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rs909253

From SNPedia

Orientationminus
Stabilizedminus
Make rs909253(C;C)
Make rs909253(C;T)
Make rs909253(T;T)
ReferenceGRCh38 38.1/141
Chromosome6
Position31572536
GeneHLA-DQA1, LTA
is asnp
is mentioned by
dbSNPrs909253
ebirs909253
HLIrs909253
Exacrs909253
Varsomers909253
Maprs909253
PheGenIrs909253
hapmaprs909253
1000 genomesrs909253
hgdprs909253
ensemblrs909253
gopubmedrs909253
geneviewrs909253
scholarrs909253
googlers909253
pharmgkbrs909253
gwascentralrs909253
openSNPrs909253
23andMers909253
23andMe allrs909253
SNP Nexus

SNPshotrs909253
SNPdbers909253
MSV3drs909253
GWAS Ctlgrs909253
GMAF0.3985
Max Magnitude
? (C;C) (C;T) (T;T) 28
[PMID 19654554OA-icon.png] The Major Histocompatibility Complex Conserved Extended Haplotype 8.1 in AIDS-Related Non-Hodgkin Lymphoma


[PMID 19167443OA-icon.png] Family-based analysis of tumor necrosis factor and lymphotoxin-alpha tag polymorphisms with type 1 diabetes in the population of South Croatia

A US study [PMID 17018637] of 1,172 lymphoma patients and 982 controls looked at 57 SNPs in 36 immune function genes. Five SNPs in two cytokine genes, tumor necrosis factor-alpha and lymphotoxin-alpha, were associated with a 1.31x increase in non-Hodgkin lymphoma (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and with a 1.64x increase in the subtype known as diffuse large B cell lymphoma (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). The other four SNPS are listed below. The cytokine genes affect inflammatory and innate immune responses.



[PMID 20459604OA-icon.png] Large-scale association analysis of TNF/LTA gene region polymorphisms in type 2 diabetes


[PMID 22615793OA-icon.png] Investigation of Host Candidate Malaria-Associated Risk/Protective SNPs in a Brazilian Amazonian Population


[PMID 22294627] Association between genetic variants in the tumour necrosis factor/lymphotoxin α/lymphotoxin β locus and primary Sjogren's syndrome in Scandinavian samples


[PMID 15726497OA-icon.png] Gene-environment interaction effects on the development of immune responses in the 1st year of life.


[PMID 16449530OA-icon.png] Cytokine polymorphisms in the Th1/Th2 pathway and susceptibility to non-Hodgkin lymphoma.


[PMID 16839190OA-icon.png] Lymphotoxin-alpha gene and risk of myocardial infarction in 6,928 cases and 2,712 controls in the ISIS case-control study.


[PMID 17174749OA-icon.png] Linkage disequilibrium with predisposing DR3 haplotypes accounts for apparent effects of tumor necrosis factor and lymphotoxin-alpha polymorphisms on type 1 diabetes susceptibility.


[PMID 17216494] Genetic variation in tumor necrosis factor and lymphotoxin-alpha (TNF-LTA) and breast cancer risk.


[PMID 17327408OA-icon.png] Prognostic significance of host immune gene polymorphisms in follicular lymphoma survival.


[PMID 17450233OA-icon.png] Parental smoking modifies the relation between genetic variation in tumor necrosis factor-alpha (TNF) and childhood asthma.


[PMID 17517687] Association of variants in the BAT1-NFKBIL1-LTA genomic region with protection against myocardial infarction in Europeans.


[PMID 17701899OA-icon.png] Flexible design for following up positive findings.


[PMID 17705862OA-icon.png] Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples.


[PMID 18423522OA-icon.png] Estimating odds ratios in genome scans: an approximate conditional likelihood approach.


[PMID 18633131OA-icon.png] 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 18687755OA-icon.png] Genetic variants in T helper cell type 1, 2 and 3 pathways and gastric cancer risk in a Polish population.


[PMID 18704761OA-icon.png] Molecular genetics of myocardial infarction.


[PMID 18805939OA-icon.png] 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 18990758OA-icon.png] Genetic variation in tumor necrosis factor and the nuclear factor-kappaB canonical pathway and risk of non-Hodgkin's lymphoma.


[PMID 19066394OA-icon.png] Organochlorine exposure, immune gene variation, and risk of non-Hodgkin lymphoma.


[PMID 19131662OA-icon.png] A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients.


[PMID 19225544OA-icon.png] Variation in the lymphotoxin-alpha/tumor necrosis factor locus modifies risk of erythema nodosum in sarcoidosis.


[PMID 19263529OA-icon.png] Genetic risk factors in recurrent venous thromboembolism: A multilocus, population-based, prospective approach.


[PMID 19281305OA-icon.png] Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populations.


[PMID 19330901OA-icon.png] Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study.


[PMID 19356949OA-icon.png] Cytokine SNPs: Comparison of allele frequencies by race and implications for future studies.


[PMID 19409079OA-icon.png] Association of MICA with rheumatoid arthritis independent of known HLA-DRB1 risk alleles in a family-based and a case control study.


[PMID 19559392OA-icon.png] A candidate gene association study of 77 polymorphisms in migraine.


[PMID 19615068OA-icon.png] The role of TNF genetic variants and the interaction with cigarette smoking for gastric cancer risk: a nested case-control study.


[PMID 19700502] Synopsis and synthesis of candidate-gene association studies in chronic lymphocytic leukemia: the CUMAGAS-CLL information system.


[PMID 20031567OA-icon.png] An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of venous thromboembolism: The Women's Genome Health Study.


[PMID 20047977OA-icon.png] Tumor necrosis factor (TNF) and lymphotoxin-alpha (LTA) polymorphisms and risk of non-Hodgkin lymphoma in the InterLymph Consortium.


[PMID 20049212OA-icon.png] Traffic-related air pollution, oxidative stress genes, and asthma (ECHRS).


[PMID 20878356] Role of ethnic variations in TNF-alpha and TNF-beta polymorphisms and risk of breast cancer in India.


[PMID 23050158OA-icon.png] Lymphotoxin-Alpha Gene Polymorphism +252A/G (rs909253, A/G) Is Associated with Susceptibility to Chronic Periodontitis: A Pilot Study


GET Evidence
rs909253
aa_change
aa_change_short
impact pharmacogenetic
qualified_impact Insufficiently evaluated pharmacogenetic
overall_frequency 0.375
summary



[PMID 23086128] Profiles of gene polymorphisms in cytokines and Toll-like receptors with higher risk for gastric cancer


[PMID 22748850] A functional polymorphism of lymphotoxin-alpha (LTA) gene rs909253 is associated with gastric cancer risk in an Asian population.


[PMID 22749237OA-icon.png] Tumor necrosis factor -308 polymorphism (rs1800629) is associated with mortality and ventilator duration in 1057 Caucasian patients.


[PMID 22882567] The +252A/G polymorphism in the lymphotoxin-alpha gene increases the risk of asthma: a meta-analysis.


[PMID 23029430OA-icon.png] Prognostic role of host cyclooxygenase and cytokine genotypes in a Caucasian cohort of patients with gastric adenocarcinoma.


[PMID 23071570OA-icon.png] Gene-gene interaction and functional impact of polymorphisms on innate immune genes in controlling Plasmodium falciparum blood infection level.


[PMID 23159874] Pro-inflammatory cytokine gene polymorphisms and threat for coronary heart disease in a North Indian Agrawal population.


[PMID 23294973] Association of TNF-alpha polymorphism rs1800629 with multisomatoform disorder in a group of German patients and healthy controls: an explorative study.


[PMID 23360674] Genetic variation may modify ovarian reserve in female childhood cancer survivors.


[PMID 23391141] Influence of polymorphisms in genes encoding immunoregulatory proteins and metabolizing enzymes on susceptibility and outcome in patients with diffuse large B-cell lymphoma treated with rituximab.


[PMID 24959879OA-icon.png] Effects of Tumor Necrosis Factor-β (TNF-β) 252A>G Polymorphism on the Development of Migraine: A Meta-Analysis


[PMID 25063351] Tumor necrosis factor beta NcoI polymorphism (rs909253) is associated with inflammatory and metabolic markers in acute ischemic stroke


[PMID 25735143] [Combinations of cytokine gene network polymorphic markers as potential predictors of myocardial infarction]


ClinVar
Risk rs909253(C;C)
Alt rs909253(C;C)
Reference rs909253(T;T)
Significance Other
Disease Myocardial infarction Psoriatic arthritis
Variation info
Gene LTA
CLNDBN Myocardial infarction Psoriatic arthritis, susceptibility to
Reversed 1
HGVS NC_000006.11:g.31540313A>G
CLNSRC OMIM Allelic Variant
CLNACC RCV000015456.3, RCV000015457.3,



[PMID 26399644] Immune-Inflammatory and Oxidative and Nitrosative Stress Biomarkers of Depression Symptoms in Subjects with Multiple Sclerosis: Increased Peripheral Inflammation but Less Acute Neuroinflammation


[PMID 24896147] Role of TNF block genetic variants in HIV-associated sensory neuropathy in black Southern Africans


[PMID 26554163] Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 (rs3765524, rs10509670) Genes and Their Correlation to Gastric Cancer Risk Based on Universal Tagged Arrays and Fe3O4 Magnetic Nanoparticles