Table 4.
The ASE pattern of genes reaching statistical significance (Illumina Assay).
| rsID | Name | Chr | Imprinting status | Average intensity >11.25 | Number of hets | Number of hets with p < 0.01 | Pattern of ASE | Alleles |
|---|---|---|---|---|---|---|---|---|
| rs1802710 | DLK1 | 14 | control | 13.57 | 15 | 14 | imprinting | |
| rs8100247 | ZNF331 | 19 | control | 12.61 | 13 | 12 | imprinting | |
| rs2075745 | H19 | 11 | control | 14.01 | 12 | 12 | imprinting | |
| rs2839702 | H19 | 11 | control | 13.48 | 11 | 11 | imprinting | |
| rs1082 | PHACTR2 | 6 | candidate | 12.09 | 14 | 10 | partial imprinting | |
| rs12982082 | ZNF331 | 19 | control | 12.27 | 12 | 10 | imprinting | |
| rs13073 | PEG10 | 7 | control | 12.09 | 11 | 10 | imprinting | |
| rs1055359 | PEG3 | 19 | control | 11.8 | 10 | 10 | imprinting | |
| rs9373409 | PLAGL1 | 6 | control | 12.48 | 11 | 9 | imprinting | |
| rs1860565 | PEG3 | 19 | control | 13.63 | 9 | 9 | imprinting | |
| rs2309428 | TJP2 | 9 | candidate | 12.86 | 9 | 8 | random ASE | |
| rs178077 | SNAP29 | 22 | candidate | 11.95 | 10 | 7 | random ASE | |
| rs1003483 | IGF2AS | 11 | control | 11.32 | 8 | 7 | imprinting | |
| rs8585 | UBE2V1 | 20 | candidate | 12.36 | 13 | 6 | preferential | A>G |
| rs1130663 | CD151 | 11 | candidate | 12.44 | 18 | 5 | random ASE | |
| rs4664114 | FMNL2 | 2 | candidate | 11.51 | 14 | 5 | random ASE | |
| rs4944960 | XRRA1 | 11 | candidate | 12.43 | 12 | 5 | preferential | G>C |
| rs2282336 | TJP2 | 9 | candidate | 12.32 | 9 | 5 | random ASE | |
| rs6633 | CDK2AP1 | 12 | candidate | 11.34 | 8 | 5 | random ASE | |
| rs4614 | VPS11 | 11 | candidate | 13.09 | 13 | 4 | random ASE | |
| rs3817672 | TFRC | 3 | candidate | 12.07 | 13 | 4 | * preferential | T>C |
| rs2905 | C14orf130 | 14 | candidate | 11.33 | 12 | 4 | random ASE | |
| rs12190287 | TCF21 | 6 | candidate | 12.88 | 10 | 4 | random ASE | |
| rs3809865 | ITGB3 | 17 | candidate | 12.09 | 10 | 4 | random ASE | |
| rs10863 | MEST | 7 | control | 12.32 | 4 | 4 | imprinting | |
| rs915894 | NOTCH4 | 6 | candidate | 13.44 | 16 | 3 | * preferential | A>C |
| rs754615 | CAST | 5 | candidate | 13.71 | 14 | 3 | preferential | G>C |
| rs838896 | SCARB1 | 12 | candidate | 12.62 | 10 | 3 | random ASE | |
| rs5758651 | TCF20 | 22 | candidate | 12.4 | 10 | 3 | random ASE | |
| rs11699879 | NCOA3 | 20 | candidate | 12.68 | 9 | 3 | random ASE | |
| rs838891 | SCARB1 | 12 | candidate | 11.85 | 9 | 3 | random ASE | |
| rs2425009 | MYH7B | 20 | candidate | 11.68 | 9 | 3 | random ASE | |
| rs9749449 | ZNF211 | 19 | candidate | 11.71 | 6 | 3 | random ASE | |
| rs4797 | SQSTM1 | 5 | candidate | 14.48 | 18 | 2 | preferential | G>A |
| rs1128933 | MAN2C1 | 15 | candidate | 12.71 | 16 | 2 | preferential | C>T |
| rs10277 | SQSTM1 | 5 | candidate | 11.78 | 16 | 2 | preferential | G>A |
| rs2249057 | NM_006031 | 21 | candidate | 13.31 | 13 | 2 | * preferential | C>A |
| rs7226091 | MGC16597 | 17 | candidate | 11.83 | 13 | 2 | * preferential | C>G |
| rs1043618 | HSPA1A | 6 | candidate | 13.6 | 12 | 2 | random ASE | |
| rs17085249 | ELL2 | 5 | candidate | 12.98 | 12 | 2 | random ASE | |
| rs2255255 | CRNKL1 | 20 | candidate | 12.86 | 12 | 2 | random ASE | |
| rs2013162 | IRF6 | 1 | candidate | 12.64 | 12 | 2 | * preferential | C>A |
| rs11121567 | PGD | 1 | candidate | 12.03 | 12 | 2 | * preferential | A>G |
| rs3780473 | ACO1 | 9 | candidate | 11.67 | 12 | 2 | random ASE | |
| rs4669 | TGFBI | 5 | candidate | 13.27 | 11 | 2 | random ASE | |
| rs7242 | SERPINE1 | 7 | candidate | 13.01 | 11 | 2 | random ASE | |
| rs2788478 | FLJ10300 | 7 | candidate | 13.04 | 10 | 2 | random ASE | |
| rs2271108 | DOCK5 | 8 | candidate | 12.85 | 10 | 2 | random ASE | |
| rs552282 | PPFIA1 | 11 | candidate | 11.58 | 10 | 2 | * preferential | C>T |
| rs1044116 | NOTCH3 | 19 | candidate | 12.21 | 9 | 2 | random ASE | |
| rs7204628 | MGC24665 | 16 | candidate | 11.84 | 9 | 2 | random ASE | |
| rs844 | FCGR2B | 1 | candidate | 13.05 | 8 | 2 | * preferential | C>T |
| rs11156878 | KIAA0391 | 14 | candidate | 12.15 | 5 | 2 | random ASE | |
| rs12780 | PRDM8 | 4 | candidate | 12.02 | 5 | 2 | random ASE | |
| rs5919 | ITGB3 | 17 | candidate | 11.55 | 4 | 2 | random ASE | |
| rs13390 | PHLDA2 | 11 | control | 12.33 | 2 | 2 | imprinting |
All SNPs had an average intensity above 11.25 and all or a subset of heterozygous samples had a significant statistical ASE test (p < 0.01). For each SNP, the ASE pattern (see text for details) was subjectively determined by examination of the bar charts, designed as in Figure 4, for all heterozygous samples. In case of preferential expression, the allele that was more expressed is indicated in the last column. *For these SNPs, the preferential bias is weaker.