rs2016105 — ELK3 ELK3 TSH regulatory variant

Intronic regulatory variant in ELK3 influencing circulating TSH levels and hypothyroidism susceptibility — the rare A allele increases risk by approximately 28% per copy

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ELK3 and the Genetic Baseline of Thyroid Stimulating Hormone

Your thyroid is calibrated to a set point — a target circulating level of thyroid-stimulating hormone (TSH)11 thyroid-stimulating hormone (TSH)
TSH is produced by the pituitary gland to signal the thyroid to produce T3 and T4; it rises when thyroid output is low and falls when it is adequate that your hypothalamic-pituitary-thyroid axis defends continuously. That set point is not the same for everyone: a substantial fraction of variation in TSH levels across individuals is genetically determined, and rs2016105 in the ELK3 gene is one of the contributors. Carriers of the rare A allele have a modestly elevated tendency toward hypothyroidism — not because their thyroid gland is diseased, but because a transcriptional regulator that fine-tunes thyroid signaling operates differently in their cells.

The Mechanism

ELK322 ELK3
ETS transcription factor ELK3; also known as NET, SAP-2, or ERP; a member of the ETS domain family recruited by serum response factor to bind serum response elements in gene promoters encodes an ETS-domain transcription factor that alternates between repressor and activator modes depending on the cellular signaling context — specifically, it suppresses transcription in the absence of Ras activity and switches to activation when Ras signaling is present. This Ras-dependent toggle positions ELK3 at the intersection of growth factor signaling and gene expression in multiple secretory cell types, including thyroid follicular and parafollicular cells.

The rs2016105 variant sits within an intron of ELK3 on chromosome 12q23.1. Intronic variants at this position can influence gene expression by disrupting or creating regulatory elements — splicing enhancers, intronic enhancers, or RNA secondary structures — without changing the protein sequence itself. The precise molecular mechanism by which this variant modulates ELK3 activity in thyroid-relevant tissues has not been characterized at functional resolution, but the strength and consistency of its GWAS signal across multiple large cohorts establishes that the variant meaningfully alters thyroid function at the population level.

In the context of thyroid endocrinology, ELK3 participates in the Ras-Raf-1-ELK3 signaling cascade33 Ras-Raf-1-ELK3 signaling cascade
Demonstrated in medullary thyroid carcinoma cells by Ma et al. 2022: RREB1 regulates C-cell differentiation and calcitonin secretion via this pathway that governs cell differentiation and hormone secretion in thyroid C cells. Normal ELK3 activity in these cells helps calibrate the output of calcitonin and, indirectly, the pituitary-thyroid axis set point.

The Evidence

The association between rs2016105 and hypothyroidism was identified in the VA Million Veteran Program GWAS44 VA Million Veteran Program GWAS
Verma A et al. Science 2024 — diversity and scale analysis of 2,068 traits in 635,969 U.S. veterans across four ancestry groups, one of the most ethnically diverse GWAS cohorts ever assembled. The G allele (carried by ~98% of the population) showed a protective effect of approximately β = −0.25 (p = 3×10-26 in the strongest association), meaning the rare A allele confers approximately 28% increased odds of hypothyroidism per copy (OR ≈ 1.28, derived from the logistic beta coefficient). Four independent association signals at this locus were identified across ancestry-stratified analyses, with p-values consistently between 2×10-16 and 3×10-26.

The 2025 Nature Genetics hypothyroidism mega-meta-analysis55 2025 Nature Genetics hypothyroidism mega-meta-analysis
Rand SA, Ahlberg G et al. GWAS and polygenic risk prediction of hypothyroidism; 113,393 cases, 1,065,268 controls; December 2025 identified 350 loci, including 179 previously unreported, with 29 linked through TSH. This study also analyzed 482,873 individuals for circulating TSH levels directly, establishing that many hypothyroidism loci alter the TSH set point before clinical disease develops. ELK3 is among the loci identified in this trans-ethnic effort, further corroborating the MVP finding.

The A allele is notably absent in East Asian populations (frequency ~0%) and rare in African populations (~0.6%), with the highest frequency in Europeans (~2.7%). This ancestry specificity means the variant is almost exclusively clinically relevant for individuals of European descent.

Practical Implications

For AG heterozygotes — the relevant genotype for 95% of A-allele carriers given the rarity of AA homozygosity — the absolute risk increase for hypothyroidism is modest (~28% relative). Hypothyroidism is common (lifetime prevalence ~5-10% in women, ~2-3% in men in European populations), so this translates to a shift from roughly 7% baseline lifetime risk to approximately 9% for AG carriers — an additional ~2 percentage points in absolute terms.

The clinical value lies primarily in interpretation: if you carry the A allele and have TSH levels at the upper end of the reference range, this genotype provides biological context supporting earlier treatment consideration. It also argues for periodic TSH monitoring rather than a single-timepoint assessment, since individuals with this variant trend toward hypothyroidism rather than against it.

Interactions

ELK3 sits in the thyroid-function gene network alongside FOXE1 (rs965513), DIO2 (rs225014), and DIO1 (rs11206244). Each of these influences thyroid hormone set point through different mechanisms — transcriptional regulation, receptor sensitivity, and T4-to-T3 conversion respectively. A carrier with multiple thyroid-axis risk alleles across these loci may have a compound shift in TSH baseline that individual SNP effects underestimate. No formal compound analysis has been published for ELK3 combined with these variants, but the convergent biology makes interaction effects plausible.

Genotype Interpretations

What each possible genotype means for this variant.

GG Typical TSH Baseline Normal

Common protective genotype — no increased hypothyroidism risk from this locus

You carry two copies of the G allele, which is the reference allele at this locus and is carried by approximately 96% of people globally. This genotype is not associated with increased hypothyroidism risk from rs2016105. Your ELK3-mediated thyroid regulatory signaling at this locus is expected to operate within the typical range for the general population.

AG Elevated TSH Risk Intermediate

One copy of the rare A allele — approximately 28% increased odds of hypothyroidism

Heterozygous AG carriers have one functional G allele and one A allele that modulates ELK3 expression or splicing in thyroid-relevant tissues. The additive inheritance pattern means one A copy confers roughly half the risk effect of two A copies. The finding was replicated across multiple ancestry groups in the VA Million Veteran Program and further supported by the 2025 Nature Genetics hypothyroidism meta-analysis (113,393 cases). The A allele is absent in East Asian populations and very rare in African populations (~0.6%), making this primarily a European-ancestry relevant finding.

Because the A allele is rare (~2% globally) and the effect size per allele is modest, AG heterozygotes represent the overwhelmingly most common A-allele carrier state. AA homozygosity occurs in only ~0.04% of the population and has not been characterized separately in published studies.

AA High TSH Risk High Risk

Two copies of the rare A allele — substantially elevated hypothyroidism susceptibility

AA homozygosity at rs2016105 represents the full dose of A-allele effect on ELK3 intronic regulation. Under an additive model, the risk is approximately the square of the per-allele OR relative to GG (i.e., OR² ≈ 1.64 for hypothyroidism). The extreme rarity of this genotype (~0.04% globally, ~0.07% in Europeans) means it has not appeared with sufficient frequency in any single published GWAS to be characterized independently — the per-allele estimates from AG carriers in large cohorts are extrapolated. Absolute lifetime hypothyroidism risk for AA carriers would be estimated at approximately 11-12% in women of European ancestry (vs ~7% baseline), with lower absolute risk in men. Selenium adequacy and vigilance for early hypothyroidism symptoms are the primary practical considerations.