Table 2

SNPs & haplotypes chosen for analysis of cis sequence effects
Gene
 N SNPs in N = 30 Cauc sample
 N tag or singleton SNPs
 N tag SNPs
 N singleton SNPs
 N haplotypes in trees
ALDH2
 4
 2
 1
 1
 3
BCL2L1
 3
 2
 0
 2
 3
BIC
 22
 9
 3
 6
 8
BIRC3
 2
 2
 0
 2
 3
BLM
 24
 9
 5
 4
 7
CCNA2
 4
 3
 0
 3
 4
CCND3
 6
 4
 0
 4
 7
CDKN1B
 3
 3
 0
 3
 6
CHEK1
 2
 2
 0
 2
 3
CYP1B1
 50
 14
 7
 7
 19
EGR1
 2
 0
 0
 0
 na
FCGR2B
 9
 6
 1
 5
 10
GADD45A
 4
 0
 0
 0
 na
IFNGR1
 2
 2
 0
 2
 3
IFNGR2
 5
 2
 0
 2
 3
IRF1
 5
 1
 1
 0
 na
JAK1
 20
 5
 2
 2
 7
LMO2
 8
 8
 0
 8
 13
LTA
 7
 10
 4
 6
 9
MGMT
 6
 4
 2
 2
 6
MSH2
 3
 1*
 na
 na
 na
MYBL2
 25
 8
 4
 4
 6
MYC
 2
 1*
 na
 na
 na
NBS1
 19
 4
 2
 2
 7
OAS1
 5
 1
 1
 0
 na
PCNA
 3
 2
 0
 2
 3
PHB
 3
 3
 0
 3
 4
PIM1
 7
 2
 1
 1
 3
PTEN
 5
 3
 0
 3
 4
TNF
 12
 10
 4
 6
 9
TP73L
 26
 9
 3
 7
 13
TYMS
 19
 4
 3
 1
 4

*There was one SNP with maf > 5% at these two genes; tag SNP analysis was not performed. The single SNP with maf > 5% at each gene was used for SNP-based analyses.

Bergen et al. BMC Genomics 2007 8:296   doi:10.1186/1471-2164-8-296