Table 2

Summary characteristics of the major genes and polygenes for traits HDL, LDL, and TGa

No.

Trait

Chr

Symbolb

Gene

SNP

Role

Total

h2

Modelc

MAF

h2 of polygenes


1

HDL

9q31.1

α1

ABCA1

rs10820738

Intron/Exon boundary

0.010

DOM

6.7

2

HDL

19q13.2

α2

CYP2B7P1

rs8103444

Exon/Intron boundary

0.002

ADD

24.4

3

HDL

15q21

α3

LIPC

rs8035006

Intron

0.003

ADD

32.5

4

HDL

8p22

α4

LPL

rs3200218

Exon downstream

0.003

DOM

21.7

5

HDL

19q13.2

δ1

CYP2B6

rs8192719

Exon/Intron boundary (Rx)

0.003

ADD (up 10%)d

24.9


Total

0.021

6

HDL

1,000 SNPs

[apoly]

0.58

ADD

min = 0.0003; max = 0.0015; avg = 0.00058


Total

0.60

1

LDL

4p16.3

β1

LRPAP1

rs7672287

Intron

0.003

ADD

22.2

2

LDL

12q13

β2

LRP1

rs1466535

Intron

0.002

ADD

31.6

3

LDL

11q13.4

β3

LRP5

rs901824

Intron/Exon boundary

0.001

ADD

10.3

4

LDL

chrom1

β4

rs10910457

0.005

ADD

1.0

5

LDL

8p22 × 4q24

β5

LPL × NFKB1

rs4648068

Intron

0.007

INT

31.0

6

LDL

22q12.2

δ2

SLC5A4

rs2294207

Intron

(Rx)

0.010

ADD (down 30%)

25.7


Total

0.028

7

LDL

1,000 SNPs

[bpoly]

0.52

ADD

min = 0.0003; max = 0.00128; avg = 0.00052


Total

0.55

1

TG

11q23

γ1

APOA5

rs603446

Downstream

0.003

OVERD

43.3

2

TG

8p22

α4

LPL

rs3200218

Exon downstream

0.004

ADD

21.7

3

TG

19q13.2

δ1

CYP2B6

rs8192719

Exon/Intron boundary (Rx)

0.003

ADD (down 15%)

24.9

4

TG

diet

0.01

Familial


Total

0.020

5

TG

1,000 SNPs

[gpoly]

0.38

ADD

min = 0.0002; max = 0.0009; avg = 0.00038


Total

0.40


aAbbreviations: MAF, Minor allele frequency; min, minimum; max, maximum; avg, average; h2, heritability; [apoly], a vector of 1,000 polygenes that contribute to HDL; [bpoly], a vector of 1,000 polygenes that contribute to LDL; [gpoly], a vector of 1,000 polygenes that contribute to TG.

bSymbol represents a locus/a vector of polygenes marked by SNPs and corresponding genes, which can be introns/exons, or a diet effect.

cEffects of genes were simulated based on ADDitive (0, 0.5, 1), DOMinant (1, 1, 0), OVERDominant (0, 1, 0), and INTeraction genetic models.

dMedication treatment lowered LDL on a varying percentage of participants dependent on visits: 2% of subjects in Visit 1, 5% of subjects in Visit 2, and 15% of subjects in Visit 3. Medication treatment increased HDL 10%, lowered LDL 30%, and lowered TG 15% for the treated subjects and in accordance with specific types of genotypes, shown in the "Model" column. For HDL on chromosome 11, 39 SNPs were simulated as a block of polygenes, starting at 110 Mbp and ending at 134 Mbp, with approximately an average equidistance of 0.5 Mbp.

Kraja et al. BMC Proceedings 2009 3(Suppl 7):S4  

Open Data