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Table 6 Characteristics and effects of 6 SCARB1 rare variants of interest

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

SNP Namea

SNP IDb

Chr12 Positionc

Location

Amino Acid Change

RegDB Scored

Major/Minor Alleles

MAF

GT

GT Count (Carrier Freq)

Adjusted Mean ± SD (mg/dL)

β

SE

R2 (%)

P

FDR

Second Assoc Trait (Effect)

HDL-C

                

 p52919

 

125296601

Intron 4

 

5

G/T

0.0013

GG

734

47.87 ± 12.71

−7.4063

2.5863

1.1050

0.0043

0.1465

ApoA-I (↓)

        

GT

2 (0.27)

24.67 ± 9.26

      

 p53372

rs115604379

125296148

Intron 5

 

5

C/T

0.0066

CC

729

47.68 ± 12.64

3.0372

1.1642

0.9140

0.0093

0.2190

 
        

CT

10 (1.35)

58.2 ± 13.03

      

 p54611

 

125294909

Intron 5

 

4

T/C

0.0007

TT

742

47.86 ± 12.68

−9.5243

3.6710

0.8920

0.0097

0.2190

ApoA-I (↓)

        

TC

1 (0.13)

19.59 ± NA

      

 p54856

 

125294664

Intron 6

 

4

C/T

0.0007

CC

742

47.85 ± 12.70

−8.4305

3.6579

0.7130

0.0215

0.3243

ApoA-I (↓)

        

CT

1 (0.13)

21.48 ± NA

      

 p77620

rs377124254

125271900

Intron 10

5

G/A

0.0007

GG

735

47.77 ± 12.67

11.5518

3.6514

1.3500

0.0016

0.1104

 
        

GA

1 (0.14)

90.2 ± NA

      

 p82264

rs141545424

125267256

Exon 12

Gly501Gly

5

C/A

0.0007

CC

739

47.77 ± 12.66

11.5850

3.6469

1.3530

0.0016

0.1104

 
        

CA

1 (0.14)

90.31 ± NA

      

ApoA-I

                

 p52919

 

125296601

Intron 4

 

5

G/T

0.0013

GG

741

136.81 ± 27.74

−13.4137

6.4689

0.5750

0.0385

0.4359

HDL-C (↓)

        

GT

2 (0.27)

97.42 ± 18.38

      

 p54611

 

125294909

Intron 5

 

4

T/C

0.0007

TT

748

136.83 ± 27.66

−19.2831

9.0970

0.5980

0.0344

0.4359

HDL-C (↓)

        

TC

1 (0.13)

80.62 ± NA

      

 p54856

 

125294664

Intron 6

 

4

C/T

0.0007

CC

748

136.87 ± 27.61

−24.0757

9.0781

0.9330

0.0082

0.2918

HDL-C (↓)

        

CT

1 (0.13)

67.98 ± NA

      
  1. ApoA-I apolipoprotein A-I, FDR false discovery rate, GT genotype, HDL-C high-density lipoprotein cholesterol, MAF minor allele frequency, RegDB RegulomeDB, SD standard deviation, SE standard error, SNP single nucleotide polymorphism; R2, the proportion of the phenotypic variance explained by the variant; ↓, decreased
  2. All alleles were on reverse stand. 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 walking or biking to work each day (jobmin) for HDL-C; sex and age for ApoA-I.
  4. Detailed single-site association results are shown in Additional file 14: Table S9 and Additional file 15: Table S10.
  5. a, cRefSeq of SCARB1: hg19, NM_005505 (CHIP Bioinformatics)
  6. bdbSNP build 139: GRCh37.p10. All 10 novel variants identified in this study have been submitted to dbSNP (batch ID: SCARB1_AB): http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?handle=KAMBOH
  7. dThe RegulomeDB (version 1.0) scoring scheme and functional assignments are described in Additional file 17: Table S12 and Additional file 18: Table S13, respectively