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 |