rs944289

badMag 4.5

This is a intergenic variant variant in the NKX2-1 gene.

Key Literature Trait Associations

Thyroid Cancer

Each copy of the T allele at rs944289 is associated with a 1.37-fold increased risk of papillary thyroid carcinoma. This variant maps to 14q13.3 near the NKX2-1 (TITF1) locus, a transcription factor critical for thyroid development and differentiation. Identified in a GWAS of 461 thyroid cancer cases and 34,109 controls from Iceland with replication in cohorts from Spain and the US (total ~3,400 cases).

Gudmundsson J et al. “Discovery of common variants associated with low TSH levels and thyroid cancer risk” Nature Genetics (2009)

Allele T

OR 1.37

p 2.0e-9

Large GWAS

Zheng J et al. “Common genetic variant on 14q13.3 contributes to thyroid cancer susceptibility: evidence based on 12 studies.” Molecular Genetics and Genomics : Mgg (2015)

Allele T

OR 1.30

p 1.0e-5

N 61,211

Preliminary work

multi-ancestry

Ai L et al. “Associations between rs965513/rs944289 and papillary thyroid carcinoma risk: a meta-analysis.” Endocrine (2014)

Allele T

OR 1.29

p —

N 51,120

Meta-analysis

multi-ancestry

Chen YH et al. “Exploration of the association between FOXE1 gene polymorphism and differentiated thyroid cancer: a meta-analysis.” Bmc Medical Genetics (2018)

Allele T

OR 1.08

p —

Meta-analysis

multi-ancestry

Ran R et al. “Genetic Variants Associated with Thyroid Cancer Risk: Comprehensive Research Synopsis, Meta-Analysis, and Cumulative Epidemiological Evidence.” Journal of Oncology (2021)

Allele T

OR —

p —

Meta-analysis

multi-ancestry

▶

GWAS Catalog Trait Associations (1)

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

thyroid carcinoma

Gudmundsson J et al. “Discovery of common variants associated with low TSH levels and thyroid cancer risk” Nature Genetics (2009)

Allele T

OR 1.37

p 2.0e-9

N 37,388

Large GWAS

European

▶

Research that mentions this SNP (2)

▶

Single nucleotide polymorphisms of ataxia telangiectasia mutated and the risk of papillary thyroid carcinoma

MethodsChang Myeon Song et al.(2015)· Environmental and Molecular Mutagenesis

This is a methods chapter describing high-resolution melting (HRM) for SNP detection in papillary thyroid carcinoma research. The paper reviews SNPs associated with PTC development and progression, including variants in FAS (rs2234978), DICER1 (rs3742330), TAS2R3/4 (rs2270009, rs2234001), ATM (rs373759, rs664143, rs4585), TITF1/TITF2 (rs944289, rs965513, rs1443434), MDM2 (rs2279744, rs3730485), BRCA1 (rs1799950, rs799917, rs16941, rs16942, rs1060915, rs1799966), VEGF-A, MMP9 (rs1562), and others associated with tumor characteristics and PTC risk.

Traits studied:Extrathyroidal extensionLymph node metastasisMultifocalityPapillary thyroid carcinomaTNM stageThyroid cancerTumor size

PubMed DOI Metascience Observatory

▶

Significant SNPs have limited prediction ability for thyroid cancer

AssociationN=1,850Shicheng Guo et al.(2014)· Cancer Medicine

Case-control study genotyping five thyroid cancer-associated SNPs (rs965513 OR=1.53, rs944289 OR=1.51, rs966423 OR=1.32, rs2439302 OR=1.40; rs116909374 not detected) in 845 Han Chinese papillary thyroid carcinoma cases and 1,005 controls. Although significant associations were confirmed, prediction accuracy was limited (AUC 0.54-0.60 across nine machine learning methods) with low sensitivity (0.28-0.48), indicating minimal clinical utility despite large odds ratios.

rs944289

Key Literature Trait Associations

Thyroid Cancer

GWAS Catalog Trait Associations (1)

thyroid carcinoma

Research that mentions this SNP (2)

Community Wiki

Comments