rs2954029

This is a intron variant variant.

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GWAS Catalog Trait Associations (24)

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

total cholesterol 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 A
OR 0.08
p 2.0e-99
N 153,950
Large GWAS
East Asian
Spracklen CN et al. “Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels.” Human Molecular Genetics 26(9):1770-1784 (2017)
Allele A
OR 0.06
p 1.0e-77
N 219,941
Large GWAS
multi-ancestry
Teslovich TM et al. “Biological, clinical and population relevance of 95 loci for blood lipids.” Nature 466(7307):707-713 (2010)
Allele A
OR 2.30
p 5.0e-36
N 100,184
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 A
OR —
β 0.071
p 1.0e-53
N 94,674
Large GWAS
multi-ancestry
Willer CJ et al. “Discovery and refinement of loci associated with lipid levels.” Nature Genetics 45(11):1274-1283 (2013)
Allele A
OR —
β 0.062
p 2.0e-65
N 94,595
Large GWAS
European
Lu X et al. “Genetic Susceptibility to Lipid Levels and Lipid Change Over Time and Risk of Incident Hyperlipidemia in Chinese Populations.” Circulation. Cardiovascular Genetics 9(1):37-44 (2016)
Allele A
OR 2.22
p 1.0e-11
N 8,344
Large GWAS
East Asian

fatty acid amount

Sun Y et al. “GWAS and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating fatty acids.” Hgg Advances 6(4):100470 (2025)
Allele T
OR —
p 4.0e-65
N 110,346
Large GWAS
European

low density lipoprotein cholesterol measurement

Spracklen CN et al. “Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels.” Human Molecular Genetics 26(9):1770-1784 (2017)
Allele A
OR 0.06
p 2.0e-56
N 205,367
Large GWAS
multi-ancestry
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 A
OR 0.05
p 2.0e-48
N 153,950
Large GWAS
East Asian
Bentley AR et al. “Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids.” Nature Genetics 51(4):636-648 (2019)
Allele A
OR 1.29
p 4.0e-17
N 125,692
Large GWAS
multi-ancestry
Teslovich TM et al. “Biological, clinical and population relevance of 95 loci for blood lipids.” Nature 466(7307):707-713 (2010)
Allele A
OR 1.84
p 3.0e-29
N 95,454
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 A
OR —
β 0.059
p 7.0e-36
N 94,674
Large GWAS
multi-ancestry
Willer CJ et al. “Discovery and refinement of loci associated with lipid levels.” Nature Genetics 45(11):1274-1283 (2013)
Allele A
OR —
β 0.056
p 2.0e-50
N 94,595
Large GWAS
European
Lee SB et al. “Dyslipidaemia-Genotype Interactions with Nutrient Intake and Cerebro-Cardiovascular Disease.” Biomedicines 10(7) (2022)
Allele A
OR 1.38
p 2.0e-13
N 58,701
Large GWAS
East Asian

phospholipids:total lipids ratio, high density lipoprotein cholesterol measurement

Karjalainen MK et al. “Genome-wide characterization of circulating metabolic biomarkers.” Nature 628(8006):130-138 (2024)
Allele A
OR 0.05
p 5.0e-40
N 136,016
Large GWAS
multi-ancestry

high density lipoprotein cholesterol measurement

Willer CJ et al. “Discovery and refinement of loci associated with lipid levels.” Nature Genetics 45(11):1274-1283 (2013)
Allele T
OR —
β 0.040
p 3.0e-29
N 94,595
Large GWAS
European
Bentley AR et al. “Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids.” Nature Genetics 51(4):636-648 (2019)
Allele T
OR 0.01
p 2.0e-14
N 133,824
Large GWAS
multi-ancestry
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 0.02
p 5.0e-10
N 115,082
Large GWAS
European
Teslovich TM et al. “Biological, clinical and population relevance of 95 loci for blood lipids.” Nature 466(7307):707-713 (2010)
Allele T
OR 0.61
p 6.0e-19
N 99,900
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 —
β 0.038
p 4.0e-24
N 94,674
Large GWAS
multi-ancestry

acetone 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 0.02
p 7.0e-29
N 450,015
Large GWAS
multi-ancestry
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 0.03
p 1.0e-9
N 115,079
Large GWAS
European

coronary artery disease

van der Harst P et al. “Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease.” Circulation Research 122(3):433-443 (2018)
Allele A
OR 0.07
p 1.0e-25
N 250,736
Large GWAS
Nelson CP et al. “Association analyses based on false discovery rate implicate new loci for coronary artery disease.” Nature Genetics 49(9):1385-1391 (2017)
Allele A
OR 1.06
p 5.0e-13
N 63,731
Large GWAS
European, NR
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Research that mentions this SNP (4)

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Sugar-sweetened beverage intake associations with fasting glucose and insulin concentrations are not modified by selected genetic variants in a ChREBP-FGF21 pathway: a meta-analysis
Meta-analysisN=34,748McKeown NM et al.(2018)· Diabetologia

Meta-analysis of 34,748 European ancestry adults from 11 CHARGE Consortium cohorts examining sugar-sweetened beverage (SSB) intake associations with glycemic traits. SSB intake was associated with higher fasting glucose (β=0.014 mmol/l, p=1.5×10⁻³) and fasting insulin (β=0.030 log pmol/l, p=2.0×10⁻¹⁰). Although a suggestive interaction between SSB and KLB-rs1542423 was observed in discovery cohorts for fasting insulin (p=0.006), this was not confirmed in replication analysis.

Traits studied:Fasting glucoseFasting insulinGlycemic traitsType 2 diabetes
PubMedDOIMetascience Observatory
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Genetic variants in five novel loci including CFB and CD40 predispose to chronic hepatitis B
AssociationN=6,033Jiang DK et al.(2015)· Hepatology

A genome-wide association study of 83 plasma proteins relevant to cardiovascular disease in 3,394 European subjects identified 79 genome-wide significant loci (p<5e-8), with 55 replicating in independent cohorts (n=2,639). Using eQTL analysis and network methods, the authors proposed plausible causal mechanisms for 25 trans-acting loci including post-translational regulation of KITLG by MMP9 and several receptor-ligand pairs. Multiple loci showed evidence of causal association with coronary artery disease risk.

Traits studied:AtherosclerosisCoronary artery diseasePlaque rupturePlasma protein levels (83 cardiovascular disease-related proteins)Thrombosis
PubMedDOIMetascience Observatory
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Common genetic variants associated with lipid profiles in a Chinese pediatric population
AssociationN=3,503Yue Shen et al.(2013)· Human Genetics

This study tested seven SNPs from European lipid-associated loci in 3,503 Chinese school-age children and found that six SNPs (rs2144300, rs1260333, rs1260326, rs10105606, rs1748195, rs964184) showed significant associations with triglyceride levels (p < 0.05 FDR-corrected), while three SNPs were associated with total cholesterol and four with LDL-cholesterol. Three SNPs (rs1260333 OR=0.82, rs1260326 OR=0.82, rs964184 OR=1.36) showed strong associations with dyslipidemia risk, demonstrating that lipid-susceptibility variants identified in European populations have similar effects in Chinese children.

Traits studied:DyslipidemiaHDL-cholesterolLDL-cholesterolTotal cholesterolTriglycerides
PubMedDOIMetascience Observatory
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Serum vitamins A and E as modifiers of lipid trait genetics in the National Health and Nutrition Examination Surveys as part of the Population Architecture using Genomics and Epidemiology (PAGE) study
AssociationN=5,576Logan Dumitrescu et al.(2012)· Human Genetics

This study investigated gene-environment interactions between 23 GWAS-identified lipid-associated SNPs and serum vitamins A and E in the National Health and Nutrition Examination Surveys (NHANES), including 5,576 participants across three racial/ethnic groups. Nine significant interactions were identified, with the most significant being APOB rs693×vitamin E associated with LDL-C in Mexican Americans (p=8.94×10⁻⁷). These nine interactions explained only 0.35-1.28% of variation in lipid traits, suggesting that gene-environment interactions account for modest proportions of the missing heritability in lipid metabolism.

Traits studied:HDL-C (High-Density Lipoprotein Cholesterol)LDL-C (Low-Density Lipoprotein Cholesterol)Triglycerides
PubMedDOIMetascience Observatory

This variant is in our database but has no known associations or PRS memberships yet.

Gene information from NCBI Gene. Variant classifications from ClinVar.

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