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Table 1 Genotyping of 12 SNPS that locate in transcription factor binding sites in low-penetrance CRC loci

From: Systematic search for enhancer elements and somatic allelic imbalance at seven low-penetrance colorectal cancer predisposition loci

Locus SNP bp* SNP ID MAF controls MAF cases OR 95% CI P Cases (n) Controls (n) Binding sequence*** TF
15q13 30 782 048 rs4779584** 0.295 0.323 1.14 1.00 - 1.31 0.05 981 1 024   
  30 806 855 rs28768389 0.088 0.073 1.24 0.97-1.57 0.08 976 837 AAYCAATCACATA GATA2-FOXL1
  30 824 927 rs11631292 0.123 0.108 1.16 0.95-1.42 0.15 1 009 823 YATCC GATA2
  30 825 051 rs62002613 monomorphic      1 011 824 KATCT GATA2
  30 806 691 rs12899808 monomorphic      976 837 MCAACAT BRCA1
  30 804 840 rs34812868 0.431 0.402 1.13 0.99-1.29 0.08 913 821 GTRTCT GATA1
10p14 8 741 225 rs10795668** 0.307 0.271 1.19 1.04-1.37 0.01 951 983   
  8 743 013 rs17485426 0.129 0.137 1.07 0.88-1.29 0.51 1 010 824 TATMTAAA FOXL1
  8 742 714 ENSSNP10169878 0.129 0.137 1.07 0.88-1.29 0.51 1 010 824 CAATCTTAWTTTTT GATA3-FOXC1
  8 783 743 rs1999638 0.123 0.136 1.12 0.92-1.37 0.24 1 010 824 RAATCT GATA3
11q23 110 676 919 rs3802842** 0.239 0.276 1.22 1.06-1.40 0.01 970 994   
  110 645 918 rs12273224 monomorphic      997 823 TAAATRTA FOXL1
  110 669 934 rs45615536 0.01 0.006 1.63 0.77-3.57 0.19 1 009 824 TKGGGG MZF1
14q22 53 480 669 rs4444235** 0.426 0.462 1.16 1.02-1.33 0.03 933 828   
  53 488 736 rs2761880 0.009 0.008 1.08 0.51-2.23 0.85 1 011 824 GTGTTTYTTTATTCTT FOXJ3
  53 484 488 rs12893484 0.384 0.414 1.13 0.99-1.29 0.07 1 010 824 GCCRCAGGC TFAP2A
  1. * Human genome build 36; **Tag SNPs genotyped in previous studies [6, 8, 9]; *** SNPs indicated as Y = C/T, K = G/T, M = A/C, R = A/G, W = A/T; MAF = minor allele frequency, TF = transcription factor; rs11631292, rs62002613, rs17485426, ENSSNP10169878, rs1999638, rs12273224, rs45615536, rs10505287, rs57897735 rs10505283, rs2761880, and rs12893484 were genotyped using Sequenom MassArray iPlex Gold; rs28768389, rs12899808, and rs34812868 were genotyped using genomic sequencing