Wilson’s disease (WD) is a rare autosomal recessive copper metabolism disorder that primarily affects hepatic and neuronal tissues. The condition is caused by mutations in the ATP7B gene. Our group conducted extensive molecular genetic studies, identifying 13 clinically diagnosed Indian WD patients lacking the coding variant of ATP7B and 17 patients with a single mutated allele. We hypothesize that in these patients, unidentified mutations may reside in cis-regulatory elements of ATP7B or that a WD-like phenotype results from the cumulative effect of hypofunctional alleles of other key genes in the copper metabolism pathway. In this study, we employed an established bioinformatic pipeline to identify and screen cis-regulatory elements of ATP7B in WD patients with missing heritability through polymerase chain reaction sequencing. Although no pathogenic variants were identified, our analysis revealed two heterozygous single nucleotide polymorphisms (rs2181891 and rs747781) in two patients. Notably, rs2181891 showed strong regulatory potential with a RegulomeDB score of 1d. The genotype-specific expression profile for rs2181891 revealed it to be an expression quantitative trait locus for ATP7B in the cerebellum. In addition, the Genotype-Tissue Expression portal data suggest that the T allele of rs2181891 is associated with higher expression of ATP7B, making it unlikely to contribute to the WD phenotype. This novel study is the first to identify and screen ATP7B cis-regulatory elements in Indian WD patients with missing heritability.