Top SNPs from meta-analysis across COG AALL0232, SJ Total XV, and Vanderbilt BioVU cohorts
| . | . | . | . | . | . | . | COG AALL0232 . | SJ Total XV . | Vanderbilt BioVU . | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP ID* . | Chr . | Position (HG19)† . | Alleles‡ . | Gene§ . | SNP function . | Meta P . | RAF . | P . | HR (95%CI) . | RAF . | P . | OR (95%CI) . | RAF . | P . | OR (95%CI) . |
| rs10989692 | 9 | 104674555 | G/A | 5′ of GRIN3A | Intergenic | 2.68 × 10−8 | 0.106 | 3.59 × 10−7 | 2.03 (1.55 - 2.66) | 0.116 | 0.063 | 1.87 (0.97 - 3.60) | 0.130 | 0.0074 | 2.26 (1.24 - 4.11) |
| rs2154490 | 21 | 30915962 | G/A | GRIK1 | Intronic | 1.28 × 10−6 | 0.222 | 0.016 | 1.29 (1.05 - 1.56) | 0.233 | 0.0078 | 1.86 (1.18 - 2.94) | 0.240 | 9.1 × 10−4 | 2.13 (1.36 - 3.32) |
| rs72733993 | 5 | 18408908 | G/A | NA | Intergenic | 2.67 × 10−6 | 0.156 | 0.043 | 1.29 (1.01 - 1.64) | 0.102 | 0.0051 | 2.62 (1.34 - 5.15) | 0.119 | 9.4 × 10−4 | 2.89 (1.54 - 5.42) |
| rs11144550 | 9 | 78261548 | G/A | 5′ of PCSK5 | Intergenic | 3.08 × 10−6 | 0.137 | 2.37 × 10−5 | 1.70 (1.33 - 2.17) | 0.136 | 0.0629 | 1.71 (0.97 - 3.01) | 0.078 | 0.046 | 2.04 (1.01 - 4.11) |
| rs1536407 | 13 | 75095567 | C/A | 5′ of KLF12 | Intergenic | 4.43 × 10−6 | 0.646 | 0.0064 | 1.32 (1.08 -1.61) | 0.638 | 0.002 | 2.13 (1.32 - 3.45) | 0.660 | 0.034 | 1.59 (1.03 - 2.44) |
| rs4789693 | 17 | 80421870 | A/C | NARF | intronic | 5.73 × 10−6 | 0.274 | 0.030 | 1.25 (1.02 - 1.54) | 0.245 | 0.013 | 1.86 (1.14 - 3.05) | 0.264 | 0.0014 | 1.95 (1.29 - 2.93) |
| rs6797178 | 3 | 137253713 | G/A | 5′ of SOX14 | Intergenic | 5.74 × 10−6 | 0.390 | 0.025 | 1.24 (1.03 - 1.49) | 0.413 | 0.0023 | 2.00 (1.28 - 3.11) | 0.430 | 0.01 | 1.63 (1.12 - 2.37) |
| rs10849004 | 12 | 4292862 | T/C | 5′ of CCND2 | Intergenic | 5.75 × 10−6 | 0.819 | 0.0029 | 1.47 (1.14 - 1.89) | 0.817 | 3.1 × 10−4 | 3.45 (1.75 -6.67) | 0.791 | 0.20 | 1.39 (0.83 - 2.27) |
| rs11594258 | 10 | 79218030 | T/A | KCNMA1 | Intronic | 8.61 × 10−6 | 0.822 | 2.8 × 10−4 | 1.59 (1.23 - 2.04) | 0.867 | 0.2 | 1.52 (0.80 - 2.86) | 0.842 | 0.0052 | 2.44 (1.30 - 4.55) |
| . | . | . | . | . | . | . | COG AALL0232 . | SJ Total XV . | Vanderbilt BioVU . | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP ID* . | Chr . | Position (HG19)† . | Alleles‡ . | Gene§ . | SNP function . | Meta P . | RAF . | P . | HR (95%CI) . | RAF . | P . | OR (95%CI) . | RAF . | P . | OR (95%CI) . |
| rs10989692 | 9 | 104674555 | G/A | 5′ of GRIN3A | Intergenic | 2.68 × 10−8 | 0.106 | 3.59 × 10−7 | 2.03 (1.55 - 2.66) | 0.116 | 0.063 | 1.87 (0.97 - 3.60) | 0.130 | 0.0074 | 2.26 (1.24 - 4.11) |
| rs2154490 | 21 | 30915962 | G/A | GRIK1 | Intronic | 1.28 × 10−6 | 0.222 | 0.016 | 1.29 (1.05 - 1.56) | 0.233 | 0.0078 | 1.86 (1.18 - 2.94) | 0.240 | 9.1 × 10−4 | 2.13 (1.36 - 3.32) |
| rs72733993 | 5 | 18408908 | G/A | NA | Intergenic | 2.67 × 10−6 | 0.156 | 0.043 | 1.29 (1.01 - 1.64) | 0.102 | 0.0051 | 2.62 (1.34 - 5.15) | 0.119 | 9.4 × 10−4 | 2.89 (1.54 - 5.42) |
| rs11144550 | 9 | 78261548 | G/A | 5′ of PCSK5 | Intergenic | 3.08 × 10−6 | 0.137 | 2.37 × 10−5 | 1.70 (1.33 - 2.17) | 0.136 | 0.0629 | 1.71 (0.97 - 3.01) | 0.078 | 0.046 | 2.04 (1.01 - 4.11) |
| rs1536407 | 13 | 75095567 | C/A | 5′ of KLF12 | Intergenic | 4.43 × 10−6 | 0.646 | 0.0064 | 1.32 (1.08 -1.61) | 0.638 | 0.002 | 2.13 (1.32 - 3.45) | 0.660 | 0.034 | 1.59 (1.03 - 2.44) |
| rs4789693 | 17 | 80421870 | A/C | NARF | intronic | 5.73 × 10−6 | 0.274 | 0.030 | 1.25 (1.02 - 1.54) | 0.245 | 0.013 | 1.86 (1.14 - 3.05) | 0.264 | 0.0014 | 1.95 (1.29 - 2.93) |
| rs6797178 | 3 | 137253713 | G/A | 5′ of SOX14 | Intergenic | 5.74 × 10−6 | 0.390 | 0.025 | 1.24 (1.03 - 1.49) | 0.413 | 0.0023 | 2.00 (1.28 - 3.11) | 0.430 | 0.01 | 1.63 (1.12 - 2.37) |
| rs10849004 | 12 | 4292862 | T/C | 5′ of CCND2 | Intergenic | 5.75 × 10−6 | 0.819 | 0.0029 | 1.47 (1.14 - 1.89) | 0.817 | 3.1 × 10−4 | 3.45 (1.75 -6.67) | 0.791 | 0.20 | 1.39 (0.83 - 2.27) |
| rs11594258 | 10 | 79218030 | T/A | KCNMA1 | Intronic | 8.61 × 10−6 | 0.822 | 2.8 × 10−4 | 1.59 (1.23 - 2.04) | 0.867 | 0.2 | 1.52 (0.80 - 2.86) | 0.842 | 0.0052 | 2.44 (1.30 - 4.55) |
Listed are 9 loci with meta P <1 × 10−5. Within each locus, only the SNP with the lowest P value is shown. RAF in each of the 3 cohorts; HR from time-dependent analysis in COG AALL0232 cohort; OR from time independent analysis in SJ Total XV and Vanderbilt BioVU cohorts.
CI, confidence interval.
Rs numbers according to the National Center for Biotechnology Information dbSNP release 139.
Physical location of SNPs based on human genome assembly (hg19).
The second allele listed is the risk allele.
Refseq gene located closest to the SNP within a distance of 1M base pairs.