ype estimates revealed that rs5883T/rs9930761C predominantly share a haplotype consisting of the main wild-type ML 176 site alleles of all high scoring SNPs in the promoter/enhancer region. Adjusting for enhancer SNP rs247616, the HDL-C association strengthened for both rs9930761 and rs5883 . rs5883 consistently scored with greater significance than rs993 0761, the latter with,1% greater allele frequency, supporting the notion that rs5883 is necessary for exon 9 skipping, while rs9930761 is insufficient but may also be required. A strong interaction was observed for effects on HDL-C between rs247616 and the splicing SNPs, consistent rs5883/rs9930761 disrupts CETP mRNA splicing to yield the D9 splice variant Formation of the D9 splice variant in human livers was associated with two SNPs in high LD with each other, intron 8 and exon 9. rs5883 appears to be necessary for enhanced deletion of exon 9, judged by the relatively low D9 splice variant content in 
two livers heterozygous only for rs9930761 but not rs5883. However, all livers with high D9 splice variant content were heterozygous for both rs9930761 and rs5883, suggesting that both may be required to achieve effective skipping of exon 9. It is remarkable that the LD between the two SNPs is nearly complete even in African populations, residing predominantly in a single haplotype stretching over at least 20 kb, suggesting this represents an evolutionarily conserved haplotype. CETP Variants Affect Splicing, HDL and Mortality with their location on different haplotypes and mechanistically distinct effects. Considering the combined effects of rs247616 and rs5883 reveals that each minor allele appears to incrementally increase the HDL levels. In particular, carriers heterozygous for both SNPs have substantially higher HDL and carriers of only the main alleles . Homozygous carriers of the minor alleles of rs247616 were at 1.55 +/2 0.43 mmole/L. The groups with other allele combinations had much fewer subjects because of the negative LD between the two SNPs, and therefore could not be evaluated. Reported rs9930761 and rs5883 allele frequencies differ between ethnic groups, while maintaining high LD and r2, ranging from 0% in Asians, and 7.5% in Caucasians to 12.5% in Yorubans. In a Yoruban population, rs9930761 allele frequency was reported to be 4% in subjects with low HDL levels, PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/22189475 and 16% in those with high HDL, suggesting a large effect on HDL in this population. Taken all results together, we conclude that rs5883 and rs9930761 have strong effects on HDL-C, independent of the upstream promoter/ enhancer SNPs for which Taq1B typically has served as a surrogate if not suboptimal marker. splicing, and to identify the regulatory variant affecting transcription. Also, our results leave open whether rs5883/ rs9930761 are risk factors independent of statin use or affect MI risk under statin therapy in males, or both. Lastly, the important conclusion that male CAD patients with specific CETP genotypes may be at elevated risk of MI incidence or other outcomes has been drawn from a patient registry not specifically designed for this study, requiring independent replication. Materials and Methods Study samples Human liver tissues. Frozen human liver samples were obtained from The Cooperative Human Tissue Network, Midwestern and Western Divisions, which is funded by the National Cancer Institute. Other investigators may have received specimens from the same subjects. CHTN specimens are derived from material that
