Table 4.
Relative risk ratio (RRR) and 95% confidence interval (CI) for the top 20 SNPs in the GxSmoke analyses.
| Analysisa | Top 20 SNPs | Chromosomal band locationb | Location of SNP in or near a given gene(s)b | p-value | q-value | RRR (95% CI) |
|---|---|---|---|---|---|---|
| Pooled | rs820930 | 7q31.1 | Nearest locus is C7orf66 | 1.06e-05 | 0.994 | 1.93 (1.44–2.58) |
| rs210625 | 6q22.2 | In DCBLD1 | 1.36e-05 | 0.994 | 1.79 (1.38–2.33) | |
| rs7258736 | 19q12 | In LOC101927210 | 1.56e-05 | 0.994 | 2.99 (1.82–4.91) | |
| rs7247342 | 19q12 | In LOC101927210 | 2.59e-05 | 0.994 | 2.89 (1.76–4.73) | |
| rs2024140 | 19q12 | In LOC101927210 | 2.91e-05 | 0.994 | 2.97 (1.78–4.94) | |
| rs6810129 | 3q26.1 | Nearest gene is CT64 | 2.94e-05 | 0.994 | 0.57 (0.44–0.74) | |
| rs1182865 | 6p21.2 | Between KCNK5 and KCNK17 | 3.43e-05 | 0.994 | 0.51 (0.37–0.70) | |
| rs1013592 | 19q12 | In LOC101927210 | 3.47e-05 | 0.994 | 2.81 (1.72–4.57) | |
| rs10085496 | 7p21 | Between pseudogenes GAPDHP68 and PER4 | 3.85e-05 | 0.994 | 0.58 (0.45–0.75) | |
| rs4805661 | 19q12 | Nearest gene is TSHZ3 | 4.05e-05 | 0.994 | 0.57 (0.43–0.74) | |
| rs2543146 | 8p22 | In TUSC3 | 4.19e-05 | 0.994 | 1.73 (1.33–2.24) | |
| rs4804843 | 19q12 | In LOC101927210 | 4.41e-05 | 0.994 | 2.86 (1.73–4.73) | |
| rs10417454 | 19q12 | In LOC101927210 | 4.63e-05 | 0.994 | 2.84 (1.72–4.69) | |
| rs244226 | 21q21 | Between pseudogenes MAPK6PS2 and ZNF299P | 4.88e-05 | 0.994 | 1.72 (1.32–2.23) | |
| rs352806 | 8p22 | In TUSC3 | 5.21e-05 | 0.994 | 0.53 (0.38–0.72) | |
| rs2191018 | 19q12 | In LOC101927210 | 5.4e-05 | 0.994 | 2.82 (1.71–4.67) | |
| rs6806286 | 3q22 | In CPNE4 | 6.37e-05 | 0.994 | 1.72 (1.32–2.25) | |
| rs2834061 | 21q22.1 | Nearest gene is OLIG2 | 6.37e-05 | 0.994 | 1.80 (1.35–2.41) | |
| rs12204228 | 6q22.1 | Between RFX6 and VGLL2 | 6.44e-05 | 0.994 | 0.40 (0.25–0.63) | |
| rs11014205 | 10p12.2 | In ARHGAP21 | 8.06e-05 | 0.994 | 0.55 (0.41–0.74) | |
| European | rs10106898 | 8q22.1 | Between pseudogenes GAPDHP30 and TUBBP7 | 4.1e-06 | 0.684 | 0.29 (0.18–0.50) |
| rs10095562 | 8q22.1 | Between pseudogenes GAPDHP30 and TUBBP7 | 1.4e-05 | 0.684 | 0.30 (0.17–0.52) | |
| rs10282921 | 8q22.1 | Between pseudogenes GAPDHP30 and TUBBP7 | 1.43e-05 | 0.684 | 0.30 (0.18–0.52) | |
| rs820930 | 7q31.1 | Between LOC646614 and LOC100421901 | 1.45e-05 | 0.684 | 2.11 (1.51–2.97) | |
| rs266642 | 5q23.2 | Nearest gene is GRAMD3 | 1.55e-05 | 0.684 | 2.69 (1.72–4.22) | |
| rs601904 | 11q13.4 | Between peudogene CYCSP27 and LIPT2 | 1.59e-05 | 0.684 | 0.49 (0.35–0.68) | |
| rs17608059 | 17p12 | Nearest gene is COX10-AS1 | 1.68e-05 | 0.684 | 1.97 (1.44–2.67) | |
| rs657339 | 11q13.4 | In LOC100287896 | 1.85e-05 | 0.684 | 0.49 (0.35–0.68) | |
| rs617989 | 11q13.4 | In LIPT2 | 1.9e-05 | 0.684 | 0.49 (0.36–0.68) | |
| rs649460 | 11q13.4 | Nearest gene is LIPT2 | 2.28e-05 | 0.684 | 0.49 (0.36–0.68) | |
| rs2509563 | 11q13.4 | Nearest gene is LIPT2 | 2.29e-05 | 0.684 | 0.50 (0.36–0.69) | |
| rs1013592 | 19q12 | In LOC101927210 | 2.45e-05 | 0.684 | 3.84 (2.05–7.17) | |
| rs1783196 | 11q13.4 | Nearest gene is LIPT2 | 2.85e-05 | 0.684 | 0.50 (0.36–0.69) | |
| rs648677 | 11q13.4 | Between LIPT2 and POLD3 | 2.85e-05 | 0.684 | 0.50 (0.36–0.69) | |
| rs10028174 | 4q22 | In CCSER1 | 3.65e-05 | 0.796 | 0.40 (0.26–0.62) | |
| rs1655475 | 11q13.4 | Between LIPT2 and POLD3 | 3.79e-05 | 0.796 | 0.51 (0.37–0.70) | |
| rs2089253 | 4q21.1 | In USO1 | 4.34e-05 | 0.858 | 0.28 (0.16–0.52) | |
| rs3317 | 5q22 | In REEP5 and SRP19 | 5.55e-05 | 0.89 | 0.53 (0.39–0.72) | |
| rs11692230 | 2q12 | In IL1RL2 | 5.67e-05 | 0.89 | 1.89 (1.39–2.58) | |
| rs4805661 | 19q12 | Nearest gene is TSHZ3 | 6.19e-05 | 0.89 | 0.53 (0.38–0.72) |
a
We were unable to assess GxSmoke effects in the Asian sample because very few of the mothers reported smoking cigarettes in the periconceptional period.
b
Location of SNP was determined using the 1,000 Genomes browser at https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/.