Intronic FCGR2A variant in linkage disequilibrium with the H131R functional polymorphism (rs1801274), tagging the high-IgG2-affinity receptor allele associated with Kawasaki disease susceptibility, autoimmune risk, and differential response to IgG2-dependent vaccines and infections

Intergenic GWAS variant on chromosome Xp22, near the testis-specific genes FAM9B and FAM9A, associated with serum testosterone levels in men; the C allele is linked to higher testosterone and the T allele (major) to lower testosterone

3'UTR variant controlling ASIP protein output; G allele reduces ASIP mRNA 12-fold, promoting eumelanin and darker skin, hair, and eye pigmentation

Promoter variant that reduces APOA5 expression, impairing lipoprotein lipase activity and raising triglycerides by 15–36%; major determinant of hypertriglyceridemia and dietary fat response

Near-gene variant tagging an IRF5 protective haplotype in the 5' promoter region that reduces type I interferon output and lowers susceptibility to lupus, rheumatoid arthritis, and related autoimmune conditions

Intronic variant in transferrin receptor 2 that tags altered TFR2 expression and iron-sensing function in hepatocytes, associating with lower transferrin saturation and serum iron in the C-allele direction

Intronic GCKR variant in strong LD with the coding P446L substitution (rs1260326); the T allele increases hepatic glucokinase activity, lowering fasting glucose and insulin while raising triglycerides, CRP, and NAFLD risk — a striking metabolic trade-off driven by excess hepatic de novo lipogenesis

Regulatory variant in a FOXO1-binding enhancer element flanking the IKZF3 gene at 17q21; the C allele maintains FOXO1/MEF2A binding and is associated with elevated ORMDL3, GSDMB, and IKZF3 expression, higher asthma susceptibility, and risk for several autoimmune conditions; the T allele disrupts these binding sites, reducing expression of all three genes and is protective for asthma but associated with increased risk for multiple sclerosis and IBD

Intronic CD58 variant that sits inside the miR-548ac stem-loop; the A allele disrupts Drosha cleavage, simultaneously lowering CD58 mRNA and raising miR-548ac levels — the functional mechanism underlying the CD58 locus MS association

3' UTR variant in the de novo DNA methyltransferase DNMT3A, associated with altered DNMT3A expression, modestly reduced gastric cancer risk in some populations, and interaction effects with folate intake and H. pylori infection on cancer and cardiovascular risk