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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.