Research — GeneOps

rs6910071 MHC-region intronic variant tagging HLA-DRB1 shared epitope haplotypes; G allele is the primary GWAS signal for seropositive rheumatoid arthritis and polymyalgia rheumatica risk in Europeans

Chromosome 6 Risk Allele G Category Interferon Signaling & Systemic Autoimmune Tags HLA, Rheumatoid Arthritis, Autoimmune, Inflammation, MHC Antigen Presentation, Immune & Autoimmune

The rs6910071 variant sits within an intron of TSBP1 (testis-expressed basic protein 1, formerly C6orf10), a gene embedded in the major histocompatibility complex (MHC) on chromosome 6p21. The MHC is the most densely associated genetic region for rheumatoid arthritis (RA), driven principally by HLA-DRB1 alleles...

rs738409 Strongest genetic risk factor for non-alcoholic fatty liver disease, progression to cirrhosis, and hepatocellular carcinoma

Chromosome 22 Risk Allele G Category Liver Fat Tags Fat Metabolism, Triglycerides, Diet, Alcohol, Cancer Risk, Liver Health, Diabetes

In 2008, a landmark genome-wide association study(https://pubmed.ncbi.nlm.nih.gov/18464913/) discovered something remarkable: a single genetic variant in the PNPLA3 gene explained more variation in liver fat content than obesity, diabetes, or alcohol consumption combined. The I148M variant (rs738409) has since been...

rs12659 Synonymous variant in the folate transporter SLC19A1 — a haplotype tag linked to altered methotrexate response

Chromosome 21 Risk Allele A Category Methylation & Detox Tags Methylation, Folate, B Vitamins, Drug Metabolism, Cancer Risk

The reduced folate carrier (RFC1, encoded by SLC19A1) is the principal route by which folates and antifolate drugs — including methotrexate — enter most human cells. Like any well-studied transporter gene, SLC19A1 carries a cluster of common variants that tend to travel together in haplotype blocks. rs12659...

rs12752133 Intronic GBA variant associated with REM sleep behavior disorder via lysosomal autophagy impairment; the T allele confers OR=2.09 for RBD in the largest GWAS of this condition to date

Chromosome 1 Risk Allele T Category Neurology & Cognition Tags Parkinson's, Neurodegeneration, Neurological Risk, Sleep, Autophagy, Brain Health

Deep inside your cells, lysosomes serve as the recycling centres responsible for breaking down worn-out proteins, lipids, and cellular debris. One enzyme is central to this process in neurons: glucocerebrosidase (GCase)(https://omim.org/entry/606463). GBA variants are already established as the strongest known...

rs12936231 Regulatory tagging SNP in the 17q21 asthma locus that is the strongest eQTL for ORMDL3 in whole blood; the C allele increases ORMDL3 expression and confers childhood asthma and early wheeze susceptibility

Chromosome 17 Risk Allele C Category Allergy & Atopic Disease Tags Asthma, Lung Health, Innate Immunity, Inflammation, Vitamin D, Autoimmune

The chromosome 17q21 locus is the most robustly replicated genetic risk region for childhood-onset asthma, identified in the landmark Moffatt et al. 2007 GWAS(https://pubmed.ncbi.nlm.nih.gov/17611496/) in Nature. Among the constellation of correlated variants in this locus, rs12936231 stands out as the most powerful...

rs13266634 Zinc transporter 8 variant affecting zinc loading into insulin granules, influencing insulin crystallization, secretion, and type 2 diabetes risk

Chromosome 8 Risk Allele C Category Blood Sugar & Diabetes Tags Zinc, Insulin, Diabetes, Diet, Cardiovascular

The SLC30A8 gene encodes zinc transporter 8() (ZnT8), a protein found almost exclusively in the insulin-producing beta cells of the pancreas. Its job is simple but critical: load zinc into the granules where insulin is stored. Zinc is essential for insulin to crystallize into its stable hexameric form — without...

rs16861205 Intronic ADIPOQ variant in LD with the promoter region; the minor A allele is associated with reduced circulating adiponectin in women and altered adiponectin dynamics during weight loss

Chromosome 3 Risk Allele A Category Fat Storage & Energy Tags Insulin Resistance, Adipogenesis, Fat Metabolism, Metabolic Health, Omega-3, Nutrition & Metabolism

Adiponectin is the body's most abundant adipokine — a hormone secreted almost exclusively by adipose tissue(https://www.ncbi.nlm.nih.gov/books/NBK537041/) that acts as a master regulator of insulin sensitivity, lipid metabolism, and metabolic inflammation. Low circulating adiponectin is one of the most consistent...

rs174616 Intronic FADS2 variant tagging the FADS1/FADS2 haplotype block; A allele carriers have reduced delta-6 desaturase activity, impairing conversion of dietary plant-based omega-3 (ALA) to EPA/DHA and omega-6 (LA) to arachidonic acid

Chromosome 11 Risk Allele A Category Triglycerides & Fatty Acids Tags Omega-3, Fat Metabolism, Cardiovascular, Diet, Inflammation, Brain Health

The FADS2 gene on chromosome 11 encodes delta-6 desaturase(), the enzyme that opens the gateway to all long-chain polyunsaturated fatty acid synthesis from plant precursors. rs174616 is an intronic FADS2 variant that tags a distinct linkage disequilibrium block within the FADS1/FADS2 cluster. Carriers of the A...

rs1799853 Decreased function variant affecting warfarin, phenytoin, and NSAIDs

Chromosome 10 Risk Allele T Category Pharmacogenomics Tags Drug Metabolism, Warfarin, Pain Medication, Cannabis, Endocannabinoid

CYP2C9 is the primary enzyme responsible for metabolizing warfarin (Coumadin), one of the most widely prescribed and dangerous medications in clinical practice. Warfarin has an extremely narrow therapeutic window| Narrow therapeutic window: small difference between effective dose and toxic dose - too little and you...

rs1800624 Promoter variant in the AGER gene that increases RAGE transcription approximately threefold, raising both membrane-bound and soluble RAGE; the elevated RAGE expression amplifies AGE-driven inflammatory signaling and is associated with diabetic microvascular complications and coronary artery ectasia

Chromosome 6 Risk Allele T Category Hormones & Sleep Tags Inflammation, Aging, Oxidative Stress, Diabetes, Cardiovascular, Sleep

AGER encodes RAGE (Receptor for Advanced Glycation End-Products), a pattern recognition receptor() found on endothelial cells, neurons, smooth muscle, immune cells, and alveolar epithelium. Unlike the Gly82Ser missense variant (rs2070600), which alters receptor structure, the −374T/A polymorphism acts upstream — it...