Intronic variant in MCF2L that acts as a synovial eQTL — A allele carriers have higher MCF2L expression in joint tissue and elevated osteoarthritis risk across large joints

Pathogenic missense variant in the MCAD enzyme causing medium-chain acyl-CoA dehydrogenase deficiency — an autosomal recessive disorder of mitochondrial fatty acid oxidation leading to hypoketotic hypoglycemia and metabolic crisis during fasting or illness

Frameshift deletion in APOB causing truncated apolipoprotein B-100, reducing LDL production and impairing fat-soluble vitamin absorption; pathogenic for familial hypobetalipoproteinemia

Ultra-rare APOE3 missense variant that dramatically reduces HSPG binding and tau propagation, conferring near-complete resistance to Alzheimer's disease in the homozygous state and a modest protective delay in heterozygotes

Pathogenic PROS1 missense variant in the SHBG-like domain that impairs protein S secretion; heterozygotes have reduced protein S activity and a substantially elevated risk of venous thromboembolism requiring specialist evaluation

Intronic variant in THADA (thyroid adenoma associated) on chromosome 2p21; the C allele is a PCOS risk allele at the THADA locus (companion tag SNP to rs13429458, the original Han Chinese GWAS lead), tagging a haplotype that reduces THADA-mediated SERCA uncoupling, impairing ER calcium homeostasis in pancreatic beta cells and predisposing to PCOS and insulin secretion defects

Intronic PTPN22 haplotype tag variant that refines autoimmune risk stratification beyond R620W and associates independently with Hashimoto's thyroiditis in Asian populations

Intronic variant in the SVCT2 vitamin C transporter — G allele associated with lower plasma vitamin C, higher glaucoma risk, and modified cognitive decline risk in APOE4 carriers

Intronic variant in the immune-response gene EPSTI1, associated in recessive models with reduced sperm concentration, total sperm count, sperm motility, and azoospermia/oligospermia risk in men.

Uromodulin promoter variant — strongest GWAS signal for chronic kidney disease risk, affecting salt handling and blood pressure via NKCC2