By mining lncRNA-SNPs in high-risk genes for MG, we demonstrated the four most significant potential mechanisms for lncRNA-SNP-gene-pathway effects: as follows: rs138852863/EPB41L4A-AS1 → VEGFA → hsa04010 (MAPK signaling pathway); rs2516515/HCP5 → RAF1 → hsa05205 (proteoglycans in cancer); rs17177030/MCM3AP-AS1 → BCL2 → hsa01521 (EGFR tyrosine kinase inhibitor resistance)/hsa01522 (Endocrine resistance); rs2476391/ DLEU2 → ESR1 → hsa05205 (proteoglycans in cancer). This evidence concerns the gene MCM3AP and myasthenia gravis.