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Table 10 Significant lipid-associated regions (global P < 0.05) that were observed in US Non-Hispanic Whites (previous studya) and African Blacks (this study)

From: Genetic contribution of SCARB1 variants to lipid traits in African Blacks: a candidate gene association study

Region #

Consecutive Haplotype Windows in 623 US Non-Hispanic Whitesa

Consecutive Haplotype Windows in 788 African Blacks

 

Trait

Chr12 Positionb (Location)

Length (bp)

The Composited Variants, 5′ to 3′ Direction

Trait

Chr12 Positionb (Location)

Length (bp)

The Composited Variants, 5′ to 3′ Direction

  

Start (5′)

End (3′)

 

SNP Namec-SNP IDd

Major/Minor Alleles

 

Start (5′)

End (3′)

 

SNP Namec-SNP IDd

Major/Minor Alleles

I

ApoB

125300551

125299369

1183

p48969-rs2343394

C/T

HDL-C

125300551

125299496

1056

p48969-rs2343394

C/T

  

(intron 2)

(intron 3)

 

p49518-rs144194221

G/A

 

(intron 2)

(intron 3)

 

p49537-rs7305310

C/T

     

p49690-rs4765615

A/G

    

p49570delC-rs145376237

W/D

     

p49978-rs5891

G/A

    

p49690-rs4765615

G/A

(p.Val135Ile)

     

p50151-rs2278986

T/C

    

p49759-rs146272788

C/T

           

p49978-rs5891

G/A

(p.Val135Ile)

           

p50024-rs368880622

G/T

       

ApoA-I

125299830

125299369

462

p49690-rs4765615

G/A

        

(intron 2)

(intron 3)

 

p49759-rs146272788

C/T

           

p49978-rs5891

G/A

(p.Val135Ile)

           

p50024-rs368880622

G/T

           

p50118-rs58710319

C/T

           

p50151-rs2278986

T/C

II

HDL-C

125269692

125262516

7177

p79828-rs838895

C/G

HDL-C

125269692

125267501

2192

p79828-rs838895

C/G

  

(intron 11)

(exon 13- 3′ UTR)

 

p80045-rs838893

G/A

 

(intron 11)

(intron 11)

 

p80045-rs838893

G/A

     

p83088-rs797729

A/G

    

p81863-rs185445624

G/A

     

p83884-rs701106

C/T

    

p82019-rs838890

C/T

     

p86436-rs10396214

C/T

HDL-C

125267501

125267086

416

p82019-rs838890

C/T

(p.Arg484Trp, isoform 2)

     

p87004-rs184715678

C/A

 

(intron 11)

(intron 12)

 

p82264-rs141545424

C/A

(p.Gly501Gly)

           

p82340-rs77483223

G/A

           

p82369-rs75446635

G/A

           

p82434-rs838889

T/C

       

HDL-C

125265636

125262553

3084

p83884-rs701106

C/T

        

(intron 12)

(exon 13- 3′ UTR)

 

p86245-rs188375019

C/T

           

p86276-rs747155

C/T

           

p86316-rs701104

G/T

           

p86481-rs701103

G/A

(p.Gly499Arg, isoform 2)

           

p86967-rs187492239

A/G

  1. ApoA-I apolipoprotein A-I, ApoB apolipoprotein B, del/D deletion, HDL-C high-density lipoprotein cholesterol, SNP single nucleotide polymorphism, UTR untranslated region, W wild type allele for deletion on RefSeq
  2. All alleles on the reverse strand
  3. Results for a US Non-Hispanic White sample were Box-Cox transformed, and adjusted for covariates: sex, age, body mass index, and smoking (past/current/never) for HDL-C; age and smoking for ApoB
  4. Results for an African Black sample were Box-Cox transformed, and adjusted for covariates: sex, age, waist, current smoking (yes/no), and minutes of walking or biking to work each day (jobmin) for HDL-C; sex and age for ApoA-I
  5. Location of each region on SCARB1 gene is shown in Fig. 4
  6. SNPs with significant evidence with the same trait in both single-site and haplotype associations (single-site P and global P < 0.05) observed in each population are shown in bold
  7. SNPs with significant evidence with the different trait in single-site and haplotype associations (single-site P and global P < 0.05) in each population are shown in italic bold
  8. aData from Niemsiri V, et al. Circ Cardiovasc Genet 2014, 7(6):838–847 (Ref [49])
  9. b, cRefSeq of SCARB1: hg19, NM_005505 (CHIP Bioinformatics)
  10. ddbSNP version 139: GRCh37.p10