rs7521902 — WNT4

Intronic variant near WNT4 on chromosome 1p36.12 associated in multiple GWAS with elevated risk of endometriosis, particularly moderate-to-severe (stage III/IV) disease, and with uterine fibroid susceptibility through disrupted Wnt signaling in the endometrium.

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WNT4 rs7521902 — When a Signaling Gene Shapes Endometriosis Risk

WNT4 encodes one of the Wnt family of secreted signaling proteins, a group essential for embryonic development of the female reproductive tract and for the monthly remodeling of the uterine lining. The protein coordinates the formation of Müllerian duct structures — the precursors to the uterus, fallopian tubes, and cervix — and continues to regulate endometrial stromal cell behavior throughout reproductive life. A common variant approximately 21 kilobases downstream of the WNT4 gene, rs7521902, has emerged from multiple large genome-wide association studies as one of the most replicated genetic risk factors for endometriosis, particularly moderate-to-severe disease.

The Mechanism

rs7521902 sits within an intronic region of an uncharacterized neighboring locus (LOC105376850) in the 1p36.12 region and does not directly alter the WNT4 protein sequence. Its functional effect is regulatory: variants in tight linkage disequilibrium11 linkage disequilibrium
LD: the tendency for nearby genetic variants to be inherited together with rs7521902 — particularly rs3820282, located in WNT4 intron 1 — have been shown to introduce a high-affinity estrogen receptor alpha binding site22 estrogen receptor alpha binding site
ERE: an estrogen response element, a DNA sequence where the estrogen receptor attaches to regulate gene transcription. The result is upregulated WNT4 transcription in endometrial stromal cells following the preovulatory estrogen peak, with a 1.5–3.3 fold increase in mouse transgenic models.

This elevated WNT4 expression in stromal cells activates non-canonical Wnt signaling33 non-canonical Wnt signaling
Wnt pathways that do not proceed through β-catenin; involved in cell polarity and invasive behavior and produces a uterine environment that is more permissive to cellular invasion. The same mechanism that may improve embryo implantation — by increasing stromal receptivity — appears to simultaneously increase the permissiveness of the endometrium to invasion by ectopic endometriotic tissue. This antagonistic pleiotropy may explain why the risk allele has been maintained at appreciable frequency despite its disease association.

WNT4 also acts downstream of BMP2 to regulate decidualization44 decidualization
the monthly transformation of endometrial stromal cells into specialized secretory cells in preparation for embryo implantation, a process frequently disrupted in endometriosis. The IHH–COUPTFII–WNT4 pathway coordinates progesterone response in the endometrium; its disruption contributes to the progesterone resistance characteristic of endometriotic tissue. In uterine fibroids, MED12 mutations — present in the majority of fibroids — directly upregulate WNT4 expression, driving cell proliferation through β-catenin signaling and mTOR activation.

The Evidence

The first genome-wide significant association between rs7521902 and endometriosis was reported in a combined Japanese–European meta-analysis55 combined Japanese–European meta-analysis
Nyholt et al. 2012, Nature Genetics (P=4.2×10⁻⁸, OR=1.19, 95% CI 1.12–1.27). A subsequent meta-analysis of eight GWAS datasets66 meta-analysis of eight GWAS datasets
Rahmioglu et al. 2014, Human Reproduction Update; PMC4132588 in 11,506 cases and 32,678 controls confirmed the association at P=1.8×10⁻¹⁵ (OR=1.18, 95% CI 1.13–1.23). Critically, the effect size strengthened for stage III/IV disease (OR=1.23, 95% CI 1.17–1.28, P=2.7×10⁻¹⁷), indicating the variant is particularly relevant to moderate and severe endometriosis, the phenotypes most likely to cause chronic pain and fertility impairment. Eight of nine genome-wide significant loci in that meta-analysis showed consistently stronger effects in stage III/IV subgroup analyses.

An Italian replication study77 Italian replication study
Pagliardini et al. J Med Genet 2013 of 305 surgically confirmed cases and 2,710 controls confirmed the association (P=5.6×10⁻³) and identified an epistatic interaction between rs7521902 and rs1250248 (OR=1.56, P=0.012). A 2024 systematic review and meta-analysis88 2024 systematic review and meta-analysis
PMID 38354602 of 10 case-control studies found the CC (homozygous reference) genotype protective: pooled OR=0.86 (95% CI 0.76–0.99). Not all populations replicate the association: a Brazilian cohort of infertile women99 Brazilian cohort of infertile women
Mafra et al. J Assist Reprod Genet 2015 found no significant association for rs7521902 (p=0.18), though rs16826658 was significant in that cohort (OR=1.44). A Chinese Han cohort similarly did not replicate rs7521902 but found rs2235529 significant for advanced disease. These population-specific results likely reflect differences in linkage disequilibrium structure around the WNT4 locus rather than absence of effect.

The WNT4 locus also shows pleiotropic association with uterine leiomyomas1010 uterine leiomyomas
fibroids; benign smooth muscle tumors of the uterus (OR=1.12–1.19), bone mineral density, and pelvic organ prolapse — consistent with WNT4's broad role in gynecological tissue maintenance.

Practical Actions

For women carrying one or two copies of the A allele, the most actionable implication is heightened awareness of endometriosis symptoms: cyclic pelvic pain, deep dyspareunia, dysmenorrhea, and unexplained infertility. Earlier investigation via gynecological ultrasound (for ovarian endometriomas and fibroids) or laparoscopy is appropriate when symptoms are present rather than waiting for symptoms to become severe. Symptom severity does not reliably correlate with disease stage, so evaluation should not depend on pain intensity alone.

No evidence supports a supplement or dietary intervention that specifically modifies WNT4 signaling in the endometrium. Progestin-based hormonal therapies are the mainstay of endometriosis management and address the progesterone-resistance pathway through which WNT4 dysregulation is thought to act — this is a medical decision to be made with a gynecologist.

Interactions

The WNT4 locus displays an epistatic interaction with rs1250248 (OR=1.56 for the interaction term; Pagliardini et al. 2013, PMID 23142796). The functional variant rs3820282, in strong LD with rs7521902 in European populations, appears to be a more direct molecular mediator of WNT4 expression change, and warrants inclusion in any compound analysis. rs16826658, also in the WNT4 region, was independently associated with endometriosis in some populations (OR=1.44 in the Brazilian cohort). Given that these variants all tag the same ~100–150 kb haplotype block on 1p36.12, users carrying risk alleles at multiple WNT4-region SNPs may reflect greater cumulative haplotype risk, though formal compound action data for this specific combination are not yet established in the literature.

Genotype Interpretations

What each possible genotype means for this variant.

CC Common Genotype Normal

Common genotype — typical endometriosis risk at this locus

The CC genotype was used as the reference group in the major GWAS meta-analyses (Nyholt et al. 2012, PMID 23104006; Rahmioglu et al. 2014, PMC4132588). No specific action is indicated based on this variant alone. Endometriosis has a complex multifactorial basis; other genetic and environmental factors remain relevant to overall risk regardless of rs7521902 status. Related WNT4-region variants such as rs16826658 and rs3820282 may capture additional risk not reflected in this single SNP result.

AC One Risk Allele Intermediate

One copy of the risk allele — modestly elevated endometriosis risk

The large meta-analysis by Rahmioglu et al. 2014 (PMC4132588) found the A allele effect under an additive model — each additional copy of A increases endometriosis risk by approximately 18–23%. For heterozygous AC carriers, this represents a partial elevation in risk. Population heterogeneity is important: some cohorts (Brazilian, Chinese Han) did not find rs7521902 significant, likely due to differences in LD structure with the functionally relevant variant rs3820282. In European populations, where LD between rs7521902 and rs3820282 is stronger, the association may be more relevant. The WNT4 locus is also associated with uterine fibroid susceptibility (OR 1.12–1.19), so gynecological evaluation may be informative for both endometriosis and fibroid surveillance.

AA Two Risk Alleles High Risk

Two copies of the risk allele — elevated endometriosis risk, especially severe disease

The large Rahmioglu et al. 2014 meta-analysis (PMC4132588, 11,506 cases and 32,678 controls) found rs7521902 significant at P=1.8×10⁻¹⁵ overall, with progressively stronger effects in stage III/IV disease (OR=1.23, 95% CI 1.17–1.28, P=2.7×10⁻¹⁷ when restricted to moderate/severe disease only). AA homozygotes, combining two additive risk copies, would be expected to fall at the upper end of genetic susceptibility at this locus. Functionally, the A allele is in linkage disequilibrium with rs3820282, which increases estrogen-receptor-alpha binding and drives elevated WNT4 expression in endometrial stromal cells during the estrogen peak — priming the endometrium for greater stromal invasibility. This mechanism is consistent with the biology of retrograde endometrial tissue implantation and is thought to contribute to the progesterone resistance seen in endometriotic lesions via disruption of the IHH–COUPTFII–WNT4 decidualization pathway.

The WNT4 1p36.12 locus is also a genome-wide significant risk locus for uterine leiomyomas (fibroids), with an odds ratio of 1.12–1.19 per risk allele. AA homozygotes may therefore face elevated risk at both phenotypes, though the fibroid association has not been independently quantified for the homozygous state.

Population heterogeneity should be noted: the association is most robustly demonstrated in European and Japanese populations. Some case-control studies in Brazilian and Chinese populations did not replicate rs7521902 specifically, attributing this to differing LD structure with the causal variant. In East Asian populations the A allele is the major allele (frequency ~50%), which may affect how population-based risk estimates translate to individuals.