rs12740374

This is a regulatory region variant variant in the CELSR2 gene.

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GWAS Catalog Trait Associations (225)

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

complement C1q tumor necrosis factor-related protein 1 measurement

Pietzner M et al. “Mapping the proteo-genomic convergence of human diseases.” Science (new York, N.y.) 374(6569):eabj1541 (2021)
Allele T
OR 0.72
p —
N 10,708
Large GWAS
European

granulins measurement

Pietzner M et al. “Mapping the proteo-genomic convergence of human diseases.” Science (new York, N.y.) 374(6569):eabj1541 (2021)
Allele T
OR 0.86
p —
N 10,708
Large GWAS
European
Thareja G et al. “Differences and commonalities in the genetic architecture of protein quantitative trait loci in European and Arab populations.” Human Molecular Genetics 32(6):907-916 (2023)
Allele T
OR 0.77
p 4.0e-104
N 2,935
Large GWAS
Greater Middle Eastern (Middle Eastern, North African or Persian)
Surapaneni A et al. “Identification of 969 protein quantitative trait loci in an African American population with kidney disease attributed to hypertension.” Kidney International 102(5):1167-1177 (2022)
Allele T
OR 0.59
p 6.0e-16
N 466
Small GWAS
African American or Afro-Caribbean

low density lipoprotein cholesterol measurement

Graham SE et al. “The power of genetic diversity in genome-wide association studies of lipids.” Nature 600(7890):675-679 (2021)
Allele T
OR 0.15
p —
N 1,320,016
Large GWAS
European
Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.07
p 8.0e-205
N 450,015
Large GWAS
multi-ancestry
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 0.12
p —
N 416,487
Large GWAS
multi-ancestry
Koskeridis F et al. “Pleiotropic genetic architecture and novel loci for C-reactive protein levels.” Nature Communications 13(1):6939 (2022)
Allele T
OR 0.01
p 3.0e-17
N 361,194
Large GWAS
European
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 0.20
p 6.0e-152
N 153,950
Large GWAS
East Asian
Richardson TG et al. “Characterising metabolomic signatures of lipid-modifying therapies through drug target mendelian randomisation.” Plos Biology 20(2):e3001547 (2022)
Allele T
OR 0.13
p 6.0e-143
N 115,082
Large GWAS
European
Hoffmann TJ et al. “A large electronic-health-record-based genome-wide study of serum lipids.” Nature Genetics 50(3):401-413 (2018)
Allele T
OR 0.18
p 4.0e-202
N 94,674
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.11
p 8.0e-91
N 88,329
Large GWAS
European
Lee SB et al. “Dyslipidaemia-Genotype Interactions with Nutrient Intake and Cerebro-Cardiovascular Disease.” Biomedicines 10(7) (2022)
Allele T
OR 5.77
p 2.0e-48
N 58,701
Large GWAS
East Asian
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 T
OR 0.15
p 9.0e-95
N 54,972
Major Consortium StudyLarge GWAS
Hispanic or Latin American
Jacobs BM et al. “Genetic architecture of routinely acquired blood tests in a British South Asian cohort.” Nature Communications 15(1):8929 (2024)
Allele T
OR 0.22
p 2.0e-137
N 38,000
Large GWAS
South Asian
Kathiresan S et al. “Common variants at 30 loci contribute to polygenic dyslipidemia.” Nature Genetics 41(1):56-65 (2009)
Allele T
OR 0.23
p 2.0e-42
N 19,840
Large GWAS
European
Gurdasani D et al. “Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.” Cell 179(4):984-1002.e36 (2019)
Allele T
OR 0.14
p 2.0e-26
N 14,126
Large GWAS
Sub-Saharan African
Choudhury A et al. “Meta-analysis of sub-Saharan African studies provides insights into genetic architecture of lipid traits.” Nature Communications 13(1):2578 (2022)
Allele T
OR 0.13
p 3.0e-15
N 10,389
Meta-analysisLarge GWAS
Sub-Saharan African
Lettre G et al. “Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.” Plos Genetics 7(2):e1001300 (2011)
Allele T
OR 0.18
p 9.0e-29
N 7,565
Large GWAS
African American or Afro-Caribbean
Moon S et al. “The Korea Biobank Array: Design and Identification of Coding Variants Associated with Blood Biochemical Traits.” Scientific Reports 9(1):1382 (2019)
Allele T
OR 0.07
p 3.0e-11
N 6,949
Large GWAS
East Asian
Ismail Umlai UK et al. “A multi-ancestry genome-wide association study and evaluation of polygenic scores of LDL-C levels.” Journal of Lipid Research 66(3):100752 (2025)
Allele T
OR 0.24
p 9.0e-20
N 5,939
Large GWAS
Greater Middle Eastern (Middle Eastern, North African or Persian)

Hypercholesterolemia

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 0.24
p 9.9e-324
N 404,034
Major Consortium StudyLarge GWAS
multi-ancestry
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 0.17
p 6.0e-115
N 394,626
Large GWAS
European
Kim YS et al. “Lifestage Sex-Specific Genetic Effects on Metabolic Disorders in an Adult Population in Korea: The Korean Genome and Epidemiology Study.” International Journal of Molecular Sciences 23(19) (2022)
Allele G
OR 0.70
p 1.0e-14
N 50,808
Large GWAS
East Asian

phospholipids in small LDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.09
p 2.0e-307
N 450,015
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.14
p 1.0e-136
N 88,329
Large GWAS
European

free cholesterol in small LDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.09
p 7.0e-300
N 450,015
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.13
p 5.0e-120
N 88,329
Large GWAS
European

drug use measurement, Hypercholesterolemia

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 0.21
p 6.0e-297
N 315,668
Major Consortium StudyLarge GWAS
European

free cholesterol to total lipids in small HDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.08
p 3.0e-252
N 450,015
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.11
p 7.0e-96
N 88,329
Large GWAS
European

free cholesterol in medium LDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.08
p 1.0e-241
N 450,015
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.12
p 4.0e-101
N 88,329
Large GWAS
European
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ClinVar annotation

Association
1 submitter3 publications

Low density lipoprotein cholesterol level quantitative trait locus 6 (LDLCQ6)

View on ClinVar →
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Research that mentions this SNP (2)

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Investigation of genetic risk factors for chronic adult diseases for association with preterm birth
AssociationN=1,792Nadia Falah et al.(2013)· Human Genetics

Case-control study of 673 preterm birth (PTB) cases vs 1,119 controls across four maternal cohorts testing 35 SNPs in cardiovascular, inflammatory, and metabolic disease genes. Found 13 statistically significant associations with PTB (P<0.05), more than expected by chance (binomial P=0.02). Most significant was HLA-DQA1 rs9272346 G allele protective effect in US White mothers (P=0.02, OR=0.65, 95% CI 0.46-0.94), which nominally replicated in Danish cohort (P=0.02, OR=0.85, 95% CI 0.75-0.97) but lost significance after correction for multiple testing.

Traits studied:Cardiovascular diseaseHeight and weightHemostasis and thrombosisHypertensionInflammatory and immunological diseaseLipids and glucose metabolismMyocardial infarctionObesityPreterm birth
PubMedDOIMetascience Observatory
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The novel genetic variant predisposing to coronary artery disease in the region of the PSRC1 and CELSR2 genes on chromosome 1 associates with serum cholesterol
AssociationN=3,974Nilesh J. Samani et al.(2008)· Journal of Molecular Medicine

This genome-wide association study investigated whether seven CAD-associated loci affect coronary artery disease risk through traditional cardiovascular risk factors. The study found that rs599839, located near PSRC1 and CELSR2 on chromosome 1p13.3, showed a strong association with serum cholesterol levels, with the risk allele A associated with 0.17 mmol/l higher total cholesterol per allele copy (P = 3.84 × 10⁻⁶) and 0.19 mmol/l higher LDL cholesterol (P = 8.56 × 10⁻⁵). This association was replicated in independent cohorts and the findings support further investigation of these genes in cholesterol metabolism and coronary risk.

Traits studied:Blood pressureBlood urateBody mass indexCoronary artery diseaseCreatinine clearanceGlucoseHDL cholesterolLDL cholesterolMyocardial infarctionTotal cholesterolWaist-hip ratio
PubMedDOIMetascience Observatory

About CELSR2

The protein encoded by this gene is a member of the flamingo subfamily, part of the cadherin superfamily. The flamingo subfamily consists of nonclassic-type cadherins; a subpopulation that does not interact with catenins. The flamingo cadherins are located at the plasma membrane and have nine cadherin domains, seven epidermal growth factor-like repeats and two laminin A G-type repeats in their ectodomain. They also have seven transmembrane domains, a characteristic unique to this subfamily. It is postulated that these proteins are receptors involved in contact-mediated communication, with cadherin domains acting as homophilic binding regions and the EGF-like domains involved in cell adhesion and receptor-ligand interactions. The specific function of this particular member has not been determined. [provided by RefSeq, Jul 2008]

View all CELSR2 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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