Open Access Open Badges Research

Single nucleotide polymorphisms in CETP, SLC46A1, SLC19A1, CD36, BCMO1, APOA5, and ABCA1 are significant predictors of plasma HDL in healthy adults

Andrew J Clifford1*, Gonzalo Rincon2, Janel E Owens3, Juan F Medrano2, Alanna J Moshfegh4, David J Baer5 and Janet A Novotny5

Author Affiliations

1 Department of Nutrition, University of California, One Shields Avenue, Davis, CA 95616, USA

2 Department of Animal Science, University of California, One Shields Avenue, Davis, CA 95616, USA

3 Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA

4 Food Surveys Research Group, US Department of Agriculture, Beltsville, MD 20705, USA

5 US Department of Agriculture, Food Components and Health Laboratory, Beltsville, MD 20705, USA

For all author emails, please log on.

Lipids in Health and Disease 2013, 12:66  doi:10.1186/1476-511X-12-66

Published: 8 May 2013



In a marker-trait association study we estimated the statistical significance of 65 single nucleotide polymorphisms (SNP) in 23 candidate genes on HDL levels of two independent Caucasian populations. Each population consisted of men and women and their HDL levels were adjusted for gender and body weight. We used a linear regression model. Selected genes corresponded to folate metabolism, vitamins B-12, A, and E, and cholesterol pathways or lipid metabolism.


Extracted DNA from both the Sacramento and Beltsville populations was analyzed using an allele discrimination assay with a MALDI-TOF mass spectrometry platform. The adjusted phenotype, y, was HDL levels adjusted for gender and body weight only statistical analyses were performed using the genotype association and regression modules from the SNP Variation Suite v7.


Statistically significant SNP (where P values were adjusted for false discovery rate) included: CETP (rs7499892 and rs5882); SLC46A1 (rs37514694; rs739439); SLC19A1 (rs3788199); CD36 (rs3211956); BCMO1 (rs6564851), APOA5 (rs662799), and ABCA1 (rs4149267). Many prior association trends of the SNP with HDL were replicated in our cross-validation study. Significantly, the association of SNP in folate transporters (SLC46A1 rs37514694 and rs739439; SLC19A1 rs3788199) with HDL was identified in our study.


Given recent literature on the role of niacin in the biogenesis of HDL, focus on status and metabolism of B-vitamins and metabolites of eccentric cleavage of β-carotene with lipid metabolism is exciting for future study.

Single nucleotide polymorphism; HDL; Folate transporter; Cholesterol