rs12880341

This is a intergenic variant variant in the SYNE2 gene.

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GWAS Catalog Trait Associations (13)

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

sphingomyelin measurement

Harshfield EL et al. “Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci.” Bmc Medicine 19(1):232 (2021)
Allele G
OR 0.06
p 6.0e-26
N 5,662
Large GWAS
South Asian
Chai JF et al. “Associations with metabolites in Chinese suggest new metabolic roles in Alzheimer's and Parkinson's diseases.” Human Molecular Genetics 29(2):189-201 (2020)
Allele G
OR 0.18
p 3.0e-15
N 1,954
Large GWAS
East Asian

cholesterol to total lipids in IDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele C
OR 0.02
p 4.0e-21
N 450,015
Large GWAS
multi-ancestry

cholesteryl esters to total lipids in IDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele C
OR 0.02
p 6.0e-21
N 450,015
Large GWAS
multi-ancestry

triglyceride measurement

Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele T
OR 0.02
p 4.0e-19
N 928,679
Large GWAS
multi-ancestry
Richardson TG et al. “Evaluating the relationship between circulating lipoprotein lipids and apolipoproteins with risk of coronary heart disease: A multivariable Mendelian randomisation analysis.” Plos Medicine 17(3):e1003062 (2020)
Allele T
OR 0.02
p 3.0e-14
N 441,016
Large 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 T
OR 0.02
p 1.0e-15
N 394,642
Large GWAS
European

polyunsaturated fatty acids to monounsaturated fatty acids ratio

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele C
OR 0.02
p 3.0e-12
N 450,015
Large GWAS
multi-ancestry

degree of unsaturation measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele C
OR 0.02
p 9.0e-11
N 450,015
Large GWAS
multi-ancestry

level of ceramide

Chai JF et al. “Associations with metabolites in Chinese suggest new metabolic roles in Alzheimer's and Parkinson's diseases.” Human Molecular Genetics 29(2):189-201 (2020)
Allele T
OR 0.21
p 9.0e-11
N 1,954
Large GWAS
East Asian

About SYNE2

The protein encoded by this gene is a nuclear outer membrane protein that binds cytoplasmic F-actin. This binding tethers the nucleus to the cytoskeleton and aids in the maintenance of the structural integrity of the nucleus. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

View all SYNE2 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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