<p>Epithelial-mesenchymal transition (EMT) is critical in tumor progression and metastasis, with long non-coding RNAs (lncRNAs) as key regulatory elements. This study explored the association between genetic variants in EMT-related lncRNAs and colorectal cancer (CRC) risk in a Chinese population. A case-control study was conducted involving 1,888 untreated CRC cases and 1,888 cancer-free controls. Multivariate logistic regression models were used to assess effects of SNPs on CRC risk, while expression quantitative trait loci (eQTL) analysis used data from the Genotype-Tissue Expression (GTEx) project, and gene expression was evaluated using The Cancer Genome Atlas (TCGA) database. Four functionally relevant SNPs (AC106786.1 rs76180806, rs2277930, LINC00578 rs28711160, and RP1-193H18.2 rs17823238) were significantly associated with CRC risk (OR = 1.52, 95% CI = 1.26–1.83, <i>P</i> = 1.57 × 10 ^− 2; OR = 1.34, 95% CI = 1.15–1.57, <i>P</i> = 3.30 × 10 ^− 2; OR = 1.21, 95% CI = 1.09–1.33, <i>P</i> = 3.30 × 10 ^− 2; OR = 0.83, 95% CI = 0.75–0.92, <i>P</i> = 3.30 × 10 ^− 2). Notably, rs28711160 exhibited a significant eQTL effect on LINC00578 expression (<i>P</i> = 2.09 × 10^− 5), and LINC00578 expression levels correlated strongly with CRC risk. These findings indicate that genetic variants in EMT-related lncRNAs (AC106786.1, LINC00578, RP1-193H18.2) may contribute to CRC susceptibility and could serve as candidate biomarkers, providing new insights into the genetic architecture of CRC.</p> Graphical Abstract <p></p>