Table 2. Allele switching during transition from iPSCs to neurons.
| chr | SNP ID | ref | alt | iPSC ref | iPSC alt | Neurons ref | Neurons alt | Genes |
| chr1 | rs12123760 | T | C | 2 | 8 | 21 | 5 | ST6GALNAC3 |
| chr1 | rs10492963 | C | T | 1 | 13 | 13 | 1 | RERE |
| chr2 | rs3811568 | A | G | 11 | 2 | 2 | 9 | FMNL2 |
| chr2 | rs6757809 | T | C | 2 | 13 | 10 | 2 | NOL10 |
| chr2 | rs4674015 | A | G | 1 | 15 | 10 | 2 | SPATS2L |
| chr3 | rs9860614 | A | G | 8 | 2 | 0 | 11 | RUVBL1 |
| chr3 | rs9817055 | G | A | 16 | 1 | 0 | 16 | CLASP2 |
| chr3 | rs1975760 | T | C | 2 | 16 | 13 | 3 | ZNF148 |
| chr3 | rs3846072 | C | T | 1 | 9 | 11 | 1 | MED12L/P2RY14 |
| chr3 | rs7644975 | G | A | 1 | 10 | 23 | 4 | ERC2 |
| chr4 | rs7678728 | T | G | 1 | 9 | 10 | 2 | ANK2 |
| chr4 | rs236985 | G | A | 2 | 8 | 9 | 2 | AFF1 |
| chr5 | rs7712332 | A | G | 13 | 2 | 2 | 11 | MSH3 |
| chr5 | rs2115436 | T | A | 2 | 10 | 13 | 2 | SCAMP1 |
| chr6 | rs9373571 | T | A | 22 | 1 | 2 | 8 | ASCC3 |
| chr6 | rs577372 | A | G | 2 | 9 | 11 | 2 | MTO1 |
| chr7 | rs2691561 | T | A | 13 | 3 | 2 | 15 | SNX13 |
| chr7 | rs258654 | C | T | 9 | 1 | 1 | 14 | CACNA2D1 |
| chr7 | rs674462 | A | T | 2 | 9 | 9 | 2 | MRPL32 |
| chr8 | rs6987331 | T | G | 12 | 3 | 1 | 9 | SNTB1 |
| chr8 | rs2980683 | G | C | 1 | 10 | 10 | 1 | AGPAT5 |
| chr9 | rs7019027 | G | A | 12 | 3 | 0 | 11 | KDM4C |
| chr9 | rs1411675 | G | A | 13 | 3 | 1 | 9 | FXN |
| chr9 | rs2297499 | C | G | 9 | 2 | 4 | 16 | TLE4 |
| chr9 | rs7020390 | A | G | 2 | 9 | 10 | 2 | UHRF2 |
| chr10 | rs1127047 | G | A | 9 | 1 | 2 | 8 | PITRM1 |
| chr10 | rs1937971 | A | C | 17 | 0 | 3 | 16 | NRG3 |
| chr10 | rs11817793 | G | A | 8 | 2 | 1 | 10 | LARP4B |
| chr10 | rs2418929 | C | G | 12 | 2 | 1 | 10 | KIF20B |
| chr10 | rs10795321 | C | G | 0 | 13 | 32 | 5 | FAM188A |
| chr10 | rs7084542 | A | G | 3 | 14 | 39 | 9 | RP11-429G19.2 |
| chr12 | rs4130296 | A | C | 3 | 15 | 22 | 3 | FBXW8 |
| chr13 | rs11619378 | T | G | 12 | 2 | 2 | 16 | ABHD13 |
| chr13 | rs7983071 | G | A | 10 | 2 | 1 | 20 | GPC6 |
| chr13 | rs9535499 | G | C | 3 | 34 | 21 | 4 | DLEU7/DLEU7-AS1 |
| chr14 | rs12893288 | C | T | 16 | 4 | 3 | 13 | intergenetic |
| chr14 | rs10131048 | T | C | 3 | 14 | 15 | 3 | ZFYVE26 |
| chr16 | rs17139246 | T | C | 10 | 2 | 0 | 14 | RBFOX1 |
| chr17 | rs2106663 | G | A | 2 | 10 | 9 | 1 | BRIP1 |
| chr17 | rs2302235 | G | A | 4 | 21 | 9 | 2 | FAM20A |
| chr17 | rs9646411 | C | T | 0 | 10 | 10 | 0 | AMAC1L3 |
| chr18 | rs7233697 | T | C | 8 | 2 | 1 | 17 | MEP1B |
Genes that showed >4 changes in allele distribution occurring during the transition from iPSCs to neurons. Abbreviations: chromosome number (chr); SNP identification number (SNP ID); reference allele (ref); alternative allele (alt); high quality reads in iPSCs (iPSC ref and iPSC alt); high quality reads in neurons (Neuron ref and Neurons alt).