cis sequence effects on gene expression

BMC Genomics

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

Gene	N SNPs analyzed SNP-wise	SAM model analysis, single P	SNP-wise regression, best P**	TreeScan, best P_permuted
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

*Statistically significant results are bolded. **See Additional file 3 for SNP details.

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