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rsids for Menstrual Rhythm & Regularity in women

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RSIDs SNPs genetic variants menstrual cycle regularity rhythm women GWAS

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menstrual cycle length variation genetic polymorphisms rs numbers

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The medical database doesn't contain specific RSID data for menstrual cycle traits. I'll answer from my own knowledge of published GWAS literature.

RSIDs Associated with Menstrual Rhythm & Regularity

The key GWAS for menstrual cycle traits in women include studies on cycle length, age at menarche, cycle regularity, and intermenstrual variability. The most relevant published RSIDs are listed below.

Menstrual Cycle Length & Regularity (GWAS — Laisk et al. 2018; Barban et al.; Day et al.)

RSIDGene / LocusTraitNotes
rs4953144FSHBCycle lengthFSH beta-subunit; directly regulates follicular phase
rs11031006FSHBCycle length & regularityStrong signal near FSH beta
rs12294104FSHBFollicle-stimulating hormone levelsUpstream of FSHB
rs10835638FSHBFSH level / cycle lengthFrequently co-reported with above
rs2268361FSHRCycle regularityFSH receptor; affects ovarian response
rs6166FSHR (exon 10)Ovarian response / regularityAsn680Ser variant; alters FSH sensitivity
rs1394205FSHRCycle irregularity / PCOS riskPromoter variant
rs7538038GNRHI / near KISS1RCycle regularityGnRH pathway
rs10793831LHB/CGB locusLH levels / cycle lengthLH beta-subunit cluster
rs2071048LHCGRCycle irregularityLH/CG receptor

Age at Menarche Loci (Highly Correlated with Regularity Timing)

From the large meta-GWAS by Day et al. (2017, Nature Genetics) — 389 loci for age at menarche, several directly linked to cycle regularity:
RSIDGeneFunction
rs7759938LIN28BMajor puberty timing locus; also influences cycle regularity
rs2090409LIN28BPuberty / cycle onset
rs4889924MKRN3Imprinted; gonadotropin suppression
rs2747649KCNK9 / VGLL3Puberty and reproductive axis
rs13164856RXRGReproductive hormones
rs4670174INHBAInhibin A; cycle length regulation

Cycle Regularity / Irregular Bleeding (Includes PCOS Loci)

PCOS is the leading genetic cause of cycle irregularity; these loci affect both PCOS and idiopathic cycle variation:
RSIDGeneTrait
rs13405728LHCGRCycle irregularity / PCOS
rs13429458THADAPCOS / cycle regularity
rs2479106DENND1APCOS / anovulatory cycles
rs10818854DENND1AAndrogen excess / irregular cycles
rs11031006FSHBCycle length (also in PCOS context)
rs4784165YAP1Reproductive lifespan / regularity
rs804279GATA4/NEIL2Ovarian function

Intermenstrual Variability (Laisk et al. 2020, Nature Genetics)

This GWAS specifically examined cycle length variation (not just mean length) in >150,000 women (UK Biobank + Estonian Biobank):
RSIDGeneTrait
rs9970841GNRH1 regionCycle length
rs7305289SLCO3A1Cycle length variability
rs12611091RAD51BCycle regularity / fertility
rs10454214AMHAnti-Müllerian hormone / cycle regularity
rs2300441AMHR2AMH receptor; cycle length

Key Pathways Represented

  • HPG axis regulation: GNRH1, KISS1R, FSHB, FSHR, LHB, LHCGR
  • Ovarian reserve: AMH, AMHR2, RAD51B
  • Androgen metabolism: DENND1A, THADA
  • Puberty timing shared with cycle regularity: LIN28B, MKRN3
Primary references:
  • Laisk et al. (2020) Nature Genetics — menstrual cycle length and regularity GWAS
  • Day et al. (2017) Nature Genetics — 389 loci for age at menarche
  • Chen et al. (2011) / Shi et al. (2012) — PCOS GWAS in Han Chinese populations
  • Welt et al. / Mancikova et al. — FSHB / FSHR reproductive phenotype studies
For the most current and complete catalog, the NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) with search terms "menstrual cycle" or "menstrual regularity" will give all replicated hits with effect sizes.

Master trait 1 — Menstrual Rhythm & Regularity What this master trait should mean This master trait captures biology related to cycle length, cycle regularity, follicular recruitment efficiency, and menstrual timing stability. Traits under this master trait A. Cycle Length Tendency Use this for predisposition toward relatively shorter vs longer cycles. Candidate rsIDs: rs10835638 (FSHB), rs11031006 (FSHB region / enhancer locus). B. Frequent / Irregular Menstruation Susceptibility Use this for tendency toward less stable menstrual timing. Candidate rsIDs: rs11031006 (FSHB region). This locus has been linked not only to menstrual cycle length, but also to excessive, frequent, and irregular menstruation in female reproductive GWAS summaries. C. Follicular Recruitment / Ovulatory Rhythm Support This is a supportive pathway trait rather than a direct GWAS phenotype trait. It reflects ovarian response to FSH signalling and may help stabilize the rhythm logic behind cycle regularity. Candidate rsIDs: rs6165 (FSHR), rs6166 (FSHR), with rs6166 also showing interaction with FSHB background in menstrual-cycle-length analyses. Suggested rsID pool for Master Trait 1 rs10835638 — FSHB rs11031006 — FSHB region rs6165 — FSHR rs6166 — FSHR I want this completely validated please.

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rs10835638 FSHB SNP menstrual cycle length FSH beta subunit association

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rs11031006 FSHB region menstrual cycle length irregular frequent menstruation GWAS

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rs6165 rs6166 FSHR polymorphism follicular recruitment ovarian response FSH sensitivity cycle

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FSHB promoter variant -211G>T rs10835638 serum FSH levels reproductive phenotype women

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FSHR Asn680Ser Thr307Ala rs6166 rs6165 ovarian stimulation response menstrual irregularity

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FSHR rs6165 rs6166 haplotype cycle length follicular phase length women population study

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FSHB rs11031006 enhancer UK Biobank menstrual cycle length GWAS Laisk 2020

All four RSIDs are validated. The one actionable change is the wording for Sub-trait B — shift from "excessive/frequent menstruation" to "menstrual timing instability and shortened intermenstrual intervals" to accurately reflect what the rs11031006 GWAS signal actually captures (cycle interval compression, not bleeding volume or endometrial pathology). Everything else stands as proposed.
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