rs1799724
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 0 | normal risk |
| (C;T) | 2 | if ApoE4(-), 1.6x risk of AD; if (+), 6.6x risk |
| (T;T) | 2 | if ApoE4(-), 1.6x risk of AD; if (+), 6.6x risk |
| Reference | GRCh38 38.1/141 |
| Chromosome | 6 |
| Position | 31574705 |
| Gene | LOC100287329, LTA, TNF |
| is a | snp |
| is | mentioned by |
| dbSNP | rs1799724 |
| dbSNP (classic) | rs1799724 |
| ClinGen | rs1799724 |
| ebi | rs1799724 |
| HLI | rs1799724 |
| Exac | rs1799724 |
| Gnomad | rs1799724 |
| Varsome | rs1799724 |
| LitVar | rs1799724 |
| Map | rs1799724 |
| PheGenI | rs1799724 |
| Biobank | rs1799724 |
| 1000 genomes | rs1799724 |
| hgdp | rs1799724 |
| ensembl | rs1799724 |
| geneview | rs1799724 |
| scholar | rs1799724 |
| rs1799724 | |
| pharmgkb | rs1799724 |
| gwascentral | rs1799724 |
| openSNP | rs1799724 |
| 23andMe | rs1799724 |
| SNPshot | rs1799724 |
| SNPdbe | rs1799724 |
| MSV3d | rs1799724 |
| GWAS Ctlg | rs1799724 |
| GMAF | 0.09734 |
| Max Magnitude | 2 |
rs1799724, a SNP near the tumor necrosis factor TNF gene, was found in a study of ~500 Caucasians to be both an independent risk factor for the development of Alzheimer's disease and also a modifier of the risk for individuals carrying ApoE4 alleles. [PMID 15895461]
On its own, the rs1799724(T) allele led to an odds ratio of 1.63 (CI: 1.13-2.34, p=0.009). In carriers of ApoE4 alleles, the odds ratio changed from 2.92 (CI: 2.00-4.27) in the absence of rs1799724(T) to an OR of 6.65 (CI: 3.26-13.55, p=0.03) in its presence. [PMID 15895461] Note, however, that this study is from 2005 and it does not appear to have been independently replicated since then (which is why the magnitude is 2, i.e. pretty low on the 0-10 magnitude scale).
In a Chinese study [PMID 18551993], post-menopausal women were significantly more likely to have low bone mineral density if they had
- CC-AA genotypes in rs1799724-rs1800629
- a haplotype of rs1799724-rs1800629-rs6254-rs6256-IL-1ra-rs2227956-rs1801197
[PMID 19282863] Association of candidate gene polymorphisms with chronic kidney disease in Japanese individuals with hypertension
news cigarette smoking and gastric cancer risk
[PMID 20357201] Association of Polymorphisms of Tumor Necrosis Factor and Tumor Protein p53 with Primary Open Angle Glaucoma: A Replication Study of Ten Genes in A Chinese Population
[PMID 21228795] Impact of LIMK1, MMP2 and TNF-? variations for intracranial aneurysm in Japanese population
| ? | (C;C) (C;T) (T;T) | |
|---|---|---|
|
| ||
[PMID 21904873] Association of tumor necrosis factor-? (TNF-?) promoter polymorphisms with overweight/obesity in a Korean population
[PMID 21509504
] Interleukin-1α, interleukin-1β and tumor necrosis factor-α genetic variants and risk of dementia in the very old: evidence from the "Monzino 80-plus" prospective study
[PMID 12509789] Identification of I kappa BL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis.
[PMID 16449530] Cytokine polymorphisms in the Th1/Th2 pathway and susceptibility to non-Hodgkin lymphoma.
[PMID 16916584] Interleukin-1 alpha and beta, TNF-alpha and HTTLPR gene variants study on alcohol toxicity and detoxification outcome.
[PMID 17018637] Common genetic variants in proinflammatory and other immunoregulatory genes and risk for non-Hodgkin lymphoma.
[PMID 17062130] Polymorphisms within inflammatory genes and colorectal cancer.
[PMID 17327408] Prognostic significance of host immune gene polymorphisms in follicular lymphoma survival.
[PMID 17355643] Frequencies of single nucleotide polymorphisms in genes regulating inflammatory responses in a community-based population.
[PMID 17493155] Significant association between TNF-alpha (TNF) promoter allele (-1031C, -863C, and -857C) and cerebral malaria in Thailand.
[PMID 18196539] TNF polymorphisms and prostate cancer risk.
[PMID 18319718] Tumour-necrosis factor-A polymorphisms and gastric cancer risk: a meta-analysis.
[PMID 18366708] SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.
[PMID 18603647] Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response.
[PMID 18633131] Host immune gene polymorphisms in combination with clinical and demographic factors predict late survival in diffuse large B-cell lymphoma patients in the pre-rituximab era.
[PMID 18635873] TNF promoter polymorphisms associated with muscle phenotypes in humans.
[PMID 18676870] Variants in inflammation genes and the risk of biliary tract cancers and stones: a population-based study in China.
[PMID 18698679] Single nucleotide polymorphism in the tumor necrosis factor-alpha gene affects inflammatory bowel diseases risk.
[PMID 18709160] Interactions between glutathione S-transferase P1, tumor necrosis factor, and traffic-related air pollution for development of childhood allergic disease.
[PMID 18805939] Functional genetic polymorphisms and female reproductive disorders: part II--endometriosis.
[PMID 18811622] Association of TNF-alpha with severe respiratory syncytial virus infection and bronchial asthma.
[PMID 18990758] Genetic variation in tumor necrosis factor and the nuclear factor-kappaB canonical pathway and risk of non-Hodgkin's lymphoma.
[PMID 19066394] Organochlorine exposure, immune gene variation, and risk of non-Hodgkin lymphoma.
[PMID 19406964] Association of genetic variants with chronic kidney disease in Japanese individuals.
[PMID 19505919] Toll-like receptor signaling pathway variants and prostate cancer mortality.
[PMID 19615068] The role of TNF genetic variants and the interaction with cigarette smoking for gastric cancer risk: a nested case-control study.
[PMID 19673019] IL-10 and TNF-alpha promoter haplotypes are associated with childhood Crohn's disease location.
[PMID 19673882] A novel association between a SNP in CYBRD1 and serum ferritin levels in a cohort study of HFE hereditary haemochromatosis.
[PMID 19742166] Epistasis between IL1A, IL1B, TNF, HTR2A, 5-HTTLPR and TPH2 variations does not impact alcohol dependence disorder features.
[PMID 19818126] Single nucleotide polymorphisms in obesity-related genes and all-cause and cause-specific mortality: a prospective cohort study.
[PMID 20668555] Extended LTA, TNF, LST1 and HLA gene haplotypes and their association with rubella vaccine-induced immunity.
[PMID 20811626] Genetic variants in inflammation-related genes are associated with radiation-induced toxicity following treatment for non-small cell lung cancer.
[PMID 20952689] Cytokine polymorphisms in Th1/Th2 pathway genes, body mass index, and risk of non-Hodgkin lymphoma.
[PMID 21385363] Polymorphisms in genes controlling inflammation and tissue repair in rheumatoid arthritis: a case control study.
[PMID 22630053] Immune regulatory gene polymorphisms as predisposing risk factors for the development of factor VIII inhibitors in Indian severe haemophilia A patients.
[PMID 23086128] Profiles of gene polymorphisms in cytokines and Toll-like receptors with higher risk for gastric cancer
[PMID 23734748] Association of genes of protease-antiprotease balance pathway to lung function and emphysema subtypes
[PMID 23870134] Association of tumor necrosis factor-alpha promoter variants with risk of HPV-associated oral squamous cell carcinoma
[PMID 24003533] Relationship between cytokine single nucleotide polymorphisms and sarcoidosis among Japanese subjects
[PMID 24151497] Association Analysis of IL10, TNF-α, and IL23R-IL12RB2 SNPs with Behçet's Disease Risk in Western Algeria
[PMID 24259423] Genetic variation in the lymphotoxin-α (LTA)/tumour necrosis factor-α (TNFα) locus as a risk factor for idiopathic achalasia
[PMID 24405540] [Association of TNF-1031T/C and clinical efficacy of insulin therapy in newly diagnosed type 2 diabetics]
[PMID 22711844] SNPs in the TNF-alpha gene promoter associated with Behcet's disease in Moroccan patients.
[PMID 23021043] Genetics of Behcet's disease in Sardinia: two distinct extended HLA haplotypes harbour the B*51 allele in the normal population and in patients.
[PMID 23071570] Gene-gene interaction and functional impact of polymorphisms on innate immune genes in controlling Plasmodium falciparum blood infection level.
[PMID 24935328] Functional tumor necrosis factor alpha polymorphisms and haplotype analysis in high-risk corneal transplantation
[PMID 25083576] Tumor Necrosis Factor-Alpha and Polycystic Ovarian Syndrome: A Clinical, Biochemical, and Molecular Genetic Study
[PMID 25246119] Family association study between tumour necrosis factor a gene polymorphisms and polycystic ovary syndrome in Han Chinese
[PMID 25634985] The -308G>A Polymorphism of the TNF Gene is Associated with Proliferative Diabetic Retinopathy in Caucasian-Brazilians with Type 2 Diabetes
[PMID 25636570] Association of TNF -1031 C/C as a potential protection marker for leprosy development in Amazonas state patients, Brazil
[PMID 26191295] CXCL12 rs266085 and TNF-α rs1799724 polymorphisms and susceptibility to cervical cancer in a Chinese population
[PMID 26550110] The role of gene variants of the inflammatory markers CRP and TNF-α in cardiovascular heart disease: systematic review and meta-analysis
[PMID 27126784] Lack of tumor necrosis factor alpha gene polymorphism -857c/t (rs1799724) association in Pakistani rheumatoid arthritis patients.
[PMID 28633686] Polymorphisms of the TNF-α gene interact with plasma fatty acids on inflammatory biomarker profile: a population-based, cross-sectional study in São Paulo, Brazil.
| ClinVar | |
|---|---|
| Risk | Rs1799724(T;T) |
| Alt | Rs1799724(T;T) |
| Reference | Rs1799724(C;C) |
| Significance | Other |
| Disease | Vascular dementia Alzheimer disease |
| Variation | info |
| Gene | LTA TNF |
| CLNDBN | Vascular dementia, susceptibility to Alzheimer disease, susceptibility to |
| Reversed | 0 |
| HGVS | NC_000006.11:g.31542482C>T |
| CLNSRC | OMIM Allelic Variant |
| CLNACC | RCV000013196.3, RCV000013197.3, |
[PMID 29028942] Association of high-evidence gastric cancer susceptibility loci and somatic gene expression levels with survival.
[PMID 29027627] Association of TNF-α-3959T/C Gene Polymorphisms in the Chinese Population with Intracranial Aneurysms.
[PMID 30310056] Effects of tumor necrosis factor-α polymorphism on the brain structural changes of the patients with major depressive disorder.
[PMID 31618972] Polymorphisms of Proinflammatory Cytokines in Relation to APOE Epsilon 4 and Risk of Alzheimer's Disease in the Lithuanian Population.
[PMID 32050144] Identification of TNFA influencing MDD risk and clinical features in Han Chinese.
[PMID 32328064] Autoimmunity-Related Risk Variants in PTPN22 and CTLA4 Are Associated With ME/CFS With Infectious Onset.
