m⁶AQTLs (m⁶A Quantitative Trait Loci) are genetic variants (e.g., SNPs) associated with variation in N⁶-methyladenosine (m⁶A) methylation levels on RNA. These associations may influence RNA stability, translation, and disease risk, but require experimental validation to establish causality. In m⁶AConquer, the association between m⁶A and SNPs were evaluated by FastQTL. The identified m⁶AQTL were functionally annotated by GWAS and ClinVar database.

1. Processed MeRIP-seq data as log-odds ratios with IP efficiency difference and GC content bias correction
2. Identified/corrected latent factors via singular value decomposition (covariate matrix for FastQTL)
3. Mapped cis-m6A QTLs restricting SNPs to gene bodies/promoters
4. Derived empirical p-values (β-distribution-adjusted FastQTL permutations; significance: empirical p < 0.05) for target m6A site identification
5. Calculated nominal p-value thresholds per target m6A site for QTL mapping
6. Computed linkage disequilibrium (PLINK v1.9.0) using 1000 Genomes Project genotypes for GWASCatalog and ClinVar
7. Variant annotation with diseases or traits