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SNP Detail For rs7138803
1.Mapping Information
| Human SNP ID | rs7138803 |
|---|---|
| Human chromosome | chr12 |
| Human SNP position | 49853685 |
| Pig chromosome | chr5 |
| Pig SNP position | 16185920 |
2.Annotation Information
| PubMed ID | 19557197 |
|---|---|
| Journal | PLoS Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19557197 |
| Study | NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. |
| Disease/Trait | Waist circumference |
| Initial sample | 31,373 European ancestry individuals |
| Replication sample | 38,641 individuals |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | BCDIN3D, FAIM2 |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-? |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.0000008 |
| Pvalue mlog | 6.09691001300805 |
| P value text | |
| Or beta | |
| %95 Ci | |
| Platform | Affymetrix, Illumina [up to 512349] |
| CNV | N |
| Mapped trait | waist circumference |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004342 |
| Study accession | GCST000427 |
| PubMed ID | 20935630 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/20935630 |
| Study | Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. |
| Disease/Trait | Body mass index |
| Initial sample | Up to 123,865 European ancestry individuals |
| Replication sample | Up to 125,931 European ancestry individuals |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | FAIM2 |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.38 |
| P value | 0.00000000000000002 |
| Pvalue mlog | 16.698970004336 |
| P value text | |
| Or beta | 0.12 |
| %95 Ci | [0.08-0.16] kg/m2 increase |
| Platform | Affymetrix, Illumina, Perlegen [~ 2800000] (imputed) |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST000830 |
| PubMed ID | 23563607 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23563607 |
| Study | Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. |
| Disease/Trait | Obesity |
| Initial sample | 93,015 European ancestry overweight individuals, 32,858 European ancestry class I obese individuals, 9,889 European ancestry class II obese individuals, 2,896 European ancestry class III obese individuals, up to 65,840 European ancestry controls |
| Replication sample | 65,332 European ancestry overweight individuals, 22,373 European ancestry class I obese individuals, 5,476 European ancestry class II obese individuals, 1,162 European ancestry class III obese individuals, up to 39,294 European ancestry controls |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | LOC144233 |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.38 |
| P value | 1E-20 |
| Pvalue mlog | 20 |
| P value text | (Obesity class I) |
| Or beta | 1.09 |
| %95 Ci | [NR] |
| Platform | Affymetrix, Illumina [~ 2800000] (imputed) |
| CNV | N |
| Mapped trait | obesity |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001073 |
| Study accession | GCST001953 |
| PubMed ID | 23563607 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23563607 |
| Study | Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. |
| Disease/Trait | Obesity |
| Initial sample | 93,015 European ancestry overweight individuals, 32,858 European ancestry class I obese individuals, 9,889 European ancestry class II obese individuals, 2,896 European ancestry class III obese individuals, up to 65,840 European ancestry controls |
| Replication sample | 65,332 European ancestry overweight individuals, 22,373 European ancestry class I obese individuals, 5,476 European ancestry class II obese individuals, 1,162 European ancestry class III obese individuals, up to 39,294 European ancestry controls |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | LOC144233 |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.38 |
| P value | 0.0000000000000001 |
| Pvalue mlog | 16 |
| P value text | (Obesity class II) |
| Or beta | 1.14 |
| %95 Ci | [NR] |
| Platform | Affymetrix, Illumina [~ 2800000] (imputed) |
| CNV | N |
| Mapped trait | obesity |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0001073 |
| Study accession | GCST001953 |
| PubMed ID | 23563607 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/23563607 |
| Study | Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. |
| Disease/Trait | Body mass index |
| Initial sample | 7,962 European ancestry high body mass index individuals, 8,106 European ancestry low body mass index individuals |
| Replication sample | 4,900 European ancestry high body mass index individuals, 4,891 European ancestry low body mass index individuals |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | LOC144233 |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.38 |
| P value | 0.000000002 |
| Pvalue mlog | 8.69897000433601 |
| P value text | |
| Or beta | 1.13 |
| %95 Ci | [NR] |
| Platform | Affymetrix, Illumina [~ 2800000] (imputed) |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST001955 |
| PubMed ID | 25231870 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/25231870 |
| Study | Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. |
| Disease/Trait | Menarche (age at onset) |
| Initial sample | Up to 182,413 European ancestry females |
| Replication sample | NA |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | BCDIN3D |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-G |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.62 |
| P value | 0.000000000002 |
| Pvalue mlog | 11.698970004336 |
| P value text | |
| Or beta | 0.04 |
| %95 Ci | [0.03-0.05] unit increase |
| Platform | Affymetrix, Illumina [2441815] (imputed) |
| CNV | N |
| Mapped trait | age at menarche |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004703 |
| Study accession | GCST002541 |
| PubMed ID | 19079260 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19079260 |
| Study | Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. |
| Disease/Trait | Weight |
| Initial sample | 72,598 European ancestry individuals, 1,160 African American individuals |
| Replication sample | Up to 11,036 European ancestry individuals, 32,615 individuals |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | BCDIN3D, FAIM2 |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.37 |
| P value | 0.0000002 |
| Pvalue mlog | 6.69897000433601 |
| P value text | |
| Or beta | 3.27 |
| %95 Ci | [2.05-4.49] percentage SD increase |
| Platform | Illumina [305846] |
| CNV | N |
| Mapped trait | body weight |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004338 |
| Study accession | GCST000299 |
| PubMed ID | 19079260 |
| Journal | Nat Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/19079260 |
| Study | Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. |
| Disease/Trait | Body mass index |
| Initial sample | 72,598 European ancestry individuals, 1,160 African American individuals |
| Replication sample | Up to 11,036 European ancestry individuals, 32,615 individuals |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | BCDIN3D, FAIM2 |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.37 |
| P value | 0.0000001 |
| Pvalue mlog | 7 |
| P value text | |
| Or beta | 3.28 |
| %95 Ci | [2.06-4.50] % SD increase |
| Platform | Illumina [305846] |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST000296 |
| PubMed ID | 25673413 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/25673413 |
| Study | Genetic studies of body mass index yield new insights for obesity biology. |
| Disease/Trait | Body mass index |
| Initial sample | up to 104,666 European ancestry male individuals, up to 132,115 European ancestry female individuals, 370 African American male individuals, 517 African American female individuals, 512 Hispanic male individuals, 764 Hispanic female individuals |
| Replication sample | up to 48,274 European ancestry male individuals, up to 39,864 European ancestry female individuals, 2,441 African American or Afro-Caribbean male individuals, 6,314 African American or Afro-Caribbean female individuals, 919 Filipino male individuals, 828 |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | BCDIN3D |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.385 |
| P value | 0.00000000006 |
| Pvalue mlog | 10.2218487496163 |
| P value text | (EA, men) |
| Or beta | 0.027 |
| %95 Ci | [0.019-0.036] kg/m2 increase |
| Platform | Affymetrix, Illumina [2550021] |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST002783 |
| PubMed ID | 25673413 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/25673413 |
| Study | Genetic studies of body mass index yield new insights for obesity biology. |
| Disease/Trait | Body mass index |
| Initial sample | up to 104,666 European ancestry male individuals, up to 132,115 European ancestry female individuals, 370 African American male individuals, 517 African American female individuals, 512 Hispanic male individuals, 764 Hispanic female individuals |
| Replication sample | up to 48,274 European ancestry male individuals, up to 39,864 European ancestry female individuals, 2,441 African American or Afro-Caribbean male individuals, 6,314 African American or Afro-Caribbean female individuals, 919 Filipino male individuals, 828 |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | BCDIN3D |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.384 |
| P value | 0.00000000000000002 |
| Pvalue mlog | 16.698970004336 |
| P value text | (EA, women) |
| Or beta | 0.035 |
| %95 Ci | [0.027-0.043] kg/m2 increase |
| Platform | Affymetrix, Illumina [2550021] |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST002783 |
| PubMed ID | 25673413 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/25673413 |
| Study | Genetic studies of body mass index yield new insights for obesity biology. |
| Disease/Trait | Body mass index |
| Initial sample | up to 104,666 European ancestry male individuals, up to 132,115 European ancestry female individuals, 370 African American male individuals, 517 African American female individuals, 512 Hispanic male individuals, 764 Hispanic female individuals |
| Replication sample | up to 48,274 European ancestry male individuals, up to 39,864 European ancestry female individuals, 2,441 African American or Afro-Caribbean male individuals, 6,314 African American or Afro-Caribbean female individuals, 919 Filipino male individuals, 828 |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | BCDIN3D |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.384 |
| P value | 8E-24 |
| Pvalue mlog | 23.096910013008 |
| P value text | (EA) |
| Or beta | 0.032 |
| %95 Ci | [0.025-0.038] kg/m2 increase |
| Platform | Affymetrix, Illumina [2550021] |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST002783 |
| PubMed ID | 25673413 |
| Journal | Nature |
| Link | www.ncbi.nlm.nih.gov/pubmed/25673413 |
| Study | Genetic studies of body mass index yield new insights for obesity biology. |
| Disease/Trait | Body mass index |
| Initial sample | up to 104,666 European ancestry male individuals, up to 132,115 European ancestry female individuals, 370 African American male individuals, 517 African American female individuals, 512 Hispanic male individuals, 764 Hispanic female individuals |
| Replication sample | up to 48,274 European ancestry male individuals, up to 39,864 European ancestry female individuals, 2,441 African American or Afro-Caribbean male individuals, 6,314 African American or Afro-Caribbean female individuals, 919 Filipino male individuals, 828 |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | BCDIN3D |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | 0.379 |
| P value | 5E-26 |
| Pvalue mlog | 25.3010299956639 |
| P value text | |
| Or beta | 0.032 |
| %95 Ci | [0.026-0.038] kg/m2 increase |
| Platform | Affymetrix, Illumina [2550021] |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST002783 |
| PubMed ID | 26604143 |
| Journal | Hum Mol Genet |
| Link | www.ncbi.nlm.nih.gov/pubmed/26604143 |
| Study | Genome-wide association analysis identifies three new susceptibility loci for childhood body mass index. |
| Disease/Trait | Childhood body mass index |
| Initial sample | 34,744 European ancestry children |
| Replication sample | 11,313 European ancestry children |
| Region | 12q13.12 |
| Chromosome id | chr12 |
| Chromosome position | 49853685 |
| Reported gene | NR |
| Mapped gene | BCDIN3D - RPL35AP28 |
| Upstream gene id | 144233 |
| Downstream gene id | 100271637 |
| SNP gene ids | |
| Upstream gene distance | 10556 |
| Downstream gene distance | 9421 |
| SNP risk allele | rs7138803-A |
| SNPs | rs7138803 |
| Merged | 0 |
| SNP id current | 7138803 |
| Context | intergenic_variant |
| Intergenic | 1 |
| Allele frequency | NR |
| P value | 0.000000000000000005 |
| Pvalue mlog | 17.3010299956639 |
| P value text | |
| Or beta | |
| %95 Ci | |
| Platform | Affymetrix, Illumina [2499691] (imputed) |
| CNV | N |
| Mapped trait | body mass index |
| Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004340 |
| Study accession | GCST003177 |
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