Table 3. HaploReg results for top-ranked ADAR3 SNP rs77027562 and its proxies from univariate analyses.
| Position (hg38) | LD (r2) | SNP (Ref>Alt) | MAF in EUR | Functional Annotation | CR | Promoter histone marks | Enhancer histone marks | DNAse site | Proteins bound | eQTL | Motifs Changed |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr10:1688744 | -- | rs77027562 (A>G) | 0.02 | Intronic | No | BRN | BLD | ERalpha-a, RXRA, Zfp281 | |||
| Chr10:1675149 | 0.94 | rs12258319 (G>T) | 0.98 | Intronic | No | BLD | Pax-5 | ||||
| Chr10:1675875 | 0.94 | rs7077743 (C>T) | 0.98 | Intronic | No | BLD | BDP1, CAC-binding-protein, HNF4, p300 | ||||
| Chr10:1676470 | 0.94 | rs6560758 (T>C) | 0.98 | Intronic | No | ||||||
| Chr10:1678882 | 0.94 | rs10751814 (A>G) | 0.98 | Intronic | No | GR, Rad21 | |||||
| Chr10:1680294 | 0.94 | rs7089727 (A>G) | 0.98 | Intronic | No | ESDR, IPSC, BLD, LNG | ESC, BLD | CTCF | |||
| Chr10:1681695 | 0.94 | rs6560759 (T>C) | 0.98 | Intronic | No | ESDR, BLD | Myc | ||||
| Chr10:1687566 | 0.94 | rs79784382 (T>A) | 0.02 | Intronic | No | BRN | Cphx, Duxl, HNF6, Hmx, Hoxa13, Pbx-1, Pbx3 |
Abbreviations: LD, linkage disequilibrium; MAF, minor allele frequency; EUR, European; CR, conserved region; eQTL, expression quantitative trait loci. Tissue groups: BRN, brain cells; BLD, blood and T-cells; ESDR, embryonic stem cell derived cells; IPSC, induced pluripotent stem cells; LNG, lung cell; ESC, embryonic stem cells. Proxies were defined as variants in LD (r2>0.8) with the index SNP rs77027562 (bolded) in 1000 genomes project Phase 1 data for Europeans. All data was accessed using HaploReg v4.1 available at: http://www.broadinstitute.org/mammals/haploreg/documentation_v4.1.html. Both conservation prediction algorithms, GERP and SiPhy-omega, were used. Only eQTLs for ADAR genes (5 genes) are given.