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arXiv · 2609.17801

GIA: Germline-Informed Aging with AlphaGenome Finds Genetically Regulated CpGs

Sean Lim
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Abstract

Epigenetic clocks estimate age and aging-related phenotypes from DNA methylation at selected CpG sites, but the extent to which these inputs are influenced by germline genetic variation is unclear. Because methylation at many CpGs is genetically regulated, some between-person variation in clock estimates may reflect inherited genetic differences rather than aging-related change alone. Here we developed GIA (Germline-Informed Aging), a framework that maps CpGs selected from 13 published epigenetic clocks to blood methylation quantitative trait loci (meQTLs) and scores associated genetic variants with AlphaGenome. We show that clock CpGs were enriched for blood meQTLs relative to matched unused Illumina 450k probes (62.7% versus 39.6%; OR 2.57), across multiple clock families, suggesting that age-informative methylation sites are heavily influenced by germline genetic variation. Ranking by predicted chromatin effect isolated rs10190186, a cis-acting variant at FHL2 predicted to increase blood chromatin accessibility (ATAC +1.00; DNase +1.64) and FHL2 RNA (+0.30). This locus illustrates how inherited variation may shape methylation features repeatedly used by epigenetic clocks, motivating direct tests of whether such variants shift baseline clock estimates or longitudinal aging trajectories.

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Sean Lim. 2026-09-15. GIA: Germline-Informed Aging with AlphaGenome Finds Genetically Regulated CpGs. https://arxiv.org/abs/2609.17801

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