Table 1

Information about genes and SNPs selected for the SNP association study
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

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.

Huhn et al.

Huhn et al. BMC Medical Genetics 2012 13:94   doi:10.1186/1471-2350-13-94

Open Data