Research — GeneOps

rs1234314 Intronic variant in TNFSF4 that reduces OX40 ligand promoter activity and is independently associated with susceptibility to systemic sclerosis and systemic lupus erythematosus

Chromosome 1 Risk Allele G Category Interferon Signaling & Systemic Autoimmune Tags Autoimmune, T-Cell Regulation, Connective Tissue, Inflammation, Rheumatoid Arthritis, Lupus

The immune system's response to tissue injury, infection, or self-antigens depends on a system of activating and restraining signals. Among the activating signals, the OX40–OX40L axis(https://www.ncbi.nlm.nih.gov/gene/8600) is one of the most potent co-stimulatory pathways in adaptive immunity. rs1234314 is an...

rs1250248 Intronic variant in the fibronectin 1 gene associated with increased susceptibility to endometriosis, particularly moderate-to-severe disease; the A allele may influence transcription factor binding and FN1 expression, altering extracellular matrix remodeling in ectopic endometrial implants

Chromosome 2 Risk Allele A Category Endometriosis & Uterine Health Tags Endometriosis, Fertility, Reproductive Health, Extracellular Matrix, Inflammation, Women's Health

Endometriosis — in which tissue resembling the uterine lining grows and implants outside the uterus — affects an estimated 10% of women of reproductive age and accounts for a major share of chronic pelvic pain, dyspareunia, and infertility. Its causes are multifactorial, but genetic factors account for roughly half...

rs1270942 Intronic variant in Complement Factor B associated with strongly elevated systemic lupus erythematosus risk through alternative complement pathway dysregulation

Chromosome 6 Risk Allele G Category B-Cell Immunity & Antibody-Mediated Disease Tags Complement System, Lupus, Autoimmune, Inflammation, Immune & Gut, Immune & Autoimmune, Immune System

Complement Factor B (CFB) is the central amplification enzyme of the alternative complement pathway(https://pubmed.ncbi.nlm.nih.gov/35296451/), the arm of the innate immune system responsible for continuous immune surveillance and the amplification of inflammation. The rs1270942 variant sits within an intron of the...

rs12720270 An intronic variant in TYK2 intron 7 that promotes exon 8 inclusion in the mature TYK2 transcript, enhancing TYK2 receptor-binding capacity and conferring protection against SLE in Caucasian populations; acts through the same exon 8 splicing mechanism as the co-associated rs2304256 (V362F) variant

Chromosome 19 Risk Allele G Category Autoimmune Tolerance & T-Cell Regulation Tags Autoimmune, Interferon, Lupus, JAK-STAT Signaling, Inflammation, Type 1 Diabetes

The TYK2 gene encodes a Janus kinase that sits at the junction of the IL-12, IL-23, and type I interferon signaling pathways — the three cytokine cascades most consistently implicated in autoimmune disease. Most protective TYK2 variants studied in depth are coding-sequence changes that impair kinase domain activity...

rs12883343 Regulatory variant near NFKBIA that specifically elevates risk for psoriatic arthritis over skin-only psoriasis, enabling early PsA risk stratification in people with psoriasis before irreversible joint damage occurs

Chromosome 14 Risk Allele G Category Psoriasis & Spondyloarthropathy Tags Autoimmune, Psoriasis, Arthritis, Inflammation, Bone & Joint, Biologic Therapy

Psoriasis affects roughly 2-3% of the global population, and one of the most consequential decisions in its management is determining which patients will go on to develop psoriatic arthritis(https://pubmed.ncbi.nlm.nih.gov/34884808/). Early PsA rarely announces itself dramatically — joint stiffness, tendon insertion...

rs12913832 Intronic enhancer variant controlling OCA2 expression and determining blue versus brown eye color, the strongest genetic predictor of iris pigmentation

Chromosome 15 Risk Allele G Category Skin & Eyes Tags Skin, Hair & Pigmentation, Eye Color, Melanoma, UV Sensitivity, Cancer Risk

The color of your eyes is determined primarily by a single nucleotide change on chromosome 15, not in a pigmentation gene itself, but in a regulatory enhancer(https://www.genome.gov/genetics-glossary/Enhancer) located deep within intron 86 of the HERC2 gene. This variant, rs12913832, functions as a dimmer switch for...

rs13207033 Intergenic protective variant near TNFAIP3 that tags a haplotype associated with enhanced A20-mediated NF-kB suppression, reducing rheumatoid arthritis and ankylosing spondylitis risk at the 6q23 locus

Chromosome 6 Risk Allele G Category TNF, NF-kB & Inflammatory Cytokines Tags Autoimmune, Inflammation, Rheumatoid Arthritis, Lupus, Immune & Gut

The 6q23 chromosomal region harbors one of the strongest known genetic influences on autoimmune disease risk. Most people know of this locus through its risk variants — but rs13207033 tells the other side of the story. This intergenic SNP, located near the TNFAIP3 gene on chromosome 6, tags a protective...

rs13236689 Intronic CD36 variant that acts as a platelet eQTL, modulating CD36 surface expression and influencing platelet activation, oxidized-LDL uptake, and postprandial lipid handling.

Chromosome 7 Risk Allele G Category Triglycerides & Fatty Acids Tags Fat Metabolism, Cardiovascular, Lipid Metabolism, Atherosclerosis, Triglycerides, Metabolic Syndrome

CD36 (also called fatty acid translocase, or FAT) is one of the body's key gatekeepers for dietary fat. It sits on the surface of cells throughout the intestine, tongue taste buds, platelets, macrophages, muscle, and adipose tissue. Its job is to bind long-chain fatty acids — the molecules that make up most of the...

rs1378577 Regulatory variant ~2kb upstream of ABCG1 that modulates transporter expression in macrophages; the G allele is associated with reduced risk of ischemic stroke, particularly the atherothrombotic subtype, likely through effects on HDL-mediated cholesterol clearance from arterial plaques

Chromosome 21 Risk Allele T Category Atherogenic Lipoproteins Tags Atherosclerosis, Cardiovascular, Cholesterol, HDL Cholesterol, Inflammation, Lipid Metabolism

When a macrophage migrates into a lipid-laden arterial wall and begins absorbing oxidized cholesterol, it faces a critical choice: offload that cargo to HDL particles and survive, or become overwhelmed by cholesterol accumulation and transform into a foam cell. This offloading depends heavily on the ABCG1...

rs1776897 Chromatin remodeling variant near HMGA1 associated with waist-to-hip ratio and height through transcriptional regulation in adipose tissue

Chromosome 6 Risk Allele G Category Liver Fat Tags Fat Metabolism, Obesity, Insulin, Cardiovascular

HMGA1 (High Mobility Group AT-Hook 1) encodes a non-histone chromosomal protein that functions as a transcriptional regulator(). It acts as an architectural transcription factor — rather than directly activating genes, it reshapes the DNA landscape to allow or prevent other regulators from doing their work. The...