Table I.
Description of genotyped SNPs
| Gene | dbSNP ID | Allele; Amino Acid Change | Location and function of SNP | dbSNP MAF Global | Study MAF Overall |
|---|---|---|---|---|---|
| miRNA coding regions | |||||
| miR-196a2 | rs11614913 | C→T | Downstream of HOXC8 and HOXC9/Noncoding RNA | 0.38 | 0.38 |
| miR-26a1 | rs7372209 | C→T | Intron variant within CTDSPL/Noncoding RNA | 0.25 | 0.27 |
| miR-27a | rs895819 | T→C | Downstream of miR-181c/d and NANOS3/Noncoding RNA | 0.36 | 0.33 |
| miR-300 | rs12894467 | C→T | Exon Chromosome 14q 32.31/Noncoding RNA | 0.43 | 0.41 |
| pre-miR-146a | rs2910164 | G→C | Upstream of miR-3142 and PTTG1 genes/Noncoding RNA | 0.38 | 0.22 |
| miRNA biogenesis genes | |||||
| AGO2 | rs4961280 | C→A | Intron variant | 0.14 | 0.19 |
| DICER1 | rs3742330 | A→G | 3′ UTR | 0.15 | 0.09 |
| DROSHA | rs10719 | C→T | 3′ UTR | 0.47 | ------ |
| DDX20 | rs197412 | T→C; [Ile⇒Thr] | Chr1: 112308953/Missense | 0.48 | 0.42 |
| GEMIN4 | rs2740348 | G→C; [Gln⇒Glu] | Chr17: 648186/Missense | 0.12 | 0.17 |
| GEMIN4 | rs7813 | C→Ta; [Arg⇒Cys] | Chr17: 744946/Missense | 0.31 | 0.39 |
| RAN | rs14035 | C→T | 3′ UTR | 0.30 | 0.31 |
| XPO5 | rs11077 | A→C | 3′ UTR | 0.38 | 0.42 |
| Genes with SNPs near or within a predicted miRNA binding siteb | |||||
| CDK6 | rs42031 | A→T | 3′ UTR; Within 30 base pairs of a putative miR-26 binding site | 0.15 | 0.20 |
| CXCL12 | rs1804429 | T→G | 3′ UTR; Within a putative miR-23a/b binding site | 0.05 | 0.03 |
| E2F2 | rs2075993 | G→Aa | 3′ UTR; Within 30 base pairs of a putative Let-7 binding site | 0.42 | 0.49 |
| HIF1A | rs2057482 | C→T | 3′ UTR; Within a putative miR-196a binding site | 0.21 | 0.16 |
| IL15 | rs10519613 | C→A | 3′ UTR; Within a putative miR-203 binding site | 0.20 | 0.10 |
| IL6R | rs4072391 | C→T | 3′ UTR; Within 30 base pairs of a putative miR-34 Family/miR-23 binding site | 0.22 | 0.20 |
| KRAS | rs9266 | C→T | 3′ UTR; Within 15 base pairs of a putative miR-181 binding site | 0.45 | 0.47 |
| RCHY1 | rs2126852 | A→G | 3′ UTR; Within 2 base pairs of a putative miR-153 binding site | 0.26 | 0.28 |
| TAB3 | rs3816757 | C→G | 3′ UTR; Within a putative miR-23 binding site | 0.21 | 0.22 |
| TP53INP1 | rs7760 | T→G | 3′ UTR; Within 30 base pairs of a putative miR-24/miR-153 binding site | 0.17 | 0.13 |
| TP53INP1 | rs896849 | T→C | 3′ UTR; Within a putative miR-155 binding site | 0.20 | 0.17 |
| WWOX | rs12828 | A→G | 3′ UTR; Within a putative miR-153 binding site | 0.44 | 0.42 |
a
Allele changes presented represent those found on HAPMAP/dbSNP. The minor alleles of two SNPs, E2F2 rs2075993 and GEMIN4 rs7813, as described in HAPMAP/dbSNP, were found to be the major alleles in our post-genotyped samples. We suspect this is due to the fact that the documented HAPMAP/dbSNP MAFs hovered around 0.50 (rs2075993: HAPMAP MAF A=0.47, major to minor GG/AG/AA; Our data MAF G=0.49 and rs7813: HAPMAP MAF T=0.49; major to minor CC/CT/TT; Our data MAF C=0.39).
b
miRNA identification and binding location predicted using Target Scan 5.2 in combination with SNP basepair location as identified in dbSNP.
MAF: minor allele frequency.
UTR: untranslated region.