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Table 2 The most statistically significant associations (P ≤ 0.005) between single nucleotide polymorphisms and the plasma homocysteine phenotype a, e

From: Folate network genetic variation, plasma homocysteine, and global genomic methylation content: a genetic association study

Gene Name

rs#

Nominal P

Effectc

Chr.

Coded allele

Coded allele frequency

Genetic Modelg

SNP Typeh

FTCD

rs2277820

3.09E-04b

7.22%

21

T

26%

O

I

SLC19A1

rs1051266

4.16E-04b

5.04%

21

A

44%

A

CN

SLC19A1

rs1131596

4.31E-04b

5.03%

21

C

44%

A

5'

SLC19A3

rs13007334

4.61E-04b

6.89%

2

C

46%

O

I

SLC19A1

rs4819130

5.65E-04b

4.94%

21

C

44%

A

I

MTHFD1L

rs11754661d

1.51E-03

49.98%

6

A

7%

R

I

DNMT1

rs2228611

2.42E-03

-6.44%

19

G

49%

D

CS

ALDH1L1

rs3772424

2.52E-03

6.14%

3

A

20%

D

I

GGH

rs4617146

2.55E-03

5.31%

8

T

19%

A

I

CELF1

rs4752843

2.74E-03

-5.72%

11

C

14%

A

I

SLC19A1

rs12482346

3.02E-03

4.08%

21

T

44%

A

I

SLC19A1

rs2297291

3.39E-03

6.07%

21

A

41%

D

I

TCN2

rs4820886

3.41E-03

-17.30%

22

G

13%

R

I

TCN2

rs9621049

3.41E-03

-17.30%

22

T

13%

R

CN

GLDC

rs7848919

3.52E-03

5.70%

9

G

32%

D

3'

SARDH

rs2502741f

3.60E-03

6.60%

9

A

50%

D

I

SLC19A1

rs1051298

3.68E-03

3.98%

21

T

44%

A

3'

CBS

rs6586282

4.06E-03

-5.80%

21

T

18%

O

I

FOLH1

rs202673

4.08E-03

-19.30%

11

G

14%

R

I

MTHFD1

rs1950902f

4.19E-03

-5.18%

14

T

16%

A

CN

  1. aModel adjusted for age, smoking, and residuals of plasma folate, plasma vitamin B-6, and plasma vitamin B-12; forward strand allele shown.
  2. bFDR-adjusted P values reached False Discovery Rate significance threshold of 0.05.
  3. cEffect is shown as percent change in plasma homocysteine levels.
  4. dSparse data (fewer than 5 individuals per category) for some genotype categories.
  5. eNo SNPs map to more than one gene.
  6. fLower quality SNP.
  7. gD:Dominant; R:Recessive; A:Additive; O:Overdominant.
  8. h5':5' region; 3':3' region; CN:Coding nonsynonymous; CS:Coding synonymous; I:Intronic.