Table 3.
Relative risk ratio (RRR) and 95% confidence interval (CI) for the top 20 SNPs in the GxVitamin analyses.
| Analysis | Top 20 SNPsa | Chromosomal band locationb | Location of SNP in or near a given gene(s)b | p-value | q-value | RRR (95% CI) |
|---|---|---|---|---|---|---|
| Pooled | rs1339221 | 1q41 | In ESRRG | 5.9e-08 | 0.011 | 0.56 (0.45–0.69) |
| rs11117745 | 1q41 | In ESRRG | 6.8e-08 | 0.011 | 0.57 (0.46–0.70) | |
| rs13027140 | 2p16 | Between FLJ30838 and LOC101927285 | 1.0e-06 | 0.117 | 1.70 (1.38–2.11) | |
| rs4233974 | 2p16 | Between FLJ30838 and LOC101927285 | 2.2e-06 | 0.15 | 1.67 (1.35–2.06) | |
| rs1316471 | 7p12 | Nearest gene is COBL | 2.2e-06 | 0.15 | 2.36 (1.66–3.38) | |
| rs16970288 | 19q13.1 | Between pseudogene EEF1A1P7a and LINC01531 | 6.2e-06 | 0.337 | 1.69 (1.35–2.13) | |
| rs2099557 | 1q41 | In ESRRG | 7.0e-06 | 0.337 | 0.62 (0.50–0.76) | |
| rs13022580 | 2q21.1 | Between pseudogenes RPL19P4 and TEKT4P3 | 8.4e-06 | 0.337 | 1.60 (1.30–1.96) | |
| rs5762534 | 22q12.1 | In TTC28 | 9.0e-06 | 0.337 | 1.90 (1.43–2.51) | |
| rs938868 | 2q21.1 | Between pseudogenes MTND5P29 and RPL19P4 | 1.02e-05 | 0.343 | 1.59 (1.29–1.95) | |
| rs10992247 | 9q22.2 | Between pseudogenes IL6RP1 and OR7E31P | 1.19e-05 | 0.367 | 0.42 (0.28–0.62) | |
| rs130413 | 22q12.1 | In TTC28 | 1.61e-05 | 0.453 | 1.81 (1.38–2.37) | |
| rs10072077 | 5q14 | Near LOC101929423 | 1.81e-05 | 0.468 | 2.35 (1.59–3.48) | |
| rs949771 | 2q21.1 | In pseudogene MTND5P29 | 1.94e-05 | 0.468 | 1.56 (1.27–1.92) | |
| rs6696232 | 1p22.2 | Between ZNF644 and HFM1 | 2.12e-05 | 0.477 | 0.60 (0.47–0.76) | |
| rs247405 | 16q23 | Nearest gene is HSBP1 | 2.59e-05 | 0.5 | 0.48 (0.34–0.67) | |
| rs621188 | 11q23.3 | In DSCAML1 | 2.63e-05 | 0.5 | 1.59 (1.28–1.97) | |
| rs6431784 | 2p25.3 | Nearest gene is SOX11 | 2.66e-05 | 0.5 | 1.74 (1.34–2.26) | |
| rs2042743 | 18p11.2 | In LDLRAD4 | 3.04e-05 | 0.539 | 1.55 (1.26–1.91) | |
| rs11676593 | 2q21.1 | Between pseudogenes RPL19P4 and TEKT4P3 | 3.18e-05 | 0.539 | 1.56 (1.26–1.92) | |
| European | rs17734557 | 7p12 | Nearest gene is COBL | 5e-07 | 0.163 | 3.22 (2.04–5.09) |
| rs1316471 | 7p12 | Nearest gene is COBL | 1e-06 | 0.168 | 3.36 (2.07–5.46) | |
| rs10875883 | 12q13.1 | Nearest gene is CCDC65 | 1.17e-05 | 0.607 | 0.49 (0.36–0.68) | |
| rs2838965 | 21q22.3 | Nearest gene is SLC19A1 | 1.29e-05 | 0.607 | 0.49 (0.35–0.67) | |
| rs7741153 | 6p23 | Nearest gene is JARID2 | 1.5e-05 | 0.607 | 0.45 (0.31–0.64) | |
| rs247405 | 16q23 | Nearest gene is HSBP1 | 1.52e-05 | 0.607 | 0.23 (0.12–0.45) | |
| rs9544295 | 13q22 | Nearest gene is KCTD12 | 1.63e-05 | 0.607 | 2.77 (1.74–4.41) | |
| rs13027140 | 2p16 | Between FLJ30838 and LOC101927285 | 1.83e-05 | 0.607 | 2.02 (1.46–2.78) | |
| rs2159963 | 12p13.3 | Between A2ML1 and PHC1 | 1.9e-05 | 0.607 | 2.35 (1.59–3.48) | |
| rs10746803 | 9q21.3 | Between C9orf170 and DAPK1 | 2.23e-05 | 0.607 | 0.34 (0.21–0.56) | |
| rs2575625 | 4q25 | Between OSTC and ETNPPL | 2.35e-05 | 0.607 | 1.96 (1.44–2.68) | |
| rs3792390 | 3q21 | In PDIA5 | 2.46e-05 | 0.607 | 0.44 (0.30–0.65) | |
| rs17651808 | 15q21.2 | Between ARPP19 and FAM214A | 2.49e-05 | 0.607 | 0.28 (0.15–0.50) | |
| rs4932844 | 19p12 | In pseudogene ZNF724 | 2.53e-05 | 0.607 | 0.51 (0.37–0.70) | |
| rs295367 | 19p12 | In pseudogene LOC100132815 | 3.21e-05 | 0.719 | 0.51 (0.38–0.70) | |
| rs9821623 | 3p22 | In ULK4 | 3.66e-05 | 0.768 | 2.19 (1.51–3.18) | |
| rs2362803 | 19p12 | Nearest gene is ZNF724P | 4.16e-05 | 0.783 | 0.52 (0.38–0.71) | |
| rs260818 | 11q22.3 | In PDGFD | 4.2e-05 | 0.783 | 1.94 (1.41–2.67) | |
| rs10743549 | 12p13.3 | Between A2ML1 and PHC1 | 4.45e-05 | 0.786 | 2.33 (1.55–3.51) | |
| rs642307 | 1p32.1 | In C1orf87 | 6.4e-05 | 0.905 | 1.89 (1.38–2.59) | |
| Asian | rs13261120 | 8p22 | In SGCZ | 3.4e-06 | 0.73 | 2.45 (1.68–3.57) |
| rs8055365 | 16q24 | Between TLDC1 and COTL1 | 6.2e-06 | 0.73 | 0.39 (0.26–0.59) | |
| rs12546303 | 8p22 | In SGCZ | 8.4e-06 | 0.73 | 2.35 (1.62–3.43) | |
| rs4773818 | 13q32 | In LOC101927284 | 9.9e-06 | 0.73 | 3.16 (1.90–5.25) | |
| rs247832 | 16q24 | Between TLDC1 and COTL1 | 1.29e-05 | 0.73 | 0.42 (0.29–0.62) | |
| rs792306 | 13q32 | In LOC101927284 | 1.33e-05 | 0.73 | 3.10 (1.86–5.17) | |
| rs12374531 | 5q32 | Between PPP2R2B and STK32A | 1.53e-05 | 0.73 | 3.22 (1.90–5.47) | |
| rs4695853 | 4q34 | Nearest gene is HAND2-AS1 | 2.34e-05 | 0.897 | 3.12 (1.84–5.29) | |
| rs6860289 | 5p15.3 | Nearest gene is MTRR | 2.65e-05 | 0.897 | 2.35 (1.58–3.50) | |
| rs1615355 | 12q24.33 | In LOC100190940 | 2.98e-05 | 0.897 | 2.29 (1.55–3.38) | |
| rs13418410 | 2p22 | Between RASGRP3 and FAM98A | 3.24e-05 | 0.897 | 2.35 (1.57–3.52) | |
| rs423909 | 1p36.2 | Nearest gene is SLC45A1 | 3.52e-05 | 0.897 | 2.18 (1.51–3.16) | |
| rs4670209 | 2p22 | Between RASGRP3 and FAM98A | 3.59e-05 | 0.897 | 2.25 (1.53–3.31) | |
| rs1448561 | 2p22 | Nearest gene is FAM98A | 4.12e-05 | 0.897 | 2.32 (1.55–3.46) | |
| rs9286945 | 1p35 | Nearest gene is PTPRU | 4.49e-05 | 0.897 | 0.45 (0.30–0.66) | |
| rs2002022 | 13q21.3 | Between pseudogenes NPM1P22 and OR7E111P | 4.6e-05 | 0.897 | 2.35 (1.56–3.54) | |
| rs17138910 | 10p13 | In RSU1 | 5.05e-05 | 0.897 | 2.22 (1.51–3.26) | |
| rs4290780 | 3q13.2 | In CCDC80 | 5.19e-05 | 0.897 | 3.85 (2.01–7.41) | |
| rs10503525 | 8p22 | In SGCZ | 5.96e-05 | 0.897 | 2.39 (1.56–3.65) | |
| rs13388224 | 2p22 | Between RASGRP3 and FAM98A | 6.04e-05 | 0.897 | 2.27 (1.52–3.39) |
a
SNPs with q-values <0.2 are shown in bold.
b
Location of SNP was determined using the 1,000 Genomes browser at https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/.