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Table 1 Information about genes and SNPs selected for the SNP association study

From: Shared ancestral susceptibility to colorectal cancer and other nutrition related diseases

Closest Candidate Gene

rs Numbera (r2)b

Status (reported / genotyped)

Position

SNPsc (ancestral / derived)

Reported associationd

Max. allele frequency difference (YRI vs. any)

Allele frequency difference YRI vs. CEU

Function or location

Ref.

AGT Angiotensin I

rs699

R/G

Chr1: 228.912.667

C/T

Hypertension, Preeclampsia

52,5%

52,5%

missense

[9, 18]

 

rs4762

R

Chr1: 228.912.850

C/T

Hypertension

3,3%

3,3%

missense

 
 

rs5051 (r2 0.948 to rs699)

R

Chr1: 228.916.745

A/G

Hypertension

52,1%

52,1%

5′UTR

 

GALNT2 Polypeptide N-acetylgalactosaminyl-transferase 2

rs4846914

R/G

Chr1: 228.362.564

G/A

HDL

58,0%

58,0%

intron

[19, 20]

rs611229

G

Chr1: 228.390.690

G/T

tagging SNP

39,4%

39,4%

intron

-

 

rs2144300 (r2 0.933 to rs4846914)

R

Chr1: 228.361.789

C/T

HDL, Triglycerides

57,0%

57,0%

intron

[20]

IFIH1 Interferon induced with helicase C domain 1

rs1990760

R/G

Chr2: 162.832.547

C/T

T2D

54,0%

54,0%

missense / benign

[21]

SLC2A Solute carrier family 2, facilitated glucose transporter member 2

rs5400

R/G.

Chr3: 172.215.244

T/C

T2D

48,1%

35,0%

missense / damaging

[9]

rs6785233

G

Chr3: 172.239.679

G/T

tagging SNP

50,8%

38,3%

-

-

 

rs8192675

G

Chr3: 172.207.577

G/A

tagging SNP

76,7%

50,0%

-

-

IGF2BP2 Insulin-like growth factor 2 mRNA binding

rs1470579

R/G

Chr3: 187.012.024

C/A

T2D

60,0%

56,8%

intron

[22]

ENPP1 Ectonucleotide pyrophosphatase

rs1044498

R/G

Chr6: 132.214.311

C/A

Insulin resistance, T2D (early onset), Myocardial infarction (early onset)

94,4%

87,3%

missense / benign

[9, 23]

 

rs9493119

G

Chr6: 132.253.111

G/A

tagging SNP

30,0%

20,8%

-

-

CYP3A_ Locus Cytochrom P450

rs776746

R/G.

Chr7: 99.108.725

A/G

Hypertension; Salt sensitivity

79,2%

79,2%

CYP3A5_ intron

[9, 18]

rs10211

G

Chr7: 99.140.930

G/A

tagging SNP

67,0%

67,0%

3′UTR_CYP3A7

-

 

rs667660

G

Chr7: 99.257.162

C/A

tagging SNP

74,3%

74,3%

upstream CYP3a3

-

MTMR9 Myotubularin related protein 9

rs10091637

G

Chr8: 11.181.724

C/T

tagging SNP

36,9%

29,2%

intron

-

rs11250127

G

Chr8: 11.207.619

G/A

tagging SNP

66,4%

26,5%

intron

-

 

rs2293855 (r2 1.00 to rs11250127)

R

Chr8: 11.215.070

G/A

Obesity

64,2%

25,2%

intron

[24]

ABCA1 ATP-binding cassette transporter

rs4149268

R/G.

Chr9: 106.687.291

T/C

HDL

51,0%

46,0%

intron

[20]

rs4149274

R

Chr9: 106.679.485

A/G

HDL

4,0%

2,0%

intron

[20]

 

rs1883025

R

Chr9: 106.704.372

T/C

HDL

13,5%

10,0%

intron

[19]

GAD2 Glutamate decarboxylase 2

rs2236418

R/G.

Chr10: 26.545.752

G/A

Obesity

74,9%

74,9%

5′UTR

[9]

rs2839670

G

Chr10: 26.544.346

A/C

tagging SNP

60,0%

60,0%

upstream

-

rs6482538

G

Chr10: 26.549.870

G/A

tagging SNP

63,6%

63,6%

intron

-

rs7076544

G

Chr10: 26.597.731

G/A

tagging SNP

68,0%

68,0%

intron

-

 

rs8190748

G

Chr10: 26.609.761

G/A

tagging SNP

60,20%

60,20%

intron

-

Chr 12q13 ERBB3 Avian erythroplastic leukemia viral oncogen homolog 3

rs11171739

R/G

Chr11: 54.757.142

C/T

T2D

56,0%

48,0%

ERBB3 ~4kb downstream

[21]

KCTD10 Potassium channel tetramerisation domain

rs7298565

G

Chr12: 108.421.917

A/G

tagging SNP

57,7%

24,1%

missense

-

 

rs2338104 (r2 0.98 to rs7298565)

R

Chr12: 108.379.801

G/C

HDL

45,0%

25,0%

KCTD10 intron; MYO1H ~9kb upstream

[19, 20]

CYP19A1 / GLDN Cytochrom P450 / Gliomedin

rs2446405

R/G

Chr15: 49.434.335

A/T

Insulin Resistance

43,0%

43,0%

GLDN intron

[25]

rs12592797

G

Chr15: 49.426.928

A/C

tagging SNP

52,5%

52,5%

GLDN intron

-

 

rs2445761

G

Chr15: 49.402.908

C/T

tagging SNP

40,9%

40,9%

CYP19A1 intron

-

BBS4 Bardet-Biedl syndrome-4

rs7178130

R/G

Chr15: 70.765.505

G/A

Bardet-Biedl Syndrome; Obesity

50,0%

50,0%

upstream 5′

[26]

C18orf8 / NCP1 Chromosome 18 open reading frame 8 / Niemann-Pick disease, type C1

rs891386

R/G

Chr18: 19.357.969

A/C

tagging SNP

42,5%

42,5%

CRC associated Protein

[27]

 

rs1805081 (r2 0.84 to rs891386)

R

Chr18: 19.394.680

A/G

BMI

46,7%

46,7%

missense

 
  1. R reported SNP; G genotyped SNP; “R/G” reported and genotyped SNP. Max. maximal; BMI body mass index, T2D type 2 diabetes, LDL low-density lipoprotein, HDL high-density lipoprotein, Ref. reference a genotyped SNPs are indicated in bold; b pair-wise linkage disequilibrium between the SNPs, if reported SNP was not genotyped directly; c reported risk allele is indicated in bold-underlined; d Next to the keywords that were used to collect and select the candidate SNPs from the literature, the table also includes all reported associations with related quantitative traits.