Skip to main content

Table 8 Significantly associated haplotype regions (global P < 0.05) with HDL-C and ApoA-I

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

Region #

Trait

Consecutive Significantly Associated Haplotype Windows (global P < 0.05)

  

Haplotype Windows #

Chr12 Positiona

The Composited Variants in the Region, 5′ to 3′ Direction

Most Relevant Haplotype

(Location)

   

Start (5′)

End (3′)

SNP Nameb-SNP IDc/Chr12 Positiona

Major/Minor Alleles

Haplotype #

Sequence

β (Min-Max)

1

HDL-C

44

125300551

125299542

p48969-rs2343394

C/T

h44.3

CCWGCGG

0.4910–1.0491

 

45

(intron 2)

(exon 3)

p49537-rs7305310

C/T

h45.2

  
 

46

  

p49570delC-rs145376237

W/D

h46.2

  
 

47

  

p49690-rs4765615

G/A

hap.base47

  
    

p49759-rs146272788

C/T

hap.base44

CCWACGG

−0.4701

    

p49978-rs5891 (p.Val135Ile)

G/A

hap.base45

  
    

p50024-rs368880622

G/T

hap.base46

  
      

h47.1

  

2

ApoA-I

47

125299830

125299369

p49690-rs4765615

G/A

h47.1

ACGGTT

(−0.8907)–3.3792

 

48

(intron 2)

(intron 3)

p49759-rs146272788

C/T

h48.1

  
 

49

  

p49978-rs5891 (p.Val135Ile)

G/A

h49.1

  
    

p50024-rs368880622

G/T

   
    

p50118-rs58710319

C/T

   
    

p50151-rs2278986

T/C

   

3

ApoA-I

70

125294893

125292516

p54627-chr12_125294893

G/C

h70.2

GCGTAG

2.0304–2.1103

 

71

(intron 5)

(intron 6)

p54856-chr12_125294664d

C/T

h71.3

  
 

72

  

p55923-rs838900

G/A

h72.3

  
    

p55963-rs7134858

C/T

   
    

p56845-rs838902

A/G

   
    

p57004-rs187562853

G/A

   

4

ApoA-I

78

125291928

125286037

p57592-rs838903

G/A

h78.5

GTTTCGCTG

4.7307–5.5715

 

79

(intron 7)

(intron 7)

p58514-rs838905

T/C

h79.6

  
 

80

  

p58664-rs865716

A/T

h80.6

  
 

81

  

p60255-rs3782287

C/T

hap.base81

  
 

82

  

p61872-rs838909

C/T

hap.base82

  
 

83

  

p62140-rs838910

G/T

hap.base83

  
    

p62409-rs838911

C/T

h78.2

GTACCTCTG

0.6384–3.8641

    

p62615-rs7138386

T/C

h79.2

  
    

p63483-rs838912

G/A

hap.base80

  
      

h81.3

  
      

h82.2

  
      

h83.4

  

5

ApoA-I

95

125277653

125272763

p71867-rs7954022

C/T

h95.5

CGTTCT

4.2363-4.7525

 

96

(intron 9)

(intron 9)

p72197-rs838861

A/G

h96.5

  
 

97

  

p72777-rs838862

C/T

h97.4

  
    

p75766-rs838866

T/C

   
    

p75778-rs7301120

C/T

   
    

p76757-rs9919713

A/T

   

6*

ApoA-I

109

125271118

125269475

p78402-rs838898

G/A

h109.6

GCCTGCA

(−3.3720)─(−1.8104)

 

110

(intron 10)

(intron 11)

p78430-rs838897

C/G

h110.6

  
 

111

  

p78747-rs2293440

T/C

h111.2

  
 

112

  

p78791-rs75289200

T/C

h112.3

  
    

p79721-rs838896

G/C

   
    

p79828-rs838895

C/G

   
    

p80045-rs838893

G/A

   

7*

HDL-C

111

125270773

125267501

p78747-rs2293440

T/C

h111.4

TTGGAGC

0.3755–2.3949

 

112

(intron 11)

(intron 11)

p78791-rs75289200

T/C

h112.2

  
 

113

  

p79721-rs838896

G/C

h113.1

  
 

114

  

p79828-rs838895

C/G

h114.1

  
    

p80045-rs838893

G/A

   
    

p81863-rs185445624

G/A

   
    

p82019-rs838890

C/T

   

8

HDL-C

117

125267501

125267086

p82019-rs838890

C/T

h117.2

TCGGC

(−1.0134)–(−0.9657)

 

118

(intron 11)

(intron 12)

p82264-rs141545424 (p.Gly501Gly)d

C/A

h118.2

  
    

p82340-rs77483223

G/A

   
    

p82369-rs75446635

G/A

   
    

p82434-rs838889

T/C

   

9

HDL-C

123

125265636

125262553

p83884-rs701106

C/T

h123.4

CCCTGA

(−1.180)–(−0.2329)

 

124

(intron 12)

(exon 13-3′ UTR)

p86245-rs188375019

C/T

h124.2

  
 

125

  

p86276-rs747155

C/T

h125.2

  
    

p86316-rs701104

G/T

   
    

p86481-rs701103 (p.Gly499Arg, isoform 2)

G/A

   
    

p86967-rs187492239

A/G

   
  1. ApoA-I apolipoprotein A-I, del/D deletion, HDL-C high-density lipoprotein cholesterol, SNP single nucleotide polymorphism, UTR untranslated region, W wild type allele for deletion on the RefSeq
  2. All alleles on the reverse strand. HDL-C and ApoA-I variables were in mg/dL and Box-Cox transformed
  3. Results were adjusted for covariates: sex, age, waist, current smoking (yes/no), and minutes of daily walking or biking to work (jobmin) for HDL-C; sex and age for ApoA-I
  4. All nine haplotype regions are shown in Fig. 3
  5. Detailed single-site associations are shown in Additional file 14: Table S9 and Additional file 15: Table S10
  6. Detailed haplotype associations are shown in Table 7 and Additional file 16: Table S11
  7. Regions with asterisk (*) indicate regions that included the haplotype window exhibiting the most significant association signal (the smallest global P) for the associated trait
  8. For each region, the most significant associated haplotype window is shown in bold
  9. SNPs with significant evidence of association with the same trait in both single-site and haplotype analyses (single-site P < 0.05 and global P < 0.05) are shown in bold
  10. SNPs with significant evidence of association with different trait in single-site and haplotype analyses (single-site P < 0.05 and global P < 0.05) are shown in italic bold
  11. a, bRefSeq of SCARB1: hg19, NM_005505 (CHIP Bioinformatics)
  12. cdbSNP build 139: GRCh37.p10
  13. dRare variants of interest with potential effects on lipid traits; see details in Table 6