rs12789028

This is a regulatory region variant variant in the LTBP3 gene.

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GWAS Catalog Trait Associations (14)

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

heart rate

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.05
p 1.0e-47
N 425,748
Major Consortium StudyLarge GWAS
European
Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele G
OR 0.02
p 2.0e-13
N 394,642
Large GWAS
European

cup-to-disc ratio measurement

Alipanahi B et al. “Large-scale machine-learning-based phenotyping significantly improves genomic discovery for optic nerve head morphology.” American Journal of Human Genetics 108(7):1217-1230 (2021)
Allele G
OR 0.07
p 1.0e-39
N 89,579
Large GWAS
European
Craig JE et al. “Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression.” Nature Genetics 52(2):160-166 (2020)
Allele G
OR —
β 0.010
p 1.0e-25
N 90,939
Large GWAS
European

type 2 diabetes mellitus

Suzuki K et al. “Genetic drivers of heterogeneity in type 2 diabetes pathophysiology.” Nature 627(8003):347-357 (2024)
Allele A
OR —
p 5.0e-27
N 2,535,601
Large GWAS
multi-ancestry
Vujkovic M et al. “Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis.” Nature Genetics 52(7):680-691 (2020)
Allele A
OR 0.05
p 4.0e-20
N 1,407,282
Meta-analysisLarge GWAS
multi-ancestry
Mahajan A et al. “Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation.” Nature Genetics 54(5):560-572 (2022)
Allele A
OR 1.06
p 2.0e-16
N 492,192
Large GWAS
multi-ancestry

dentin matrix acidic phosphoprotein 1 amount

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele A
OR 0.06
p 2.0e-20
N 47,745
Large GWAS
European

HbA1c measurement

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.03
p 2.0e-20
N 338,857
Major Consortium StudyLarge GWAS
European

glaucoma

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.06
p 5.0e-20
N 430,721
Major Consortium StudyLarge GWAS
European

open-angle glaucoma

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.07
p 4.0e-19
N 434,033
Major Consortium StudyLarge GWAS
European

prostate specific antigen amount

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.03
p 1.0e-14
N 254,586
Major Consortium StudyLarge GWAS
European

diabetic retinopathy

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.07
p 5.0e-13
N 432,209
Major Consortium StudyLarge GWAS
European

optic cup area

Bonnemaijer PWM et al. “Multi-trait genome-wide association study identifies new loci associated with optic disc parameters.” Communications Biology 2:435 (2019)
Allele A
OR 0.02
p 1.0e-10
N 24,493
Large GWAS
European
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Research that mentions this SNP (1)

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lncRNA Neat1 Stimulates Osteoclastogenesis Via Sponging miR-7
FunctionalN=426,824Yan Zhang et al.(2020)· Journal of Bone and Mineral Research

This functional study establishes that the long noncoding RNA NEAT1 stimulates osteoclastogenesis via sponging miR-7, relieving inhibition of PTK2 expression. A distal GWAS SNP rs12789028 functions as an allele-specific enhancer regulating NEAT1 expression; the G-allele increases NEAT1 expression leading to enhanced bone resorption and osteoporosis risk. The mechanism links a NEAT1 locus variant to bone mineral density through lncRNA-mediated osteoclastogenesis.

Traits studied:Bone mineral densityBone resorptionOsteoclastogenesisOsteoporosis
PubMedDOIMetascience Observatory

About LTBP3

The protein encoded by this gene forms a complex with transforming growth factor beta (TGF-beta) proteins and may be involved in their subcellular localization. Activation of this complex requires removal of the encoded binding protein. This protein also may play a structural role in the extracellular matrix. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]

View all LTBP3 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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