Table 3 SNPs identified for various cohorts using the stringent filter (Part 2).
Cohort(s) | SNP/identity (degeneracy) | Chr: Pos. (hg17) and orientation | Duplicon length | Characterized genes and pseudogenes in duplicons | |
|---|---|---|---|---|---|
CD | rs11060028 | 12: | 128 M→ | 1.5 kb | GLT1D1 |
93.4% (P) | 10: | 102 M← | 1.2 kb | [ABCC2] | |
T1D | rs3805006 | 3: | 4,775 K→ | 402 | ITPR1, [EGO] |
93.4% (P) | 3: | 4,773 K← | 407 | ITPR1, [EGO] | |
BD, HT | rs9378249 | 6: | 31.4 M→ | 27 kb | HLA-B, DHFRP2 |
92.9% (F) | 6: | 31.3 M→ | 35 kb | HLA-C | |
HT | rs841245 | 12: | 27.1 M→ | 84 kb | - |
92.0% (P) | 12: | 27.6 M→ | 82 kb | PPFIBP1 | |
BD | rs12070036 | 1: | 224 M→ | 9 kb | ZNF678 |
91.9% | 12: | 7 M← | 3.5 kb | [PEX5] | |
91.1% | 12: | 123 M← | 10 kb | [RILPL1], [TMED2] | |
90.9% | 11: | 26 M← | 2.7 kb | - | |
RA | rs4988327 | 11: | 68 M→ | 104 kb | LRP5 |
91.2% | 22: | 24 M← | 64 kb | LRP5L | |
T2D | rs11010908 | 10: | 37.2 M→ | 6 kb | - |
90.6% | 10: | 27.2 M← | 12 kb | - | |
90.0% | 10: | 27.6 M→ | 6 kb | - | |
CAD | rs295470 | 3: | 141 M→ | 1.9 kb | ACTGP1, [RBP2] |
89.5% | 17: | 77 M← | 2.3 kb | ACTG1, [FSCN2] | |
89.1% | 1: | 92 M← | 866 | - | |
87.8% | X: | 53 M← | 636 | - | |
86.6% | 2: | 108 M→ | 568 | - | |
86.5% | 17: | 17 M→ | 696 | [FLCN] | |
85.9% | 3: | 12 M→ | 1.9 kb | SYN2 | |
BD, HT | rs2122231 | 3: | 35 M→ | 4.9 kb | - |
88.8% | 6: | 117.0 M→ | 4 kb | [NT5DC1] | |
88.6% | 18: | 5 M→ | 3.9 kb | - | |
88.5% | 2: | 194 M→ | 1 kb | - | |
87.9% | 1: | 96 M→ | 4.9 kb | - | |
87.3% | 10: | 117 M→ | 4.2 kb | - | |
86.3% | 20: | 24 M→ | 728 | - | |
BD, HT | SNP_A-1948953 | 17: | 17 M→ | 894 | LNX1 pseudogene LOC644909 |
87.0% (P) | 4: | 54 M← | 21 kb | LNX1 | |
CD | rs9839841 | 3: | 16 M→ | 110 kb | RFTN1 |
86.8% (F) | Y: | 7.6 M→ | 100 kb | RFTN1-pseudogene LOC360015, [TTTY12], [TTTY16] | |
BD, T2D | rs4850057 | 2: | 4 M→ | 4.7 kb | - |
86.8% | 9: | 35 M→ | 4.5 kb | UNC13B | |
86.1% | 11: | 5 M→ | 3.0 kb | [TRIM68], [OR51D1], [OR51E1] | |