Impact of Genetic Variants in Human Scavenger Receptor Class B Type I (SCARB1) on Plasma Lipid TraitsCLINICAL PERSPECTIVE by Vipavee Niemsiri, Xingbin.

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Impact of Genetic Variants in Human Scavenger Receptor Class B Type I (SCARB1) on Plasma Lipid TraitsCLINICAL PERSPECTIVE by Vipavee Niemsiri, Xingbin Wang, Dilek Pirim, Zaheda H. Radwan, John E. Hokanson, Richard F. Hamman, M. Michael Barmada, F. Yesim Demirci, and M. Ilyas Kamboh Circ Genom Precis Med Volume 7(6):838-847 December 16, 2014 Copyright © American Heart Association, Inc. All rights reserved.

Single-site association P values of 39 SCARB1 variants with minor allele frequency (MAF) ≥5% for high-density lipoprotein cholesterol (HDL-C) and apolipoprotein B (ApoB; top), gene structure of SCARB1 (middle), and linkage disequilibrium (LD) plot of 7 variants associated with HDL-C (n=3) or ApoB (n=4; P<0.05; bottom). Single-site association P values of 39 SCARB1 variants with minor allele frequency (MAF) ≥5% for high-density lipoprotein cholesterol (HDL-C) and apolipoprotein B (ApoB; top), gene structure of SCARB1 (middle), and linkage disequilibrium (LD) plot of 7 variants associated with HDL-C (n=3) or ApoB (n=4; P<0.05; bottom). The −log10P values are in the Y axis. A total of 39 variants with MAF≥5% are on SCARB1 (5′→3′; RefSeq: hg19, NM_005505) in the X axis. Marker names are shown as SNP name-SNP ID (dbSNP build 139)/chromosome 12 position (for novel variants). Dash line indicates the significance threshold (P=0.05). Shades and values (r2×100) in each square of LD plot indicate pairwise LD: black indicating complete LD (r2=1), white indicating no LD (r2=0), and shade intensity indicating the degree of LD (r2 between 0 and 1). FDR indicates false discovery rate; and SNP, single nucleotide polymorphism. Vipavee Niemsiri et al. Circ Cardiovasc Genet. 2014;7:838-847 Copyright © American Heart Association, Inc. All rights reserved.

Haplotype association plots for high-density lipoprotein cholesterol (HDL-C) and apolipoprotein B (ApoB; top) and linkage disequilibrium (LD) structure (bottom) of 69 SCARB1 variants. Haplotype association plots for high-density lipoprotein cholesterol (HDL-C) and apolipoprotein B (ApoB; top) and linkage disequilibrium (LD) structure (bottom) of 69 SCARB1 variants. The −log10P values are in the Y axis. Total 69 variants are on SCARB1 (5′→3′; RefSeq: hg19, NM_005505) in the X axis. Marker names are shown as SNP name-SNP ID (dbSNP build 139)/chromosome 12 position (for novel variants). Dash line indicates the significance threshold (global P=0.05). Highlighted areas in the haplotype plots represent 4 haplotype regions significantly associated with HDL-C (regions: 1, 4) and apoB (regions: 2, 3). The degree of shades and values (r2×100) in each square of LD plot indicate pairwise LD: black indicating complete LD (r2=1), white indicating no LD (r2=0), and shade intensity indicating the degree of LD (r2 between 0 and 1). MAF indicates minor allele frequency; and SNP, single nucleotide polymorphism. Vipavee Niemsiri et al. Circ Cardiovasc Genet. 2014;7:838-847 Copyright © American Heart Association, Inc. All rights reserved.