Table 2 Most of the eleven variants presented were found six or more times in the TGCA or LocusZoom. In the presented LocusZoom studies, at least one variant satisfying -log10(p-value) > 5 was discovered
dbSNP rs number | Gene symbol | cancer | GWAS studies | Location (hg19) | Ref | Alt | Classification | -log10(PV) range |
|---|---|---|---|---|---|---|---|---|
rs1060901 | MYLIP | COAD (n = 1) | LZ0048511, LZ0054179, LZ0079035, LZ0279362, LZ0622873, LZ0694421 (n = 6) | chr6:16145242 | C | T | Silent | 28.02488-36.0667 (n = 6) |
rs113337987 | MTTP | COAD (n = 1) | LZ0048511, LZ0054179, LZ0079035, LZ0279362, LZ0622873, LZ0656755, LZ0694421 (n = 7) | chr4:99611445 | G | A | Missense_Mutation | 8.078993-13.79644 (n = 7) |
rs12438025 | STRC | COAD (n = 1) | LZ0041192, LZ0185011, LZ0194301, LZ0230841, LZ0465704, LZ0549442, LZ0707867 (n = 7) | chr15:43600649 | G | C | Silent | 13.99787-30.17285 (n = 7) |
rs141502002 | PCSK9 | STAD (n = 1), UCEC (n = 1) | LZ0048511, LZ0065547, LZ0079035, LZ0346909, LZ0694421, LZ0725414, LZ0898954, LZ0919709 (n = 8) | chr1:55058549 | C | T | Missense_Mutation | 7.713815-19.52549 (n = 8) |
rs151135411 | SLC22A3 | UCEC (n = 1) | LZ0048511, LZ0054179, LZ0065547, LZ0079035, LZ0279362, LZ0346909, LZ0622873, LZ0656755, LZ0694421 (n = 9) | chr6:160410764 | G | A | Missense_Mutation | 6.27433-31.41669 (n = 9) |
rs2075799 | HSPA1L | COAD (n = 1) | LZ0048511, LZ0185011, LZ0194301, LZ0230841, LZ0549442, LZ0725414, LZ0919709 (n = 7) | chr6:31810752 | C | T | Silent | 7.458832-19.77592 (n = 7) |
rs3135506 | APOA5 | COAD (n = 1) | LZ0041192, LZ0048511, LZ0054179, LZ0079035, LZ0185011, LZ0194301, LZ0230841, LZ0279362, LZ0465704, LZ0549442, LZ0622873, LZ0656755, LZ0694421, LZ0707867, LZ0722350, LZ0898954 (n = 16) | chr11:116791691 | G | C | Missense_Mutation | 6.043769-Inf (n = 16) |
rs41269255 | POM121L2 | COAD (n = 1) | LZ0048511, LZ0279362, LZ0622873, LZ0656755, LZ0694421, LZ0796235 (n = 6) | chr6:27309272 | C | T | Missense_Mutation | 5.999566-16 (n = 6) |
rs41288783 | APOB | STAD (n = 1) | LZ0048511, LZ0054179, LZ0065547, LZ0079035, LZ0279362, LZ0346909, LZ0622873, LZ0694421, LZ0725414, LZ0919709 (n = 10) | chr2:21019741 | G | A | Missense_Mutation | 20.4329-76.95933 (n = 10) |
rs74830677 | SCARB1 | UCEC (n = 1) | LZ0048511, LZ0279362, LZ0465704, LZ0707867, LZ0725414, LZ0919709 (n = 6) | chr12:124800125 | G | A | Missense_Mutation | 5.07808-20.47277 (n = 6) |
rs762703502 | HNF1A | COAD (n = 4), UCEC (n = 2) | LZ0656755 (n = 1) | chr12:120994312 | CG | C | Frame_Shift_Del | 7.290137 (n = 1) |