Intronic tag SNP in NEGR1 affecting neuronal cell adhesion, hippocampal neurogenesis, and monoaminergic neurotransmission — the G allele is associated with increased risk of major depression, anxiety disorders, and elevated BMI through shared hypothalamic circuits

Intronic IL12RB2 variant associated with IL-12 signaling pathway variation and susceptibility to Th1-mediated autoimmune conditions including primary biliary cholangitis, allergic rhinitis, and endometriosis

Synonymous variant in Toll-Like Receptor 2 affecting mRNA stability and splicing, associated with pulmonary tuberculosis susceptibility, cancer risk modification, and anti-TNF treatment response in inflammatory bowel disease

Intronic STAT3 variant where the T allele (reference, ~66%) increases risk for autoimmune thyroid disease, Crohn's disease, and lung cancer while the protective C allele correlates with higher STAT3 expression

Missense variant in the elastin-crosslinking enzyme LOXL1; the common G allele is one of the strongest known genetic risk factors for exfoliation syndrome and exfoliation glaucoma, a leading cause of secondary glaucoma worldwide

Rare missense variant near the BTD active site (p.Val89Gly) that likely reduces biotinidase enzyme activity; heterozygous carriers have partial enzyme reduction while biallelic inheritance causes biotinidase deficiency

Regulatory variant in the IL2RA locus altering LEF1 transcription factor binding and soluble IL-2 receptor levels — the C allele increases type 1 diabetes susceptibility while the minor A allele raises Graves' disease risk

Intronic variant in TTC39B (9p22) that increases endometriosis susceptibility; the T allele carries an OR of 1.29 for endometriosis, with a stronger effect on stage III/IV disease (OR 1.35). TTC39B is a regulator of LXR protein stability that controls HDL cholesterol metabolism, suggesting the endometriosis association may act through lipid-mediated inflammatory signalling in the peritoneal environment.

Intronic regulatory variant in TNFAIP3 — the primary NF-kB brake gene — with the C allele independently increasing psoriasis susceptibility (OR 1.23) and showing pleiotropic associations across multiple autoimmune conditions

Missense variant in the VWF A2 domain that destabilizes the protein and increases ADAMTS13 cleavage, causing loss of high-molecular-weight multimers and von Willebrand disease type 2A with mucocutaneous bleeding