Table 5.
Bioinformatics analyses on replicable risk CHRN SNPs.
| SNP | Chr | Position | Location | Allele Frequency | 2nd RNA Alteration | Bioinformatics | |||
|---|---|---|---|---|---|---|---|---|---|
| (Build 37) | Allele | European | African | Asian | |||||
| rs10958725 | 8 | 42524584 | 5′ to CHRNB3 | G | 0.822 | 0.239 | 0.792 | Highly significant | -- |
| rs10958726 | 8 | 42535909 | 5′ to CHRNB3 | T | 0.807 | 0.328 | 0.816 | no | -- |
| rs13273442 | 8 | 42544017 | 5′ to CHRNB3 | G | 0.825 | 0.35 | 0.826 | Significant | -- |
| rs4736835 | 8 | 42547033 | 5′ to CHRNB3 | C | 0.825 | 0.35 | 0.826 | Significant | LncRNA |
| rs1955186 | 8 | 42549491 | 5′ to CHRNB3 | C | 0.833 | 0.326 | 0.875 | Mild | TFBS, LncRNA |
| rs1955185 | 8 | 42549647 | 5′ to CHRNB3 | T | 0.822 | 0.233 | 0.836 | no | TFBS, LncRNA |
| rs13277254 | 8 | 42549982 | 5′ to CHRNB3 | A | 0.833 | 0.435 | 0.875 | no | TFBS, LncRNA |
| rs13277524 | 8 | 42550057 | 5′ to CHRNB3 | T | 0.833 | 0.326 | 0.875 | Significant | TFBS, LncRNA |
| rs6474412 | 8 | 42550498 | 5′ to CHRNB3 | T | 0.81 | 0.309 | 0.824 | Significant | TFBS, LncRNA |
| rs6474413 | 8 | 42551064 | 5′ to CHRNB3 | T | 0.833 | 0.235 | 0.875 | no | TFBS, LncRNA |
| rs7004381 | 8 | 42551161 | 5′ to CHRNB3 | G | 0.825 | 0.339 | 0.826 | Mild | TFBS, LncRNA |
| rs4950 | 8 | 42552633 | 5′UTR of CHRNB3 | A | 0.828 | 0.182 | 0.826 | no | TFBS, LncRNA |
| rs13280604 | 8 | 42559586 | Intron 1 of CHRNB3 | A | 0.825 | 0.178 | 0.826 | no | LncRNA |
| rs4952 | 8 | 42587065 | Exon 6 of CHRNB3 | C | 0.983 | 1 | 1 | Highly significant | -- |
| rs4954 | 8 | 42587796 | Intron 6 of CHRNB3 | A | 0.973 | 0.773 | 0.885 | no | chromatin |
| rs16969968 (Asp398Asn) | 15 | 78882925 | Exon 5 of CHRNA5 | G | 0.587 | 1 | 0.982 | Highly significant | splicing,tolerated, benign,conservative |
| rs1051730 | 15 | 78894339 | Exon 7 of CHRNA3 | G | 0.608 | 0.876 | 0.982 | no | CpG |
| rs6495308 | 15 | 78907656 | Intron 6 of CHRNA3 | T | 0.792 | 0.661 | 0.244 | no | -- |
| rs2236196 | 20 | 61977556 | 3′UTR of CHRNA4 | A | 0.744 | 0.458 | 0.889 | no | chromatin |
2nd RNA alteration, the alteration of secondary RNA structure predicted using MFOLD; LncRNA, these SNPs are located in LncRNAs; TFBS, these SNPs are located in the transcription factor binding sites; chromatin, this SNP is located in an open chromatin region; splicing, this SNP is located in an exonic splicing silencer or enhancer; tolerated/benign, these SNPs are predicted by SIFT/Polyphen not to significantly affect protein function or structure; conservative, this SNP is predicted to be conservative; CpG, this SNP is located within a 234 bp methylated CpG island.