Table 5.
Relative risk ratio (RRR) and 95% confidence interval (CI) for the top 20 SNPs in the GxAlcohol analyses.
| Analysisa | Top 20 SNPsb | Chromosomal band locationc | Location of SNP in or near a given gene(s)c | p-value | q-value | RRR (95% CI) |
|---|---|---|---|---|---|---|
| Pooled | rs17023089 | 3p24.1 | Nearest gene is RBMS3 | 7.4e-06 | 0.858 | 0.32 (0.19–0.53) |
| rs7164773 | 15q22.2 | In RORA | 9.8e-06 | 0.858 | 1.73 (1.35–2.20) | |
| rs6748903 | 2q14.3 | Near LOC101927881 | 1.65e-05 | 0.858 | 0.51 (0.38–0.69) | |
| rs11691558 | 2q21.1 | In LOC101927881 | 1.72e-05 | 0.858 | 0.51 (0.38–0.69) | |
| rs4132008 | 1q32.1 | In PLEKHA6 | 1.94e-05 | 0.858 | 1.75 (1.35–2.27) | |
| rs2118769 | 2q22.3 | Nearest gene is ACVR2A | 2.04e-05 | 0.858 | 0.58 (0.46–0.75) | |
| rs1335594 | 13q33 | In ITGBL1 | 2.3e-05 | 0.858 | 1.74 (1.35–2.25) | |
| rs3805025 | 3p26 | In ITPR1 | 2.77e-05 | 0.858 | 1.96 (1.43–2.69) | |
| rs30306 | 5q32 | Nearest gene is ADBR2 | 3.58e-05 | 0.858 | 1.66 (1.30–2.11) | |
| rs6685648 | 1p36.2 | In CASP9 | 3.89e-05 | 0.858 | 0.59 (0.46–0.76) | |
| rs2064317 | 6p21.3 | In TULP1 | 4.45e-05 | 0.858 | 1.65 (1.30–2.11) | |
| rs686805 | 11q13.4 | In SHANK2 | 4.66e-05 | 0.858 | 2.24 (1.52–3.30) | |
| rs9653456 | 2q12 | Nearest gene is EDAR | 4.76e-05 | 0.858 | 1.85 (1.37–2.49) | |
| rs2163752 | 5q32 | Between HTR4 and ADRB2 | 4.77e-05 | 0.858 | 1.64 (1.29–2.09) | |
| rs13086826 | 3q22 | In CPNE4 | 4.94e-05 | 0.858 | 0.59 (0.45–0.76) | |
| rs4810165 | 20q13.3 | Between EDN3 and peudogene PIEZO1P1 | 5.01e-05 | 0.858 | 1.75 (1.34–2.30) | |
| rs4859190 | 3q27 | Nearest gene is MCF2L2 | 5.12e-05 | 0.858 | 0.58 (0.45–0.76) | |
| rs2740882 | 8p23.3 | In CSMD1 | 5.15e-05 | 0.858 | 0.48 (0.33–0.68) | |
| rs13077768 | 3q22 | In CPNE4 | 5.29e-05 | 0.858 | 0.59 (0.45–0.76) | |
| rs11076508 | 16q12.1 | Between ZNF423 and pseudogene RPL34P29 | 5.56e-05 | 0.858 | 0.61 (0.48–0.78) | |
| European | rs9653456 | 2q12 | Between EDAR and SH3RF3 | 4e-07 | 0.148 | 2.40 (1.71–3.37) |
| rs921876 | 2q12 | Nearest gene is EDAR | 9e-07 | 0.153 | 2.09 (1.56–2.81) | |
| rs11076508 | 16q12.1 | Between ZNF423 and pseudogene RPL34P29 | 2.25e-05 | 0.892 | 0.54 (0.40–0.72) | |
| rs7713774 | 5q14 | In ACOT12 | 3.05e-05 | 0.892 | 0.51 (0.37–0.70) | |
| rs10784765 | 12q15 | Between CPM and CPSF6 | 4.76e-05 | 0.892 | 0.41 (0.27–0.63) | |
| rs893912 | 15q22.3 | Between LCTL and SMAD6 | 5.04e-05 | 0.892 | 2.28 (1.53–3.39) | |
| rs17199679 | 9q31 | Between pseudogene RPL36AP35 and ACTL7B | 5.1e-05 | 0.892 | 2.86 (1.72–4.76) | |
| rs3020054 | 11q21 | Nearest gene is CCDC67 | 6.7e-05 | 0.892 | 0.52 (0.38–0.72) | |
| rs2192926 | 2p12 | Nearest gene is TACR1 | 7.24e-05 | 0.892 | 0.50 (0.36–0.71) | |
| rs7862797 | 9q31 | Between pseudogene RPL36AP35 and ACTL7B | 7.49e-05 | 0.892 | 2.77 (1.67–4.58) | |
| rs851674 | 7q35 | In CNTNAP2 | 7.85e-05 | 0.892 | 1.87 (1.37–2.56) | |
| rs6581864 | 12q15 | Between CPM and CPSF6 | 8.72e-05 | 0.892 | 1.81 (1.34–2.43) | |
| rs6495940 | 15q14 | Between TMCO5A and SPRED1 | 8.82e-05 | 0.892 | 0.41 (0.26–0.64) | |
| rs6822683 | 4q34 | Nearest gene is GALNT7 | 9.58e-05 | 0.892 | 1.82 (1.35–2.46) | |
| rs2276049 | 11q24 | In VWA5A | 9.78e-05 | 0.892 | 0.48 (0.33–0.69) | |
| rs2417976 | 9q31 | Between TMEM245 and FRRS1L | 9.82e-05 | 0.892 | 2.04 (1.42–2.91) | |
| rs10759878 | 9q33 | In ASTN2 | 9.89e-05 | 0.892 | 1.93 (1.39–2.69) | |
| rs4778036 | 15q26.1 | Between SLCO3A1 and pseudogene DUXAP6 | 0.0001033 | 0.892 | 1.80 (1.34–2.43) | |
| rs17104078 | 10q23.1 | Nearest gene is CCSER2 | 0.0001042 | 0.892 | 2.48 (1.57–3.93) | |
| rs12540601 | 7p15.3 | Between TRA2A and pseudogene LOC442517 | 0.0001044 | 0.892 | 0.56 (0.42–0.75) |
a
We were unable to assess GxAlcohol effects in the Asian sample because very few of the mothers reported drinking alcohol in the periconceptional period.
b
SNPs with q-values <0.2 are shown in bold.
c
Location of SNP was determined using the 1,000 Genomes browser at https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/.