Expressive

rs11762896 (CHRM2): Vaginal Bacteriome Variant

Key takeaways

  • This variant appeared in a genome-wide study of vaginal bacterial communities in 359 pregnant women, as one of 72 genome-wide significant associations.
  • The alternate allele reduces CHRM2 expression in cultured fibroblasts, based on GTEx data from 953 donors.
  • Two additional genes show reduced expression in colon tissue, though what that means biologically is not yet established.
  • Evidence is early-stage: a single small cohort study with no independent replication reported in the available sources.

Key takeaways

  • This variant was identified in a genome-wide association study of vaginal bacterial traits in 359 pregnant women, as one of 72 genome-wide significant associations (P < 5 x 10^-8).
  • The alternate allele reduces CHRM2 (cholinergic receptor muscarinic 2) expression in cultured fibroblasts, based on GTEx eQTL data from 953 donors.
  • Two additional genes show reduced expression in colon tissue, though the biological significance is not yet established.
  • Evidence is early-stage: a single small cohort study with no independent replication reported in the available sources.
  • No lifestyle or drug-response data are on file for this variant.

What the research says A genome-wide association study (GWAS) in 359 pregnant Chinese women identified 72 genetic variant-vaginal bacterial trait (VBT) associations at genome-wide significance (P < 5 x 10^-8); most associated variants had a minor allele frequency below 0.05, and the study reported a genomic inflation factor below 1.1, indicating acceptable control for population stratification. The CHRM2 - PTN locus was identified in that study among those 72 associations, though the specific VBT linked to this variant is not described in the available study text. GTEx eQTL (expression quantitative trait locus) data from 953 donors independently links the alternate allele to reduced CHRM2 expression in cultured fibroblasts GTEx Portal.

Reported associations

  • Vaginal bacterial traits (pregnant women): Listed among 72 genome-wide significant variant-VBT associations (P < 5 x 10^-8) in a cohort of 359 pregnant women whose bacterial communities were characterized into five community state types (CSTs) via 16S rRNA sequencing; the specific CST or bacterial taxon linked to rs11762896 is not described in the available study text. (Fan W et al., mSystems 2021)

Evidence quality The vaginal bacteriome association comes from a single cohort of 359 pregnant Chinese women, which is small by current GWAS standards. The study reports a genomic inflation factor below 1.1, indicating acceptable statistical control for population stratification (a form of confounding in genetic studies). Most of the 72 genome-wide significant variants had low minor allele frequencies (below 0.05), which can elevate false-positive rates in small samples. No replication cohort is described in the provided sources, and no PMID was included in the study metadata, limiting independent verification. The GTEx eQTL associations are based on 953 donors; these data describe changes in gene activity levels across tissues and do not constitute evidence of disease association. Overall, evidence for this locus is early-stage and should be interpreted cautiously. (Fan W et al., mSystems 2021; GTEx Portal)

Tissue-specific expression effects

  • CHRM2: The alternate allele is associated with reduced expression in cultured fibroblasts GTEx Portal
  • KRT8P51: The alternate allele is associated with reduced expression in sigmoid colon GTEx Portal
  • ENSG00000234352: The alternate allele is associated with reduced expression of this uncharacterized locus in transverse colon GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is the CHRM2 gene?

CHRM2 encodes the muscarinic acetylcholine receptor M2, a protein involved in cholinergic signaling. GTEx data link the alternate allele at rs11762896 to reduced CHRM2 expression in cultured fibroblasts, though the functional consequences of this change are not yet established from the available sources.

Is rs11762896 linked to vaginal health or pregnancy complications?

A genome-wide association study of 359 pregnant women listed this variant among 72 associations with vaginal bacterial traits, but the specific bacterial community trait linked to rs11762896 is not described in the available study text. The evidence is preliminary and has not been independently replicated in the available sources.

What tissues does rs11762896 affect gene expression in?

According to GTEx data from 953 donors, the alternate allele is associated with reduced expression of CHRM2 in cultured fibroblasts, KRT8P51 in sigmoid colon, and an uncharacterized gene (ENSG00000234352) in transverse colon. These are expression-level effects and do not directly indicate disease risk.

How reliable is the research on rs11762896?

The vaginal bacteriome association comes from one small cohort (n=359) with no independent replication reported in the available sources. The GTEx eQTL data are based on 953 donors and carry stronger statistical support, but expression effects describe gene regulation rather than clinical outcomes. Overall, the evidence is early-stage.