Table 2.
SNPs in NR1I2 Located in A Predicted or Confirmed NF-κB Binding Site 1.
| SNP | Variation | Location | Allele Frequency | In Binding Site (Proximity) of: | Distance to Binding Site (bp) | Binding Spot Predicted in: |
|---|---|---|---|---|---|---|
| rs10934498 | G > A, C, T | intron | G = 0.5024 | NFκB1-p105 subunit | 0 | GTRD |
| A = 0.4976 | ||||||
| rs1403526 | A > C, G | Intron | A = 0.64900 | RelA-p65 subunit | 0 | Alggen PROMO |
| G = 0.35100 | ||||||
| rs12721602 | G > A | 5 -UTR | G = 0.98303 | RelA-p65 subunit | 13 | Alggen PROMO |
| A = 0.01697 | ||||||
| rs1054191 | G > A, C | 3′-UTR | G = 0.87745 | NF-κB, NF-κB1 p105 | 17 | Alggen PROMO |
| A = 0.12255 |
1 To cover relevant NF-kB binding sites, we took into consideration the human NF-κB p105 subunit, the NF-κB p100 subunit, and the RelA-p65 subunit binding sites. An arbitrary threshold of 25 base pairs from confirmed or predicted NF-κB binding spot was set to identify relevant NR1I2 SNPs [98]. Matching score to consensus sequence was set at 85% for the Alggen PROMO database. For the GTRD, CHIP-seq derived data was collected from the meta clusters data set. Allele frequencies were obtained from the GnomeAD or 1000Genomes database.