Table 1.
SNPs selected for DNA methylation and genotype measured by the Nsp microarray.
| Rank | SNPs | |||
|---|---|---|---|---|
| 50 | SNP_A-1825620 | SNP_A-2213037 | SNP_A-2145008 | SNP_A-2309865 |
| SNP_A-4233167 | ||||
| 100 | SNP_A-2172952 | SNP_A-2234716 | SNP_A-1984943 | SNP_A-2121000 |
| SNP_A-2085071 | ||||
| 150 | SNP_A-2040111 | SNP_A-4195285 | SNP_A-4199352 | SNP_A-2089983 |
| SNP_A-1944699 | SNP_A-1988914 | SNP_A-1834529 | SNP_A-1950742 | |
| SNP_A-2105346 | SNP_A-4235277 | |||
| 200 | SNP_A-4229534 | SNP_A-4226834 | SNP_A-4196078 | SNP_A-2199615 |
| SNP_A-1919825 | SNP_A-2276203 | SNP_A-1961374 | ||
| 250 | SNP_A-1989613 | SNP_A-1845324 | SNP_A-1880907 | SNP_A-2142865 |
| SNP_A-2124767 | SNP_A-1810962 | SNP_A-4193660 | SNP_A-1852621 | |
| SNP_A-1961109 | SNP_A-4212314 | SNP_A-2042678 | SNP_A-1886593 | |
| SNP_A-1980533 | SNP_A-2143521 | SNP_A-2088571 | ||
| 300 | SNP_A-2043441 | SNP_A-2287632 | SNP_A-2056366 | SNP_A-2185001 |
| SNP_A-1910539 | SNP_A-4213049 | SNP_A-2007288 | SNP_A-4228665 | |
| SNP_A-4236336 | SNP_A-2063926 | SNP_A-1911642 | SNP_A-1950919 | |
| SNP_A-2053247 | SNP_A-4197286 | SNP_A-4204073 | SNP_A-2221049 | |
| SNP_A-2065785 | ||||
The 59 selected SNPs (probes) that exhibited significant differences between blood, and normal and tumor tissues, within the top N (= 50, 100, 150, 200, 250, and 300) outliers for both DNA methylation and genotype. Top 300 outliers are shown in red in Fig. 3. For detailed annotations, including associated genes, of the selected SNPs, see Additional file 1 (sheet name Nsp).