{{Rsnum
|rsid=909253
|Gene=LTA
|Chromosome=6
|position=31572536
|Orientation=minus
|GMAF=0.3985
|Gene_s=HLA-DQA1,LTA
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(C;C)
|geno2=(C;T)
|geno3=(T;T)
}}{{ population diversity
| geno1=(C;C)
| geno2=(C;T)
| geno3=(T;T)
| CEU | 7.7 | 55.4 | 36.9
| HCB | 17.8 | 51.1 | 31.1
| JPT | 18.2 | 50.0 | 31.8
| YRI | 27.1 | 44.1 | 28.8
| ASW | 0.0 | 0.0 | 0.0
| CHB | 17.8 | 51.1 | 31.1
| CHD | 0.0 | 0.0 | 0.0
| GIH | 0.0 | 0.0 | 0.0
| LWK | 0.0 | 0.0 | 0.0
| MEX | 0.0 | 0.0 | 0.0
| MKK | 0.0 | 0.0 | 0.0
| TSI | 0.0 | 0.0 | 0.0
| HapMapRevision=28
}}
{{PMID Auto
|PMID=19654554
|Title=The Major Histocompatibility Complex Conserved Extended Haplotype 8.1 in AIDS-Related Non-Hodgkin Lymphoma
|OA=1
}}

{{PMID Auto
|PMID=19167443
|Title=Family-based analysis of tumor necrosis factor and lymphotoxin-alpha tag polymorphisms with type 1 diabetes in the population of South Croatia
|OA=1
}}

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.

* [[rs1800629]]
* [[rs361525]]
* [[rs1799724]]
* [[rs2239704]]

{{PharmGKB
|RSID=rs909253
|Name_s=intron 1 c.-10+90 (G/A)
|Gene_s=LTA, TNF
|Feature=
|Evidence=PubMed ID:19837266
|Annotation=Risk or phenotype-associated allele, tested allele: unspecified; minor allele designation varies by ethnicity in dbSNP Phenotype: In 114 cases and 414 controls (n = 528), univariate analysis of disease association showed OR = 1.03 for heterozygote, OR = 0.57 for homozygous, versus homozygous wild type, in ALL, with P(trend) OR = 0.83, p = 0.23 using an additive model. Study size: 528. Study population/ethnicity: Childhood acute lymphoblastic leukemia (<=14 years) and healthy newborn controls (1988 to 1999) from South Wales in the United Kingdom. Significance metric(s): Non-significant finding p = 0.23. Type of association: CO.
|Drugs=
|Drug Classes=
|Diseases=Precursor Cell Lymphoblastic Leukemia-Lymphoma
|Curation Level=Curated
|PharmGKB Accession ID=PA165110230
}}

{{PMID Auto
|PMID=20459604
|Title=Large-scale association analysis of TNF/LTA gene region polymorphisms in type 2 diabetes
|OA=1
}}

{{PMID Auto
|PMID=22615793
|Title=Investigation of Host Candidate Malaria-Associated Risk/Protective SNPs in a Brazilian Amazonian Population
|OA=1
}}

{{PMID Auto
|PMID=22294627
|Title=Association between genetic variants in the tumour necrosis factor/lymphotoxin Î±/lymphotoxin Î² locus and primary Sjogren's syndrome in Scandinavian samples
}}

{{PMID Auto
|PMID=15726497
|Title=Gene-environment interaction effects on the development of immune responses in the 1st year of life.
|OA=1
}}

{{PMID Auto
|PMID=16449530
|Title=Cytokine polymorphisms in the Th1/Th2 pathway and susceptibility to non-Hodgkin lymphoma.
|OA=1
}}

{{PMID Auto
|PMID=16839190
|Title=Lymphotoxin-alpha gene and risk of myocardial infarction in 6,928 cases and 2,712 controls in the ISIS case-control study.
|OA=1
}}

{{PMID Auto
|PMID=17174749
|Title=Linkage disequilibrium with predisposing DR3 haplotypes accounts for apparent effects of tumor necrosis factor and lymphotoxin-alpha polymorphisms on type 1 diabetes susceptibility.
|OA=1
}}

{{PMID Auto
|PMID=17216494
|Title=Genetic variation in tumor necrosis factor and lymphotoxin-alpha (TNF-LTA) and breast cancer risk.
}}

{{PMID Auto
|PMID=17327408
|Title=Prognostic significance of host immune gene polymorphisms in follicular lymphoma survival.
|OA=1
}}

{{PMID Auto
|PMID=17450233
|Title=Parental smoking modifies the relation between genetic variation in tumor necrosis factor-alpha (TNF) and childhood asthma.
|OA=1
}}

{{PMID Auto
|PMID=17517687
|Title=Association of variants in the BAT1-NFKBIL1-LTA genomic region with protection against myocardial infarction in Europeans.
}}

{{PMID Auto
|PMID=17701899
|Title=Flexible design for following up positive findings.
|OA=1
}}

{{PMID Auto
|PMID=17705862
|Title=Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples.
|OA=1
}}

{{PMID Auto
|PMID=18423522
|Title=Estimating odds ratios in genome scans: an approximate conditional likelihood approach.
|OA=1
}}

{{PMID Auto
|PMID=18633131
|Title=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.
|OA=1
}}

{{PMID Auto
|PMID=18687755
|Title=Genetic variants in T helper cell type 1, 2 and 3 pathways and gastric cancer risk in a Polish population.
|OA=1
}}

{{PMID Auto
|PMID=18704761
|Title=Molecular genetics of myocardial infarction.
|OA=1
}}

{{PMID Auto
|PMID=18805939
|Title=Functional genetic polymorphisms and female reproductive disorders: part II--endometriosis.
|OA=1
}}

{{PMID Auto
|PMID=18811622
|Title=Association of TNF-alpha with severe respiratory syncytial virus infection and bronchial asthma.
}}

{{PMID Auto
|PMID=18990758
|Title=Genetic variation in tumor necrosis factor and the nuclear factor-kappaB canonical pathway and risk of non-Hodgkin's lymphoma.
|OA=1
}}

{{PMID Auto
|PMID=19066394
|Title=Organochlorine exposure, immune gene variation, and risk of non-Hodgkin lymphoma.
|OA=1
}}

{{PMID Auto
|PMID=19131662
|Title=A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients.
|OA=1
}}

{{PMID Auto
|PMID=19225544
|Title=Variation in the lymphotoxin-alpha/tumor necrosis factor locus modifies risk of erythema nodosum in sarcoidosis.
|OA=1
}}

{{PMID Auto
|PMID=19263529
|Title=Genetic risk factors in recurrent venous thromboembolism: A multilocus, population-based, prospective approach.
|OA=1
}}

{{PMID Auto
|PMID=19281305
|Title=Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populations.
|OA=1
}}

{{PMID Auto
|PMID=19330901
|Title=Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study.
|OA=1
}}

{{PMID Auto
|PMID=19356949
|Title=Cytokine SNPs: Comparison of allele frequencies by race and implications for future studies.
|OA=1
}}

{{PMID Auto
|PMID=19409079
|Title=Association of MICA with rheumatoid arthritis independent of known HLA-DRB1 risk alleles in a family-based and a case control study.
|OA=1
}}

{{PMID Auto
|PMID=19559392
|Title=A candidate gene association study of 77 polymorphisms in migraine.
|OA=1
}}

{{PMID Auto
|PMID=19615068
|Title=The role of TNF genetic variants and the interaction with cigarette smoking for gastric cancer risk: a nested case-control study.
|OA=1
}}

{{PMID Auto
|PMID=19700502
|Title=Synopsis and synthesis of candidate-gene association studies in chronic lymphocytic leukemia: the CUMAGAS-CLL information system.
}}

{{PMID Auto
|PMID=20031567
|Title=An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of venous thromboembolism: The Women's Genome Health Study.
|OA=1
}}

{{PMID Auto
|PMID=20047977
|Title=Tumor necrosis factor (TNF) and lymphotoxin-alpha (LTA) polymorphisms and risk of non-Hodgkin lymphoma in the InterLymph Consortium.
|OA=1
}}

{{PMID Auto
|PMID=20049212
|Title=Traffic-related air pollution, oxidative stress genes, and asthma (ECHRS).
|OA=1
}}

{{PMID Auto
|PMID=20878356
|Title=Role of ethnic variations in TNF-alpha and TNF-beta polymorphisms and risk of breast cancer in India.
}}

{{PMID Auto
|PMID=23050158
|Title=Lymphotoxin-Alpha Gene Polymorphism +252A/G (rs909253, A/G) Is Associated with Susceptibility to Chronic Periodontitis: A Pilot Study
|OA=1
}}

{{GET Evidence
|impact=pharmacogenetic
|qualified_impact=Insufficiently evaluated pharmacogenetic
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs909253
|overall_frequency_n=48
|overall_frequency_d=128
|overall_frequency=0.375
|n_genomes=33
|n_genomes_annotated=0
|n_haplomes=42
|n_articles=1
|n_articles_annotated=0
|in_pharmgkb=Y
|autoscore=1
|webscore=N
}}

{{PMID Auto
|PMID=23086128
|Title=Profiles of gene polymorphisms in cytokines and Toll-like receptors with higher risk for gastric cancer
}}

{{PMID Auto
|PMID=22748850
|Title=A functional polymorphism of lymphotoxin-alpha (LTA) gene rs909253 is associated with gastric cancer risk in an Asian population.
}}

{{PMID Auto
|PMID=22749237
|Title=Tumor necrosis factor -308 polymorphism (rs1800629) is associated with mortality and ventilator duration in 1057 Caucasian patients.
|OA=1
}}

{{PMID Auto
|PMID=22882567
|Title=The +252A/G polymorphism in the lymphotoxin-alpha gene increases the risk of asthma: a meta-analysis.
}}

{{PMID Auto
|PMID=23029430
|Title=Prognostic role of host cyclooxygenase and cytokine genotypes in a Caucasian cohort of patients with gastric adenocarcinoma.
|OA=1
}}

{{PMID Auto
|PMID=23071570
|Title=Gene-gene interaction and functional impact of polymorphisms on innate immune genes in controlling Plasmodium falciparum blood infection level.
|OA=1
}}

{{PMID Auto
|PMID=23159874
|Title=Pro-inflammatory cytokine gene polymorphisms and threat for coronary heart disease in a North Indian Agrawal population.
}}

{{PMID Auto
|PMID=23294973
|Title=Association of TNF-alpha polymorphism rs1800629 with multisomatoform disorder in a group of German patients and healthy controls: an explorative study.
}}

{{PMID Auto
|PMID=23360674
|Title=Genetic variation may modify ovarian reserve in female childhood cancer survivors.
}}

{{PMID Auto
|PMID=23391141
|Title=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 Auto
|PMID=24959879
|Title=Effects of Tumor Necrosis Factor-β (TNF-β) 252A&gt;G Polymorphism on the Development of Migraine: A Meta-Analysis
}}

{{PMID Auto
|PMID=25063351
|Title=Tumor necrosis factor beta NcoI polymorphism (rs909253) is associated with inflammatory and metabolic markers in acute ischemic stroke
}}
{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | FTDNA2}}
{{on chip | HumanOmni1Quad}}