Leopard Complex spotting (LP), the result of an incompletely dominant mutation in TRPM1, produces a collection of unique pigmentation patterns in several breeds of horse. While the LP mutation allows for expression of the various patterns, other loci are responsible for modification of the extent of patterning. Pedigree analysis of families segregating for high levels of patterning (80-100% white hair coat) indicated a single dominant gene (PATN1) as a major effect modifier for LP. Previous linkage analysis identified an 11 Mb region on ECA3p associated with PATN1. Whole transcriptome sequencing of pigmented and unpigmented skin samples from a LP/LP horse with PATN1 was performed to identify SNPs for fine mapping, as well as to examine the effects of PATN1 on the skin transcriptome. These two samples were compared to transcriptome data from pigmented and unpigmented skin in horses carrying the LP/LP or LP/lp genotype but not the PATN1 allele. The PATN1 samples contained 100 polymorphisms, three of which were non-synonymous, in the 11 Mb region that were not found in the non-PATN1 samples. In combination with additional SNPs from EquCab2.0, these PATN1-specific markers comprise a custom designed Sequenom assay to fine-map in an 192 individuals. Analysis of mapping and differential expression data is currently on-going.