ArticleAmerican journal of human genetics2015
Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol.
Article in American journal of human genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it, 59 citations in OpenAlex.
- The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases.BMC medical genomics · 2022Pooled it
- Genome-Wide Differentiation, Inbreeding, and Candidate Selection Loci in Local Vietnamese Pig Breeds.International journal of molecular sciences · 2026Article
- PDIA3 rs2788, a risk factor for metabolic syndrome, interacted negatively with antihypertensive medications.Scientific reports · 2025Article
- An evolving understanding of multiple causal variants underlying genetic association signals.American journal of human genetics · 2025Review
- Functional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cells.bioRxiv : the preprint server for biology · 2025Article
- Genome-wide association study for metabolic syndrome reveals APOA5 single nucleotide polymorphisms with multilayered effects in Koreans.Lipids in health and disease · 2024Article
- GALNT2 expression is associated with glucose control and serum metabolites in patients with type 2 diabetes.Acta diabetologica · 2024Article
- Apolipoprotein-CIII O-Glycosylation Is Associated with Micro- and Macrovascular Complications of Type 2 Diabetes.International journal of molecular sciences · 2024Article
- Apolipoprotein-CIIIInternational journal of molecular sciences · 2023Article
- Global mapping of GalNAc-T isoform-specificities and O-glycosylation site-occupancy in a tissue-forming human cell line.Nature communications · 2022Article
- Role of GALNT2 on Insulin Sensitivity, Lipid Metabolism and Fat Homeostasis.International journal of molecular sciences · 2022Review
- Subcutaneous adipose tissue splice quantitative trait loci reveal differences in isoform usage associated with cardiometabolic traits.American journal of human genetics · 2022Article
- PolypeptideMolecules (Basel, Switzerland) · 2021Review
- Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases.International journal of molecular sciences · 2021Review
- Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation.Genome medicine · 2021Review
- Effect of vitamin E and alpha lipoic acid on intestinal development associated with wooden breast myopathy in broilers.Poultry science · 2021Article
- Global view of human protein glycosylation pathways and functions.Nature reviews. Molecular cell biology · 2020Review
- Adiponectin GWAS loci harboring extensive allelic heterogeneity exhibit distinct molecular consequences.PLoS genetics · 2020Article
- PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence.PloS one · 2020Article
- Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits.G3 (Bethesda, Md.) · 2019Article
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Authors and funding
22 authors at 8 institutions in 3 countries.
Funding
Abstract
Genome-wide association studies (GWASs) have identified more than 150 loci associated with blood lipid and cholesterol levels; however, the functional and molecular mechanisms for many associations are unknown. We examined the functional regulatory effects of candidate variants at the GALNT2 locus associated with high-density lipoprotein cholesterol (HDL-C). Fine-mapping and conditional analyses in the METSIM study identified a single locus harboring 25 noncoding variants (r(2) > 0.7 with the lead GWAS variants) strongly associated with total cholesterol in medium-sized HDL (e.g., rs17315646, p = 3.5 × 10(-12)). We used luciferase reporter assays in HepG2 cells to test all 25 variants for allelic differences in regulatory enhancer activity. rs2281721 showed allelic differences in transcriptional activity (75-fold [T] versus 27-fold [C] more than the empty-vector control), as did a separate 780-bp segment containing rs4846913, rs2144300, and rs6143660 (49-fold [AT(-) haplotype] versus 16-fold [CC(+) haplotype] more). Using electrophoretic mobility shift assays, we observed differential CEBPB binding to rs4846913, and we confirmed this binding in a native chromatin context by performing chromatin-immunoprecipitation (ChIP) assays in HepG2 and Huh-7 cell lines of differing genotypes. Additionally, sequence reads in HepG2 DNase-I-hypersensitivity and CEBPB ChIP-seq signals spanning rs4846913 showed significant allelic imbalance. Allelic-expression-imbalance assays performed with RNA from primary human hepatocyte samples and expression-quantitative-trait-locus (eQTL) data in human subcutaneous adipose tissue samples confirmed that alleles associated with increased HDL-C are associated with a modest increase in GALNT2 expression. Together, these data suggest that at least rs4846913 and rs2281721 play key roles in influencing GALNT2 expression at this HDL-C locus.
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