rs1360590 — CDKN2BAS

Intronic variant in ANRIL at the 9p21.3 locus — the shared susceptibility region for coronary artery disease and periodontitis; the C allele elevates inflammatory signaling through ANRIL dysregulation and increases susceptibility to aggressive and chronic periodontitis

See your personal result for CDKN2BAS

Upload your DNA data to find out which genotype you carry and what it means for you.

Upload your DNA data

Works with 23andMe, AncestryDNA, and other DNA test exports. Results in under 60 seconds.

ANRIL at the Crossroads of Gum Disease and Heart Disease

The 9p21.3 locus on chromosome 9 is the most replicated common genetic risk region for coronary artery disease (CAD) ever identified — and it doubles as a susceptibility locus for periodontitis. rs1360590 sits within an intron of CDKN2B-AS1 (ANRIL)11 CDKN2B-AS1 (ANRIL)
Antisense Non-coding RNA in the INK4 Locus — a long non-coding RNA transcribed antisense to the tumor suppressor genes CDKN2A and CDKN2B at chromosome 9p21.3, one of several tag SNPs at this locus validated for both cardiovascular and periodontal disease risk.

The C allele at rs1360590 was identified as a susceptibility variant for aggressive and chronic periodontitis in two independent European cohorts22 two independent European cohorts
Schaefer AS et al. CDKN2BAS is associated with periodontitis in different European populations and is activated by bacterial infection. J Med Genet. 2011;48(1):38-47.. The same chromosomal region had previously been shown to confer shared risk for coronary heart disease and aggressive periodontitis — diseases linked by chronic systemic inflammation.

The Mechanism

ANRIL operates as a master regulator of the CDKN2A/CDKN2B gene cluster, which encodes the cyclin-dependent kinase inhibitors p16-INK4a and p15-INK4b. These proteins control cellular senescence — when cells stop dividing after accumulating damage. The 9p21.3 risk haplotype disrupts the ANRIL regulatory architecture, impairing the balance between proliferation and senescence in vascular smooth muscle cells and macrophages33 vascular smooth muscle cells and macrophages
Two cell types central to atherosclerotic plaque formation — VSMCs proliferate abnormally in atherogenesis, while macrophages drive inflammatory plaque instability.

ANRIL exists in two molecular forms with opposing effects. Linear ANRIL interacts with the transcription factor YY1 to upregulate pro-inflammatory cytokines44 upregulate pro-inflammatory cytokines
Including IL-6 and IL-8 — key mediators of systemic and vascular inflammation that promote atherosclerosis and periodontal tissue destruction. Circular ANRIL (circANRIL), by contrast, is protective: it binds the ribosomal assembly factor PES1, inducing nucleolar stress and p53-mediated apoptosis in vascular cells55 inducing nucleolar stress and p53-mediated apoptosis in vascular cells
circANRIL suppresses smooth muscle cell proliferation, a key atherogenic process; the ratio of circANRIL to linear ANRIL inversely correlates with coronary stenosis severity. Risk variants at this locus shift the balance toward linear ANRIL, tilting cells toward a pro-inflammatory, pro-proliferative state.

A critical functional finding is that oral bacterial challenge powerfully induces ANRIL. Stimulation of gingival fibroblasts with Porphyromonas gingivalis66 Porphyromonas gingivalis
The primary periodontal pathogen — a Gram-negative anaerobe that invades gingival tissue and triggers systemic inflammatory responses extending beyond the oral cavity increased CDKN2BAS expression 25-fold in human gingival fibroblasts and 4-fold in gingival epithelial cells. This demonstrates that C-allele carriers are not just constitutively primed for inflammatory signaling — they are also acutely vulnerable to oral bacterial infection as an ANRIL amplifier.

The Evidence

The initial 9p21.3 association with aggressive periodontitis and CHD was established by Schaefer et al. (2009)77 Schaefer et al. (2009)
Identification of a shared genetic susceptibility locus for coronary heart disease and periodontitis. PLoS Genetics., who identified the lead SNP rs1333048 with OR 1.99 (95% CI 1.33–2.94, p=6.9×10⁻⁴) for generalized aggressive periodontitis — a finding that simultaneously placed this locus as a shared causal region for two of the most prevalent inflammatory diseases globally.

rs1360590 was among three tag SNPs subsequently validated across Dutch and German cohorts (combined n=1,577)88 validated across Dutch and German cohorts (combined n=1,577)
Schaefer AS et al., J Med Genet 2011, aggressive and chronic periodontitis; validated after adjustment for smoking, gender, and diabetes for both aggressive and chronic periodontitis. An independent replication in 469 individuals99 469 individuals
Ernst et al. BMC Med Genet 2010 — independent case-control cohort with meta-analysis; confirmed 9p21.3 association with generalized aggressive periodontitis further confirmed the 9p21.3 periodontitis association using overlapping tag SNPs.

The mechanistic link to cardiovascular risk was elucidated through circANRIL biology: higher circANRIL expression is associated with the protective 9p21.3 haplotype, while risk variants show relatively less circANRIL and more linear ANRIL — translating to greater vascular inflammation and less apoptotic regulation in plaques. The circANRIL-to-linear ANRIL ratio inversely correlates with coronary artery stenosis severity in human patients1010 inversely correlates with coronary artery stenosis severity in human patients
Holdt LM et al. Nat Commun 2016; the ratio measured in circulating blood cells reflected disease state.

Practical Actions

For C-allele carriers, two distinct risk pathways require attention: the oral inflammatory gateway (periodontitis–ANRIL induction–systemic inflammation) and the direct vascular senescence pathway shared with the broader 9p21.3 haplotype.

The most genotype-specific intervention is rigorous periodontal hygiene and monitoring. Bacterial infection is a documented ANRIL amplifier — P. gingivalis specifically upregulates CDKN2BAS expression 25-fold in gingival tissue. This is not general dental advice; it is a genotype-specific inflammatory control strategy. C-allele carriers who develop periodontal disease are not merely risking tooth loss — they are activating an ANRIL-mediated systemic inflammatory cascade that shares a molecular pathway with coronary artery disease risk.

Cardiovascular monitoring with inflammatory biomarkers — specifically high-sensitivity CRP and lipid panels — is appropriate given the shared locus biology. The 9p21.3 haplotype that rs1360590 tags is the strongest common genetic signal for CAD in humans.

Interactions

rs1360590 is in linkage disequilibrium with other 9p21.3 risk variants including rs4977574 and rs1333049 (primary CAD-associated SNPs) and rs2811712 (ANRIL functional aging variant). Together these tag SNPs capture the broad 9p21.3 risk haplotype. Carriers of risk alleles across multiple 9p21.3 SNPs carry greater cumulative ANRIL dysregulation burden than any single variant predicts.

The periodontitis–CAD inflammatory link at this locus suggests a specific interaction pathway: oral bacterial dysbiosis activates ANRIL → elevated IL-6 and IL-8 → systemic pro-inflammatory state → accelerated atherosclerotic plaque instability. This mechanistic chain makes periodontal status a uniquely important modifiable variable for carriers of the 9p21.3 risk haplotype.

Genotype Interpretations

What each possible genotype means for this variant.

TT Low Genetic Risk Normal

Reference genotype — no elevated ANRIL-mediated inflammatory risk

You carry two copies of the T reference allele at rs1360590. About 29% of people of European descent share your TT genotype, though frequencies vary substantially by ancestry — TT is more common in Europeans and South Asians (~39–54%) than in African or East Asian populations (~5–9%). The TT genotype is not associated with elevated CDKN2BAS-driven susceptibility to periodontitis or the associated cardiovascular inflammatory pathway at this locus.

CT Elevated Inflammatory Risk Intermediate

One C risk allele — moderately elevated ANRIL locus inflammatory susceptibility

The 9p21.3 locus where rs1360590 sits encodes ANRIL, a long non-coding RNA that controls cellular senescence and inflammation in vascular and gingival tissue. The C risk allele shifts the balance between protective circANRIL (which induces apoptosis and suppresses vascular cell proliferation) and pro-inflammatory linear ANRIL (which upregulates IL-6 and IL-8).

A critical amplification mechanism: oral bacterial infection with Porphyromonas gingivalis induces CDKN2BAS expression 25-fold in gingival fibroblasts. This means periodontal disease is not only a comorbidity for CT carriers — it is a trigger that can substantially amplify ANRIL-mediated systemic inflammatory signaling. The shared 9p21.3 CAD-periodontitis locus suggests this amplification reaches vascular tissue through IL-6 and IL-8 pathways.

CC High Inflammatory Risk High Risk

Two C risk alleles — highest ANRIL locus inflammatory susceptibility

The 9p21.3 risk haplotype encodes ANRIL in a configuration that favors linear over circular isoforms. Linear ANRIL acts via YY1 to upregulate IL-6 and IL-8, while protective circANRIL suppresses vascular smooth muscle cell proliferation and induces apoptosis through PES1 binding and p53 activation. As a CC homozygote, both alleles carry the risk configuration — maximizing the shift toward inflammatory linear ANRIL in vascular and gingival tissue.

The bacterial amplification mechanism is particularly relevant for CC carriers: P. gingivalis infection induces CDKN2BAS expression 25-fold in gingival fibroblasts. This means untreated periodontal disease in CC carriers represents a sustained high-level ANRIL activation event, continuously driving elevated IL-6 and IL-8 into systemic circulation. Periodontal pathogens have been detected in atherosclerotic plaque, and systemic inflammation from periodontal disease is a documented independent cardiovascular risk factor.

The circANRIL:linear ANRIL ratio inversely correlates with coronary artery stenosis severity in human studies. CC carriers at this locus show the least favorable isoform balance, which translates to the greatest ANRIL-mediated atherosclerotic burden from this genetic signal.