Table 3.
Illustrative examples of SNPs representing different regulatory features. The chromosomal coordinates of the change, the harboring gene, the functional annotation, and the respective number of variation and wild type calls are presented for each SNP.
| Feature (putative) | Position and Change | Gene | SNP ID | Annotation | Number of reads (var/wt)* | |||
|---|---|---|---|---|---|---|---|---|
| NE | NT | TE | TT | |||||
| Imprinting | chr15:23931507 G>A | NDN | rs2192206 | Coding-synonymous | 26 / 18 | 40 / 0 | 11 / 5 | 15 / 1 |
| Expression Advantage | chrX:80373961 C>T | HMGN5 | rs73231013 | Coding-synonymous | 37 / 38 | 37 / 2 | 21 / 18 | 4 / 0 |
| Loss of Heterozygosity LOH) | chr2:218682771 A>G | TNS1 | rs3796026 | Coding-synonymous | 9 / 12 | 27 /49 | 2 / 1 | 12 / 2 |
| chr2:219209796 C>A | PNKD | rs921970 | 3’ UTR | 4 / 3 | 7 / 1 | 5 / 0 | 6 / 1 | |
| chr2:219503113 C>T | ZNF142 | rs1803383 | Coding-synonymous | 5 / 6 | 9 / 6 | 7 / 0 | 37 / 4 | |
| chr2:220431631 G>T | OBSL1 | rs1043537 | Coding-synonymous | 9 / 9 | 41 / 42 | 8 / 1 | 82 / 4 | |
| Growth Advantage | chr1:9305335 C>T | H6PD | rs138024142 | Coding-synonymous | 32 / 35 | 34 / 29 | 34 / 20 | 22 / 2 |
| Somatic Mutation | chr17:7578203 C>T | TP53 | COSM10667 | Missense; V216M | 0 / 0 | 0 / 0 | 19 / 34 | 93 / 9 |
| RNA Editing | chr1:160319987 A>G | NCSTN | NA | Missense;S177G | 0 / 0 | 0 / 0 | 0 / 0 | 42 / 89 |
*
Total number of reads, before filtering for MQV; reads will MQV< 20 were removed from further analysis