Table 1 Summary of the functional prediction and eQTL analysis results of the 11 selected SNPs in the TCPTP pathways in silico.
SNP | Gene | Chr. | Allelea | SNPinfo | Regulome DB Score | HaploReg | P b | ||
|---|---|---|---|---|---|---|---|---|---|
P (additive model) | P (dominant model) | P (recessive model) | |||||||
rs7538978 | PIK3R3 | 1 | A/G | — | 1 f | Enhancer histone marks: 9 tissues; DNAse: CRVX; Motifs changed: 6 altered motifs | 0.722 | 0.249 | 0.175 |
rs11707731 | ATR | 3 | G/T | — | 4 | Promoter histone marks: 4 tissues; Enhancer histone marks: 4 tissues; DNAse: ESC; Motifs changed: 4 altered motifs | 0.579 | 0.719 | 0.420 |
rs706714 | PIK3R1 | 5 | A/C | TFBS | 5 | Enhancer histone marks: 7 tissues; DNAse: GI; Motifs changed: GATA,Nkx2,Nkx3 | 0.281 | 0.137 | 0.714 |
rs2740762 | EGFR | 7 | C/A | TFBS | 5 | Enhancer histone marks: 13 tissues; DNAse: IPSC,MUS,PANC; Motifs changed: Foxo,NF-AT,Pax-4 | 0.053 | 0.008 | 0.338 |
rs845553 | EGFR | 7 | G/A | — | 4 | Promoter histone marks: 4 tissues; Enhancer histone marks: 17 tissues; DNAse: 17 tissues; Proteins bound: 7; Motifs changed: 5 altered motifs | 0.396 | 0.683 | 0.280 |
rs17172432 | EGFR | 7 | T/C | — | 4 | Promoter histone marks: 7 tissues; Enhancer histone marks: 18 tissues; DNAse: 6 tissues; Motifs changed: 4 altered motifs | 0.359 | 0.614 | 0.280 |
rs34280975 | MET | 7 | A/G | — | 2c | Enhancer histone marks: SKIN; DNAse: 4 tissues; Proteins bound: CEBPB; Motifs changed: 7 altered motifs | 0.421 | 0.197 | 0.538 |
rs3744483 | STAT3 | 17 | T/C | miRNA | 4 | bound: 7; DNAse: 11 tissues; Motifs changed: Foxa,p300 | 0.907 | 0.856 | 0.467 |
rs1135669 | STAT5A | 17 | C/T | Splicing | 4 | Enhancer histone marks: BLD, THYM; DNAse: OVRY,BRST; Motifs changed: BATF, Pbx3, STAT | 0.062 | 0.079 | 0.255 |
rs2847297 | PTPN2 | 18 | A/G | — | — | DNAse: BLD; Motifs changed: Nkx2,Pax-5 | 0.005 | 0.017 | 0.005 |
rs2847282 | PTPN2 | 18 | T/G | — | 5 | Promoter histone marks: STRM, LIV, BLD; Enhancer histone marks: 9 tissues; DNAse: 4 tissues; Motifs changed: 26 altered motifs | 0.029 | 0.001 | 0.029 |
