Table 1 Annotations of Korean only SNVs and shared SNVs
Category | SNV-11 (%) | SNV-352 (%) | Shared with 1KGP & HapMap (%) | Shared with 1KGP (%) | Shared with 1KGP or HapMap (%) | |
|---|---|---|---|---|---|---|
CDS3 and splicing regions | Synonymous Variant | 3,587 (0.296) | 29 (0.229) | 13,978 (0.522) | 25,988 (0.354) | 26,030 (0.355) |
| Â | Missense Variant | 6,620 (0.545) | 40 (0.316) | 14,147 (0.528) | 26,835 (0.366) | 26,909 (0.367) |
| Â | Stop Gained Variant | 173 (0.014) | 1 (0.008) | 129 (0.005) | 343 (0.005) | 348 (0.005) |
| Â | Stop Lost Variant | 20 (0.002) | 0 (0) | 70 (0.003) | 105 (0.001) | 106 (0.001) |
| Â | Stop Retained Variant | 5 (0.000) | 0 (0) | 22 (0.001) | 45 (0.001) | 45 (0.001) |
| Â | Initiator Codon Variant | 18 (0.001) | 0 (0) | 62 (0.002) | 104 (0.001) | 104 (0.001) |
| Â | Incomplete Terminal Codon Variant | 4 (0.000) | 0 (0) | 8 (0.000) | 16 (0.000) | 16 (0.000) |
| Â | Coding Sequence Variant | 5 (0.000) | 0 (0) | 15 (0.001) | 29 (0.000) | 29 (0.000) |
| Â | Splice Donor Variant | 162 (0.013) | 0 (0) | 226 (0.008) | 557 (0.008) | 562 (0.008) |
| Â | Splice Acceptor Variant | 95 (0.008) | 0 (0) | 165 (0.006) | 357 (0.005) | 359 (0.005) |
| Â | Splice Region Variant | 1,496 (0.123) | 18 (0.142) | 3,983 (0.149) | 8,298 (0.113) | 8,312 (0.113) |
Regulatory region and adjacent regions to CDS | 5' Prime UTR4 Variant | 3,358 (0.277) | 22 (0.174) | 8,462 (0.316) | 19,526 (0.266) | 19,568 (0.267) |
| Â | 3' Prime UTR Variant | 13,638 (1.124) | 99 (0.783) | 37,145 (1.387) | 76,397 (1.042) | 76,547 (1.043) |
| Â | Regulatory Region Variant | 117,783 (9.705) | 1,186 (9.383) | 267,822 (10.002) | 649,464 (8.859) | 650,799 (8.864) |
| Â | TF Binding Site Variant | 1,645 (0.136) | 11 (0.087) | 2,511 (0.094) | 6,913 (0.094) | 6,927 (0.094) |
| Â | Upstream Gene Variant | 185,499 (15.285) | 2,010 (15.902) | 343,491 (12.827) | 989,954 (13.503) | 991,984 (13.511) |
| Â | Downstream Gene Variant | 192,188 (15.836) | 1,999 (15.815) | 370,173 (13.824) | 1,028,139 (14.024) | 1,030,243 (14.032) |
non-coding regioins | NMD5 Transcript Variant | 127,138 (10.476) | 634 (5.016) | 287,027 (10.719) | 779,516 (10.633) | 780,572 (10.631) |
| Â | Mature miRNA Variant | 48 (0.004) | 1 (0.008) | 20 (0.001) | 146 (0.002) | 146 (0.002) |
| Â | Noncoding Exon Variant | 28,539 (2.352) | 292 (2.310) | 62,513 (2.334) | 143,214 (1.953) | 143,617 (1.956) |
| Â | Noncoding Transcript Variant | 376,646 (31.035) | 4,590 (36.313) | 815,372 (30.449) | 2,191,354 (29.890) | 2,195,528 (29.903) |
Intron Variant | 602,464 (49.642) | 5,272 (41.709) | 1,379,647 (51.521) | 3,703,303 (50.513) | 3,708,842 (50.515) | |
Intergenic Variant | 462,916 (38.144) | 5,264 (41.646) | 1,030,973 (38.501) | 2,876,064 (39.230) | 2,879,598 (39.220) | |
Total SNVs | 1,213,613 | 12,640 | 2,677,812 | 7,331,322 | 7,342,113 | |