Table 1.
Polymorphisms identified by POU5F1 re-sequencing
| Site1 | Location | NCBI rsnumber2 | Major allele | Minor allele | Minor Allele Frequency | Site | Location | NCBI rsnumber | Major allele | Minor allele | Minor Allele Frequency | ||
| AD3 | ED | AD | ED | ||||||||||
| -2812 | 5' | rs2269712 | C | T | 0.15 | 0.22 | 1736 | Intron 1 | rs3130502 | C | T | 0.17 | 0.20 |
| -2730 | 5' | rs2269713 | T | C | 0.17 | 0.00 | 1825 | Intron 1 | rs9263809 | T | C | 0.17 | 0.13 |
| -2482 | 5' | rs17197241 | C | T | 0.08 | 0.00 | 1827 | Intron 1 | A | G | 0.02 | 0.07 | |
| -2411 | 5' | rs6910473 | C | T | 0.15 | 0.13 | 2524 | Intron 1 | C | T | 0.06 | 0.13 | |
| -2361 | 5' | G | A | 0.02 | 0.00 | 2578 | Intron 1 | T | A | 0.02 | 0.00 | ||
| -2344 | 5' | rs1265158 | G | C | 0.46 | 0.35 | 2625 | Intron 1 | A | C | 0.06 | 0.13 | |
| -2218 | 5' | rs9501065 | G | A | 0.21 | 0.04 | 2665 | Intron 1 | + | - | 0.38 | 0.46 | |
| -2135 | 5' | rs885948 | C | T | 0.33 | 0.46 | 2679 | Intron 1 | + | - | 0.06 | 0.13 | |
| -2121 | 5' | rs6909939 | C | T | 0.15 | 0.13 | 2697 | Intron 1 | A | G | 0.17 | 0.20 | |
| -1892 | 5' | C | T | 0.02 | 0.00 | 3679 | Intron 1 | + | - | 0.17 | 0.20 | ||
| -1827 | 5' | G | C | 0.04 | 0.00 | 3738 | Intron 1 | + | - | 0.04 | 0.00 | ||
| -1823 | 5' | rs885949 | A | G | 0.19 | 0.16 | 3781 | Intron 1 | T | C | 0.06 | 0.13 | |
| -1772 | 5' | rs3132518 | C | G | 0.42 | 0.36 | 3807 | Intron 1 | C | T | 0.17 | 0.13 | |
| -1755 | 5' | rs885950 | T | G | 0.40 | 0.48 | 3815 | Intron 1 | rs11965454 | A | G | 0.15 | 0.00 |
| -1694 | 5' | rs885951 | G | T | 0.40 | 0.48 | 4083 | Intron 1 | G | A | 0.06 | 0.13 | |
| -1691 | 5' | rs3132519 | G | A | 0.40 | 0.36 | 4202 | Intron 1 | C | T | 0.02 | 0.00 | |
| -1676 | 5' | rs3094190 | T | C | 0.44 | 0.36 | 4231 | Intron 1 | rs3132526 | A | G | 0.40 | 0.46 |
| -1671 | 5' | G | A | 0.00 | 0.02 | 4284 | Intron 1 | T | G | 0.00 | 0.09 | ||
| -1650 | 5' | rs1265159 | C | T | 0.21 | 0.23 | 4285 | Intron 1 | + | - | 0.08 | 0.17 | |
| -1611 | 5' | rs3132520 | G | A | 0.40 | 0.55 | 4322 | Intron 1 | rs1265163 | G | C | 0.17 | 0.20 |
| -1566 | 5' | rs28383834 | -4 | + | 0.04 | 0.09 | 4466 | Exon 16 | rs3130932 | T | G | 0.23 | 0.33 |
| -1107 | 5' | rs1108746 | G | T | 0.11 | 0.10 | 4515 | Exon 16 | rs9501063 | C | G | 0.15 | 0.00 |
| -1093 | 5' | rs885952 | G | A | 0.43 | 0.55 | 4539 | Exon 16 | C | T | 0.06 | 0.13 | |
| -1055 | 5' | rs879882 | G | A | 0.50 | 0.21 | 4746 | Intron 2 | A | G | 0.06 | 0.13 | |
| -985 | 5' | rs5875289 | - | + | 0.17 | 0.17 | 4787 | Intron 2 | rs9281233 | + | - | 0.23 | 0.33 |
| -734 | 5' | rs17197220 | A | G | 0.04 | 0.04 | 4834 | Intron 2 | + | - | 0.35 | 0.33 | |
| -643 | 5' | rs9263818 | G | T | 0.17 | 0.14 | 4908 | Intron 2 | rs2106074 | T | C | 0.23 | 0.33 |
| -520 | 5' | rs9263817 | C | T | 0.17 | 0.14 | 5724 | Intron 4 | rs3064866 | + | - | 0.23 | 0.33 |
| -513 | 5' | rs3094191 | A | G | 0.10 | 0.23 | 5763 | Intron 4 | rs9263795 | A | G | 0.00 | 0.13 |
| -400 | 5' | rs9263816 | C | A | 0.17 | 0.14 | 5770 | Intron 4 | rs2394882 | G | T | 0.23 | 0.33 |
| -310 | 5' | rs17190839 | C | T | 0.15 | 0.00 | 6005 | Exon 5 | rs1061118, rs17197178 | T | C | 0.25 | 0.25 |
| -75 | 5' | rs17197199 | G | A | 0.15 | 0.00 | 6116 | 3' UTR | rs3734864 | G | A | 0.02 | 0.00 |
| 21 | Exon 15 | rs2077010 | G | A | 0.42 | 0.50 | 6279 | 3' | rs13409 | C | T | 0.41 | 0.48 |
| 27 | Exon 15 | rs1265160 | C | T | 0.15 | 0.20 | 6334 | 3' | rs3130933 | G | A | 0.00 | 0.11 |
| 291 | Exon 1 | rs1062630 | C | T | 0.20 | 0.20 | 6466 | 3' | T | C | 0.02 | 0.00 | |
| 561 | Intron 1 | rs3130504 | A | T | 0.17 | 0.20 | 6582 | 3' | rs17190811 | T | A | 0.06 | 0.13 |
| 594 | Intron 1 | rs3094192 | C | G | 0.17 | 0.20 | 6623 | 3' | C | T | 0.02 | 0.00 | |
| 600 | Intron 1 | G | A | 0.25 | 0.17 | 6712 | 3' | rs9501062 | A | G | 0.12 | 0.00 | |
| 601 | Intron 1 | C | T | 0.04 | 0.00 | 6808 | 3' | G | T | 0.17 | 0.20 | ||
| 624 | Intron 1 | rs3094193 | A | C | 0.33 | 0.33 | 6810 | 3' | A | T | 0.17 | 0.20 | |
| 639 | Intron 1 | rs3132522 | G | A | 0.17 | 0.20 | 6813 | 3' | + | - | 0.17 | 0.20 | |
| 653 | Intron 1 | rs9263811 | G | A | 0.17 | 0.13 | 6822 | 3' | G | A | 0.02 | 0.00 | |
| 663 | Intron 1 | C | G | 0.19 | 0.04 | 6851 | 3' | rs3132528 | A | G | 0.17 | 0.20 | |
| 679 | Intron 1 | - | + | 0.42 | 0.50 | 7144 | 3' | rs17190798 | T | A | 0.06 | 0.14 | |
| 683 | Intron 1 | T | C | 0.04 | 0.07 | 7211 | 3' | rs17190783 | T | C | 0.06 | 0.14 | |
| 690 | Intron 1 | C | T | 0.19 | 0.04 | 7555 | 3' | rs17190776 | C | T | 0.06 | 0.13 | |
| 709 | Intron 1 | T | G | 0.02 | 0.00 | 7599 | 3' | rs1044870 | G | A | 0.17 | 0.13 | |
| 742 | Intron 1 | C | T | 0.10 | 0.00 | 7660 | 3' | rs1841 | T | C | 0.04 | 0.07 | |
| 770 | Intron 1 | rs9263810 | C | G | 0.17 | 0.13 | 7827 | 3' | rs1419881 | T | C | 0.44 | 0.50 |
| 1424 | Intron 1 | A | G | 0.02 | 0.00 | 7845 | 3' | rs9501503 | G | C | 0.02 | 0.00 | |
| 1570 | Intron 1 | rs3132523 | G | A | 0.17 | 0.20 | 7918 | Exon7 | rs1065461 | G | A | 0.17 | 0.20 |
| 1650 | Intron 1 | rs17840029 | T | C | 0.04 | 0.04 | 8128 | Intron7 | G | A | 0.02 | 0.00 | |
| 1688 | Intron 1 | rs3132524 | G | A | 0.17 | 0.20 | 8169 | Intron7 | rs3216869 | + | - | 0.12 | 0.00 |
1Polymorphism sites are named according to the number of bases from the first transcription start site, 2National Center for Biotechnology Information (NCBI) rsnumbers are included if they have been previously published, 3AD, African-descent and ED, European-descent populations, 4 (-), deletion and (+), insertion polymorphisms. The (+) allele for each loci is as follows: -1566 = G, -985 = G, 679 = TCTG, 2665 = G, 2679 = AG, 3679 = GAG, 3738 = TG, 4284 = CTC, 4787 = CT, 4834 = GGGCTT, 5724 = TC, 6813 = A, 8169 = GAAG, 5Exon for POU5F1 isoform 1 only, 6Exon for POU5F1 isoform 2 only, 7Loci are 3' of the POU5F1 gene, and in the exon/intron of the flanking TCF 19 gene.