Visual backward masking (BM) deficits are often proposed to be trait markers for schizophrenia, revealing the genetic underpinnings of the disease. Here, we show that masking deficits in the shine-through effect are associated with polymorphisms in the nicotinic receptor 7 subunit gene (CHRNA7). In the shine-through effect, two vertical bars are slightly offset in the horizontal direction. Observers indicate this offset direction. When the vernier is followed by a grating, vernier offset discrimination deteriorates for controls but much more strongly for the patients. We found these masking deficits of the patients to be strongly correlated with mutations on the rs904952 SNP and a related haplotype. The results further support the significance of CHRNA7 as an important candidate gene for schizophrenia. We propose that because of the deficient cholinergic system, the neural activity of the vernier briefly presented cannot be enhanced and is vulnerable to masking.