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Table 2 SNPs & haplotypes chosen for analysis of cis sequence effects

From: cis sequence effects on gene expression

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
  1. *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.
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