Table 2.
Painful crisis association results
| SNP | Chromosome (position) | Effect allele/other allele | Effect allele frequency | CSSCD discovery | CSSCD replication | Combined CSSCD | Duke | Gene (annotation) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| β (SE) | P value | β (SE) | P value | β (SE) | P value | OR (95% CI) | P value | |||||
| rs12720497 | 1 (185097043) | T/C | 0.10 | 0.529 (0.125) | 3.9 × 10−5 | 0.336 (0.194) | .08 | 0.470 (0.107) | 1.2 × 10−5 | NA | NA | PLA2G4A (intron) |
| rs540006 | 2 (70636930) | T/C | 0.98 | −0.723 (0.167) | 2.9 × 10−5 | −0.310 (0.338) | .36 | −0.637 (0.154) | 3.5 × 10−5 | 0.94 [0.08, 10.65] | .96 | Intergenic |
| rs3917296 | 2 (102151265) | A/G | 0.98 | −0.773 (0.172) | 1.5 × 10−5 | 1.393 (1.013) | .17 | −0.708 (0.176) | 5.5 × 10−5 | 8.5 × 10−8 [-inf, 0] | 1.00 | IL1R1 (intron) |
| rs324035 | 3 (115351544) | A/C | 0.74 | −0.303 (0.076) | 1.2 × 10−4 | 0.061 (0.170) | .72 | −0.239 (0.071) | 8.3 × 10−4 | NA | NA | DRD3 (intron) |
| rs10513478 | 3 (156723359) | T/C | 0.02 | 0.836 (0.209) | 1.1 × 10−4 | −1.779 (2.450) | .47 | 0.816 (0.216) | 1.5 × 10−4 | 0.59 [0.13, 2.72] | .50 | PLCH1 (intron) |
| rs11732673 | 4 (2652853) | A/G | 0.77 | −0.338 (0.089) | 2.2 × 10−4 | −0.374 (0.154) | .02 | −0.347 (0.079) | 9.9 × 10−6 | NA | NA | FAM193A (intron) |
| rs6858735 | 4 (37592622) | T/C | 0.12 | 0.375 (0.095) | 1.4 × 10−4 | −0.165 (0.218) | .45 | 0.283 (0.090) | 1.6 × 10−3 | NA | NA | TBC1D1 (intron) |
| rs13113915 | 4 (187702958) | A/G | 0.40 | 0.261 (0.067) | 1.6 × 10−4 | 0.245 (0.131) | .06 | 0.258 (0.061) | 2.5 × 10−5 | NA | NA | MTNR1A (intron) |
| rs10942625 | 5 (90446448) | A/G | 0.25 | −0.362 (0.091) | 1.2 × 10−4 | −0.329 (0.178) | .07 | −0.355 (0.083) | 2.0 × 10−5 | 0.93 [0.68, 1.28] | .66 | GPR98 (intron) |
| rs1851426 | 7 (99220872) | A/G | 0.68 | −0.290 (0.074) | 1.6 × 10−4 | 0.269 (0.145) | .07 | −0.168 (0.068) | 0.01 | NA | NA | CYP3A4 (intergenic) |
| rs10107231 | 8 (18098691) | T/C | 0.83 | −0.375 (0.096) | 1.7 × 10−4 | −0.105 (0.203) | .61 | −0.322 (0.089) | 3.1 × 10−4 | NA | NA | NAT1 (intron) |
| rs7034457 | 9 (77807918) | A/G | 0.90 | −0.418 (0.102) | 7.1 × 10−5 | 0.045 (0.249) | .86 | −0.348 (0.097) | 3.3 × 10−4 | NA | NA | PCSK5 (intron) |
| rs7899453 | 10 (79469965) | A/C | 0.22 | 0.317 (0.079) | 1.1 × 10−4 | 0.179 (0.149) | .23 | 0.285 (0.072) | 7.3 × 10−5 | NA | NA | RPS24 (missense) |
| rs11817401 | 10 (108823893) | T/C | 0.08 | 0.602 (0.110) | 1.2 × 10−7 | −0.176 (0.273) | .52 | 0.487 (0.105) | 3.4 × 10−6 | NA | NA | SORCS1 (intron) |
| rs17101814 | 11 (103367886) | T/C | 0.09 | 0.444 (0.100) | 1.8 × 10−5 | 0.128 (0.196) | .51 | 0.375 (0.091) | 4.1 × 10−5 | 0.82 [0.50, 1.35] | .44 | PDGFD (intron) |
| rs9933611 | 16 (52331386) | A/G | 0.93 | −0.449 (0.116) | 1.8 × 10−4 | −0.245 (0.272) | .37 | −0.415 (0.110) | 1.5 × 10−4 | NA | NA | FTO (intron) |
| rs445683 | 17 (71913117) | T/C | 0.67 | 0.311 (0.079) | 1.5 × 10−4 | 0.089 (0.142) | .53 | 0.256 (0.071) | 3.2 × 10−4 | 0.91 [0.68, 1.23] | .56 | UBE2O (intron) |
| rs7507634 | 19 (10297562) | T/C | 0.02 | 0.899 (0.226) | 1.2 × 10−4 | −0.821 (0.674) | .22 | 0.714 (0.221) | 1.2 × 10−3 | NA | NA | RAVER1 (intron) |
| rs2872817 | 23 (153211612) | A/G | 0.70 | −0.249 (0.058) | 3.0 × 10−5 | −0.158 (0.121) | .19 | −0.231 (0.053) | 1.5 × 10−5 | NA | NA | TKTL1 (3′UTR) |
We genotyped 19 SNPs with P < 1 × 10−4 in the CSSCD Discovery dataset (before GC correction) in an independent subset of the CSSCD. We combined results from the discovery and replication cohorts using an inverse variance meta-analysis approach. Only 1 SNP (rs11732673, in bold) replicated at nominal significance, but no SNPs reached array-wide significance (P < 2 × 10−6) in the combined analysis. We also report results for the analysis of painful crisis as a dichotomous trait in the Duke cohort. P values for the CSSCD Discovery cohort are G -corrected. Genomic positions are on NCBI build 37.1.
NA, not available; SE, standard error.