rs12537

This is a regulatory region variant variant in the MTMR3 gene.

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GWAS Catalog Trait Associations (5)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

body height

Yengo L et al. “A saturated map of common genetic variants associated with human height.” Nature 610(7933):704-712 (2022)
Allele T
OR 0.01
p 6.0e-99
N 5,314,291
Large GWAS
European, Hispanic or Latin American, East Asian, African unspecified, South Asian

hypothyroidism

White SL et al. “Global multi-ancestry genome-wide analyses identify genes and biological pathways associated with thyroid cancer and benign thyroid diseases.” Nature Genetics 58(2):307-316 (2026)
Allele T
OR 0.04
p 4.0e-18
N 2,444,128
Large GWAS
multi-ancestry

IGA glomerulonephritis

Li M et al. “Identification of susceptibility loci and relevant cell type for IgA nephropathy in Han Chinese by integrative genome-wide analysis.” Frontiers of Medicine 18(5):862-877 (2024)
Allele T
OR 0.74
p 1.0e-12
N 14,033
Large GWAS
East Asian
Li M et al. “Identification of new susceptibility loci for IgA nephropathy in Han Chinese.” Nature Communications 6:7270 (2015)
Allele T
OR 1.41
p 3.0e-9
N 12,095
Large GWAS
East Asian
Yu XQ et al. “A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy.” Nature Genetics 44(2):178-82 (2011)
Allele T
OR 1.28
p 1.0e-11
N 5,704
Large GWAS
East Asian

erythrocyte volume

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele T
OR 0.03
p 2.0e-9
N 129,832
Large GWAS
East Asian
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ClinVar annotation

Benign★★★☆
2 submitters1 publication
View on ClinVar →
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Research that mentions this SNP (2)

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Relationships between SNPs and prognosis of breast cancer and pathogenic mechanism
AssociationN=1,665Yaning He et al.(2019)· Molecular Genetics &amp; Genomic Medicine

Case-control study in Chilean women examining SNPs in driver genes SMAD4, KMT2C, and SF3B1 in relation to familial breast cancer risk (n=453 cases, n=1212 controls). The C allele of rs3819122 (SMAD4) was significantly associated with increased breast cancer risk (OR=1.3 [95% CI 1.1-1.5], p=0.0008), particularly with Luminal A subtype. The T allele of rs16865677 (SF3B1) showed association with early-onset sporadic breast cancer (p=0.030). The rs13231116 (KMT2C) variant showed no significant association with breast cancer risk.

Traits studied:Breast cancerEarly-onset breast cancerFamilial breast cancerHER-2 positive breast cancerLuminal A breast cancerLuminal B breast cancerTriple negative breast cancer
PubMedDOIMetascience Observatory
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A functional polymorphism in MIR196A2 is associated with risk and prognosis of gastric cancer
ReviewShizhi Wang et al.(2013)· Molecular Carcinogenesis

This comprehensive review analyzes microRNA-related single nucleotide polymorphisms (SNPs) in gastric cancer, focusing on the most commonly studied variants including pre-miR-146a rs2910164, pre-miR-196a2 rs11614913, pre-miR-149 rs2292832, and pre-miR-499 rs3746444. The paper reviews 45 studies examining associations between miRNA polymorphisms and gastric cancer risk, including 18 studies on rs2910164 showing conflicting results (OR range 0.81-1.58), 13 studies on rs11614913 with no overall significant association, and analysis of pri-miRNA, pre-miRNA, promoter, and 3'-UTR variants. Additional variants identified include rs712 in let-7 (OR = 3.05; 95% CI = 1.53-6.08), rs12904 in miR-200c (OR = 0.65; 95% CI = 0.50-0.85), and rs12537 in miR-181a (OR = 1.72; 95% CI = 1.36-2.16).

Traits studied:Digestive system cancerGastric cancerGastrointestinal cancerNon-small cell lung cancer
PubMedDOIMetascience Observatory

About MTMR3

This gene encodes a member of the myotubularin dual specificity protein phosphatase gene family. The encoded protein is structurally similar to myotubularin but in addition contains a FYVE domain and an N-terminal PH-GRAM domain. The protein can self-associate and also form heteromers with another myotubularin related protein. The protein binds to phosphoinositide lipids through the PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The encoded protein has been observed to have a perinuclear, possibly membrane-bound, distribution in cells, but it has also been found free in the cytoplasm. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

View all MTMR3 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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