We identified a total of 27 genome-wide significant loci, most of which are associated with both non-oral LP and OLP, but some loci are specific or have a stronger association to one subgrouping of LP (non-OLP: HLA-DQB1, CLEC16A; OLP: IFIH1, CASP8, CEP43, GRAF2, C12orf42, and ZFP36L1). This evidence concerns the gene C12orf42 and oral lichen planus.