.698970004336 |
| P value text | |
| Or beta | 1.1 |
| %95 Ci | [1.05-1.16] |
| Platform | Affymetrix, Illumina [~ 1100000] (imputed) |
| CNV | N |
| Mapped trait | ulcerative colitis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000729 |
| Study accession | GCST000964 |
| PubMed ID | 21533022 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21533022 |
| Study | Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk. |
| Disease/Trait | Bone mineral density |
| Initial sample | 900 European ancestry female individuals with low hip bone mineral density, 1,055 European ancestry female individuals with high hip bone mineral density |
| Replication sample | 20,898 European ancestry female individuals |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | ZBTB40 |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-G |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.0000009 |
| Pvalue mlog | 6.04575749056067 |
| P value text | (total hip) |
| Or beta | 0.44 |
| %95 Ci | [NR] unit decrease |
| Platform | Illumina [2543887] (imputed) |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST001050 |
| PubMed ID | 21533022 |
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/21533022 |
| Study | Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk. |
| Disease/Trait | Bone mineral density |
| Initial sample | 900 European ancestry female individuals with low hip bone mineral density, 1,055 European ancestry female individuals with high hip bone mineral density |
| Replication sample | 20,898 European ancestry female individuals |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | ZBTB40 |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-G |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.000001 |
| Pvalue mlog | 6 |
| P value text | (femoral neck) |
| Or beta | 0.14 |
| %95 Ci | [NR] unit decrease |
| Platform | Illumina [2543887] (imputed) |
| CNV | N |
| Mapped trait | bone density |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003923 |
| Study accession | GCST001050 |
| PubMed ID | 19915572 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19915572 |
| Study | Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. |
| Disease/Trait | Ulcerative colitis |
| Initial sample | 2,361 European ancestry cases, 5,417 European ancestry controls |
| Replication sample | 2,321 European ancestry cases, 4,818 European ancestry controls |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | intergenic |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-A |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.83 |
| P value | 0.0000003 |
| Pvalue mlog | 6.52287874528033 |
| P value text | |
| Or beta | 1.1 |
| %95 Ci | [1.00-1.21] |
| Platform | Affymetrix [NR] |
| CNV | N |
| Mapped trait | ulcerative colitis |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0000729 |
| Study accession | GCST000527 |
| PubMed ID | 21732829 |
| Journal | N Engl J Med |
| Link | www.ncbi.nlm.nih.gov/pubmed/21732829 |
| Study | Wnt signaling and Dupuytren__s disease. |
| Disease/Trait | Dupuytren__s disease |
| Initial sample | 856 European ancestry cases, 2,836 European ancestry controls |
| Replication sample | 1,298 European ancestry cases, 7,136 European ancestry controls |
| Region | 1p36.12 |
| Chromosome id | chr1 |
| Chromosome position | 22371954 |
| Reported gene | RP11-415K20.1, WNT4 |
| Mapped gene | LOC101060363 - LOC105376856 |
| Upstream gene id | 101060363 |
| Downstream gene id | 105376856 |
| SNP gene ids | |
| Upstream gene distance | 48623 |
| Downstream gene distance | 44377 |
| SNP risk allele | rs7524102-G |
| SNPs | rs7524102 |
| Merged | 0 |
| SNP id current | 7524102 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.21 |
| P value | 0.000000003 |
| Pvalue mlog | 8.52287874528033 |
| P value text | |
| Or beta | 1.28 |
| %95 Ci | [1.17-1.41] |
| Platform | Illumina [234939] |
| CNV | N |
| Mapped trait | Dupuytren Contracture |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004229 |
| Study accession | GCST001144 |
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and Xi'an University of Technology ©2014-2017 All Rights Reserved.
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