Table 1.
Characteristics and frequencies of variants observed in the COGA data set
| Gene | Amino acid position | CHR | hg19 position | A1 | A2 | PhyloP score | SIFT | Polyphen | Frequency in COGA EAs | Frequency in COGA AAs | Frequency in COGEND EAs | Frequency in COGEND AAs |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CHRNB3 | L250P | 8 | 42587199 | C | T | 5.117 | + | ++ | 0.0021 | 0 | 0 | 0 |
| CHRNB3 | S326T | 8 | 42587426 | T | A | 0.672 | + | 0 | 0.0028 | 0 | 0.0022 | |
| CHRNB3 | H329Y | 8 | 42587435 | C | T | 3.982 | + | ++ | 0.0019 | 0.0120 | 0.0020 | 0 |
| CHRNB3 | V368M | 8 | 42587552 | A | G | 4.767 | 0.0188 | 0 | 0 | 0 | ||
| CHRNB3 | K451E | 8 | 42591735 | G | A | 2.350 | 0.0096 | 0.0423 | 0.0007 | 0.0515 | ||
| CHRNA6 | N447S | 8 | 42611002 | T | C | 3.502 | + | ++ | 0.0007 | 0 | 0 | 0.0006 |
| CHRNA6 | K408E | 8 | 42611120 | C | T | 3.527 | 0.0028 | 0 | 0 | 0 | ||
| CHRNA6 | V314G | 8 | 42611401 | C | A | 7.129 | + | ++ | 0.0087 | 0.0005 | 0 | 0 |
| CHRNA6 | I226T | 8 | 42611665 | C | T | 5.214 | + | 0.0069 | 0 | 0 | 0 | |
| CHRNA6 | V110I | 8 | 42612117 | C | T | 2.128 | 0.0035 | 0 | 0 | 0 | ||
| CHRNA6 | R96H | 8 | 42612158 | C | T | 0.939 | + | + | 0.0007 | 0.0002 | 0 | 0.0010 |
| CHRNA6 | S43P | 8 | 42620300 | A | G | 1.234 | + | 0.0034 | 0.0110 | 0.0003 | 0.0145 | |
| CHRNA5 | F76V | 15 | 78873272 | T | G | 4.712 | ++ | 0.0021 | 0 | 0 | 0 | |
| CHRNA5 | V134I | 15 | 78880752 | A | G | 6.721 | + | ++ | 0.0175 | 0.0042 | 0.0147 | 0.0011 |
| CHRNA5 | K167R | 15 | 78882233 | A | G | 5.403 | + | ++ | 0.0007 | 0.0158 | 0.0003 | 0.0157 |
| CHRNA5 | L317V | 15 | 78882682 | G | C | 2.262 | + | ++ | 0.0038 | 0.0014 | 0 | 0 |
| CHRNA5 | L363Q | 15 | 78882821 | T | A | 4.767 | + | + | 0.0034 | 0.0433 | 0.0005 | 0.0576 |
| CHRNA5 | D398N | 15 | 78882925 | A | G | 3.766 | 0.2920 | 0.0520 | 0.3494 | 0.0478 | ||
| CHRNA3 | E363D | 15 | 78893895 | G | C | 3.285 | 0.0042 | 0 | 0 | 0 | ||
| CHRNA3 | R37H | 15 | 78911230 | C | T | 2.671 | + | ++ | 0.0458 | 0.0116 | 0.0521 | 0.0088 |
| CHRNB4 | M467V | 15 | 78917573 | T | C | 1.584 | 0.0192 | 0.0637 | 0 | 0.0759 | ||
| CHRNB4 | A435V | 15 | 78921343 | A | G | −0.549 | + | ++ | 0.0145 | 0.0007 | 0 | 0 |
| CHRNB4 | A435T | 15 | 78921344 | T | C | 3.053 | + | + | 0 | 0.0011 | 0 | 0 |
| CHRNB4 | R421X | 15 | 78921386 | A | G | 1.653 | + | + | 0.0014 | 0 | 0 | 0 |
| CHRNB4 | T375I | 15 | 78921523 | G | A | 2.262 | + | 0 | 0.0168 | 0 | 0.0169 | |
| CHRNB4 | R349C | 15 | 78921602 | A | G | 1.960 | + | ++ | 0.0842 | 0.0030 | 0.0072 | 0.0006 |
| CHRNB4 | V311I | 15 | 78921716 | T | C | 2.402 | + | 0.0062 | 0 | 0 | 0 | |
| CHRNB4 | S140G | 15 | 78922229 | C | T | 2.269 | + | 0.0555 | 0.0410 | 0.0040 | 0.0434 | |
| CHRNB4 | R136Q | 15 | 78922240 | C | T | 0.410 | 0.1243 | 0.0024 | 0.0114 | 0.0016 | ||
| CHRNB4 | T91I | 15 | 78923505 | A | G | 2.161 | 0.3911 | 0.0074 | 0.0457 | 0.0067 | ||
| CHRNB4 | R18C | 15 | 78933424 | A | G | 5.625 | 0.0014 | 0 | 0 | 0 |
For SIFT predictions, variants predicted to be damaging are depicted with +. For polyphen predictions, variants predicted to be ‘possibly damaging’ are depicted with + and variants predicted to be ‘probably damaging’ are depicted with ++.