Intergenic variant near MC4R with genome-wide significant association with antipsychotic-induced weight gain, particularly olanzapine and clozapine; also tags the MC4R locus for general BMI effects

Intronic variant in TSBP1-AS1 (LOC101929163), a non-coding antisense RNA in the HLA region between TSBP1 and BTNL2 on chromosome 6p21.32; the G allele is associated with increased risk of non-obstructive azoospermia in Han Chinese men, with an odds ratio of approximately 1.42 in a large multi-stage GWAS

Intronic NEDD4L variant influencing ubiquitin ligase isoform expression and salt-sensitive blood pressure regulation via the ENaC pathway

A2 domain missense variant in von Willebrand factor associated with type 2A von Willebrand disease; the proline substitution destabilizes the A2 domain, increasing susceptibility to ADAMTS13 proteolysis and depleting high-molecular-weight multimers required for platelet adhesion

Intronic PXK variant; the G allele is a replicated GWAS risk allele for systemic lupus erythematosus in Europeans, acting through impaired receptor endocytosis and disrupted B-cell immune signalling

Intronic SLC2A9 variant tagging a urate-transport regulatory haplotype; the protective T allele (~48% global frequency) is enriched in populations with lower gout prevalence and is associated with more efficient renal urate clearance, while the risk C allele — common in East Asians (~90%) where gout prevalence is highest — tags reduced GLUT9-mediated reabsorption efficiency and elevated serum uric acid

Intronic variant near the CYP19A1 promoter region, falling within MIR4713HG but mapping to the CYP19A1 RefSeqGene locus; associated with breast cancer histological grade and tumor size in a Swedish cohort, consistent with its position in the aromatase regulatory zone

Rare likely-pathogenic missense variant in the LDLR EGF-like repeat domain causing impaired LDL receptor processing and familial hypercholesterolemia with severely elevated LDL-C and premature coronary artery disease risk

Intronic tag SNP in HLA-DPB1 (and upstream of HLA-DPA1) that marks the HLA-DP haplotype controlling antigen-presenting cell surface expression; the G allele is strongly associated with chronic hepatitis B infection susceptibility and impaired hepatitis B vaccine antibody response across multiple populations

An intronic variant in the DENND1A locus on chromosome 9q33.3, a robustly replicated PCOS susceptibility region; the A allele tags regulatory variation that drives DENND1A overexpression in theca cells, elevating androgen biosynthesis