Table 2 Selection of SNPs as neutral markers surrounding the mutant allele.
Gene | Nucleotide variants | SNP ID | Distance to SGCB c.544 T > G (bp) | Ancestral Allele | MAF (1KGP3-ALL) | MAF (1KGP3-SAS) | MAF (gnomAD-ALL) | MAF (gnomAD-SAS) |
|---|---|---|---|---|---|---|---|---|
DCUN1D4 | G/A | rs10009426 | ( −) 184,060 | G | 0.456 (A) | 0.491 (A) | 0.44 (G) | 0.472 (G) |
DCUN1D4 | A/G | rs6824707 | ( −) 183,788 | A | 0.458 (G) | 0.491 (G) | 0.436 (A) | 0.471 (A) |
DCUN1D4 | C/G | rs6851073 | ( −) 180,462 | C | 0.477 (C) | 0.497 (C) | 0.581 (C) | 0.400 (C) |
DCUN1D4 | T/A | rs2271046 | ( −) 142,161 | T | 0.455 (A) | 0.491 (A) | 0.357 (T) | 0.45 (T) |
LRRC66 | G/A | rs225160 | ( −) 10,734 | G | 0.644(G) | 0.67(G) | 0.563 (G) | 0.648 (G) |
SGCB | T/G | rs751427686 | 0 | T | 0 (G) | 0 (G) | 1.193e − 05 (G) | 9.8e − 05 (G) |
SGCB | A/G | rs225170 | ( +) 1077 | A | 0.644 (A) | 0.673 (A) | 0.564 (A) | 0.648 (A) |
SPATA18 | C/A | rs999634 | ( +) 32,140 | C | 0.642 (C) | 0.688(C) | NA | NA |
SPATA18 | T/C | rs3860707 | ( +) 43,270 | T | 0.616 (T) | 0.661 (T) | 0.508 (T) | 0.605 (T) |
SPATA18 | C/G | rs35414474 | ( +) 53,861 | C | 0.158 (G) | 0.299 (G) | 0.127 (G) | 0.277 (G) |
SPATA18 | A/T | rs17611952 | ( +) 54,039 | A | 0.157 (T) | 0.3 (T) | 0.125 (T) | 0.276 (T) |
