RS_Number | Position | Alleles | MAF | Distance | Dprime | R2 | Correlated_Alleles | FORGEdba | RegulomeDBb | Function |
|---|
rs3918262 | chr20:44643770 | (A/G) | 0.370 | 4989 | 1.000 | 0.332 | A = A, G = G | 8 | 2b | NA |
rs17577 | chr20:44643111 | (G/A) | 0.168 | 4330 | 0.166 | 0.010 | NA | 10 | 2b | missense |
rs3918251 | chr20:44638781 | (A/G) | 0.361 | 0 | 1.000 | 1.000 | A = A, G = G | 8 | 4 | NA |
rs2250889 | chr20:44642406 | (G/C) | 0.250 | 3625 | 1.000 | 0.591 | G = A, C = G | 8 | 4 | missense |
rs3918254 | chr20:44640391 | (C/T) | 0.188 | 1610 | 0.929 | 0.112 | C = A, T = G | 9 | 4 | NA |
rs9509 | chr20:44645153 | (T/C) | 0.221 | 6372 | 0.478 | 0.037 | NA | 8 | 6 | NA |
- 5 SNPs with high regulatory potentials were selected by securing FORGEdb and RegulomeDB. SNPs selected for subsequent analyses were marked in bold
- Abbreviations: MAF Minor Allele Frequency, MAF was presented as (MAF in cases)/(MAF in controls), Dprime SNP haplotype frequency, R2 SNP correlation, Correlated alleles refer to alleles that are correlated if linkage disequilibrium is present (R2 > 0.1). rs3918251 was used as reference SNP
- aFORGEdb scores indicated the regulatory potentials for SNPs (https://forge2.altiusinstitute.org/files/forgedb.html). FORGEdb scores of from 0 to 10 and higher scores indicate greater likelihood that the SNP is a regulatory variant
- bRegulomeDB scores indicated the regulatory potentials for SNPs (https://regulomedb.org/regulome-search). RegulomeDB scores of 1–6 indicate most to least likely to affect binding and expression of target gene. A score 2b denotes that the SNP was within a potential regulatory region supported by TF binding, binding motif, DNase Foorprint, and DNase peak data
