Table 1.
Gene-based tests of association with alcohol dependence in the COGA case/control sample
| Gene | Protein | NSNP | NSIG | ISIG | p-value |
|---|---|---|---|---|---|
| ACTB | ACTIN | 4 | 0 | 0 | 1.000 |
| ACTL6A | BAF53A | 24 | 3 | 2 | 0.163 |
| ACTL6B | BAF53B | 16 | 0 | 0 | 1.000 |
| ARID1A | BAF250A | 116 | 4 | 3 | 0.342 |
| ARID1B | BAF250B | 810 | 19 | 9 | 0.957 |
| ARID2 | BAF200 | 119 | 2 | 1 | 0.712 |
| BCL11A | CTIP1 | 153 | 5 | 3 | 0.038* |
| BCL11B | CTIP2 | 150 | 2 | 2 | 0.739 |
| BCL7A | BCL7A | 57 | 7 | 3 | 0.262 |
| BCL7B | BCL7B | 59 | 1 | 1 | 0.042* |
| BCL7C | BCL7C | 11 | 0 | 0 | 1.000 |
| BRD7 | BRD7 | 85 | 3 | 1 | 0.021* |
| BRD9 | BRD9 | 71 | 2 | 2 | 0.315 |
| DPF1 | BAF45B | 30 | 0 | 0 | 1.000 |
| DPF2 | BAF45D | 36 | 11 | 1 | 0.066 |
| DPF3 | BAF45C | 523 | 28 | 10 | 0.303 |
| PBRM1 | PBRM1 | 262 | 36 | 2 | 0.300 |
| PHF10 | BAF45A | 37 | 0 | 0 | 1.000 |
| SMARCA2 | hBRM | 289 | 22 | 11 | 0.233 |
| SMARCA4 | BRG1 | 280 | 11 | 1 | 0.928 |
| SMARCB1 | BAF47/INI1 | 202 | 136 | 5 | 0.042* |
| SMARCC1 | BAF155 | 207 | 14 | 6 | 0.184 |
| SMARCC2 | BAF170 | 10 | 0 | 0 | 1.000 |
| SMARCD1 | BAF60A | 19 | 3 | 1 | 0.016* |
| SMARCD2 | BAF60B | 20 | 0 | 0 | 1.000 |
| SMARCD3 | BAF60C | 77 | 0 | 0 | 1.000 |
| SMARCE1 | BAF57 | 33 | 2 | 2 | 0.405 |
| SS18 | SS18 | 119 | 3 | 3 | 0.294 |
| SS18L1 | CREST | 123 | 52 | 2 | 0.008** |
Note: For each gene, NSNP= number of SNPs; NSIG= number of significant SNPs; ISIG= number of independent significant SNPs.
*
p-value <0.05;
**
p-value ≤ 0.01.
Accordingly, test statistics are corrected for multiple testing with each gene, but not across all genes. We note that these analyses are presented as secondary analyses to supplement the primary test of the overall gene set and provide insight into the genes in the set most strongly driving the overall association signal for the SWI/SNF complex.