Evidence linking mutations in ATP-binding-cassette transporter gene 1 (ABC1) to Tangier disease suggests it functions in the active transport of free cholesterol out of cells. Since its mRNA level is regulated in response to cellular cholesterol stores it is of interest to explore its promoter response elements, and to investigate polymorphisms for their contributions to the prevalence of low levels of HDL in the population that promotes premature coronary heart disease. Investigation of the 5' end of the gene by 5' RACE analysis revealed 455 nucleotides additional to published sequences, and predicts another 60 amino acid N-terminal residues, resulting in a 2261-residue protein. Protein sequence analysis predicts a membrane-spanning region and possible signal peptide. The 5' flanking region was located by a Human Research Project BLAST search. This region contains regulatory elements that potentially control ABC1 gene expression. In addition to numerous SP1 binding sites there are four putative sterol regulatory elements (SREs). Our studies uncovered three single nucleotide substitution polymorphisms, one in the promoter region and two in the 5' untranslated region (5'UTR), plus an insertion/deletion polymorphism,