The sine oculis homeobox homolog 4 (SIX4) gene belongs to the SIX gene family,which plays a critical role in muscle regeneration and early stages of ontogeny.This study aimed to detect genetic variations of bovine SIX4 genes in Qinchuan cattle,and to evaluate the effect of these variations on economically important body measurement traits.Quantitative real-time PCR (qPCR) results showed that the mRNA expression levels of SIX4 gene were found significantly highest in longissimus thoracis tissue and individual before attaining the stage of physiological maturity.Using sequencing technology on a total of 428 Qinchuan cattle,seven single nucleotide polymorphisms (SNPs) were identified in the promoter region of SIX4,and seven haplotypes representing 18 potential transcription factor compositions of polymorphic potential cis-acting elements.Association analysis indicated that the H3-H3 diplotype performed greater withers height,chest depth,chest circumference,back fat thickness and ultrasound loin muscle area (P < 0.05) than H5-H6,which were consistent with the promoter activity of Hap3 haplotype was higher than the Hap5 and Hap6 haplotype in vitro.These potential transcription factor information and combined genotypes H3-H3 of the SIX4 gene can be used as a molecular marker for selection of economic traits in Qinchuan cattle.