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Table 3 SNP and haplotype-based cis sequence effects on gene expression*

From: cis sequence effects on gene expression

Gene N SNPs analyzed SNP-wise SAM model analysis, single P SNP-wise regression, best P** TreeScan, best Ppermuted
ALDH2 2 0.482 0.577 0.796
BCL2L1 2 0.283 0.488 0.191
BIC 9 0.010 0.016 0.056
BIRC3 2 0.110 0.550 0.092
BLM 9 0.941 0.266 0.882
CCNA2 3 0.142 0.085 0.635
CCND3 4 0.601 0.519 0.819
CDKN1B 3 0.142 0.059 0.259
CHEK1 2 0.542 0.290 0.577
CYP1B1 14 did not compute 0.032 0.438
FCGR2B 6 0.011 0.003 0.024
IFNGR1 2 0.981 0.854 0.902
IFNGR2 2 0.175 0.096 0.374
IRF1 1 0.160 0.282 Na
JAK1 5 0.194 0.375 0.123
LMO2 8 0.830 0.181 0.024
LTA 103 0.785 0.380 0.992
MGMT 4 0.330 0.064 0.329
MSH2 1 0.388 0.409 Na
MYBL2 8 0.105 0.008 0.095
MYC 1 0.303 0.409 Na
NBS1 4 0.005 0.000 0.197
OAS1 1 0.186 0.206 Na
PCNA 2 0.138 0.064 0.006
PHB 3 0.902 0.651 0.937
PIM1 2 0.689 0.419 0.721
PTEN 3 0.257 0.236 0.569
TNF 103 0.619 0.394 0.756
TP73L 9 0.305 0.024 0.563
TYMS 4 0.127 0.100 0.185
  1. *Statistically significant results are bolded. **See Additional file 3 for SNP details.
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