Table 2.
Strongest single nucleotide polymorphism (SNP)-phenotype associations in meta-analysis for covert MRI-defined brain infarcts.
| SNP rs# | SNP function | Chr position |
Minor allele |
MAF | OR (95%CI) |
p-value | PAR | Closest Gene | 2nd Closest Gene | Additional SNPs at p<10−5 |
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Name | Distance | Name | Distance | |||||||||
| rs2208454 | intronic | 20:14213415 | T | 0.20 | 0.76 (0.68–0.84) |
4.64E-07 | 0.12 | MACROD2 | in gene | FLRT3 | 39.2 | 22 intronic |
| rs1834018 | intronic | 16:56864743 | G | 0.12 | 1.32 (1.18–1.48) |
1.59E-06 | 0.07 | CCDC113 | in gene | KLKBL4 | 6.7 | 1 intronic, 2 upstream |
| rs2869036 | intergenic | 15:76454627 | G | 0.22 | 0.76 (0.68–0.85) |
3.36E-06 | 0.13 | CRABP1 | 27.0 | IREB2 | 62.9 | 0 |
| rs1471895 | intronic | 11:11297762 | A | 0.06 | 1.44 (1.23–1.68) |
3.90E-06 | 0.05 | GALNTL4 | in gene | EIF4G2 | 510.6 | 1 intronic |
| rs4335430 | intronic | 1:215166854 | T | 0.16 | 1.27 (1.15–1.41) |
4.31E-06 | 0.08 | ESRRG | in gene | USH2A | 503.5 | 0 |
| rs17695069 | intronic | 18:54801916 | G | 0.11 | 1.34 (1.18–1.52) |
4.54E-06 | 0.07 | ZNF532 | in gene | SEC11C | 156.2 | 0 |
| rs2284038 | intronic | 22:35965001 | G | 0.36 | 1.20 (1.11–1.30) |
5.98E-06 | 0.13 | RAC2 | in gene | SSTR3 | 26.7 | 3 intronic |
| rs12885474 | intronic | 14:24451217 | A | 0.12 | 0.75 (0.66–0.85) |
6.90E-06 | 0.08 | STXBP6 | in gene | GZMB | 277.9 | 13 intronic |
| rs11746929 | intronic | 5:149114067 | A | 0.27 | 0.81 (0.73–0.89) |
8.35E-06 | 0.12 | PPARGC1B | in gene | PDE6A | 103.6 | 0 |
The reference single nucleotide polymorphism (SNP) number (rs#), function, and chromosome (chr) position are listed. Odds ratios (OR), 95% confidence intervals (CI), and p-values as powers of 10 (E) are based on the meta-analysis. Each row lists only the SNP-phenotype association with the lowest p-value for that locus. The last column shows the number of additional SNPs at the same locus, within 250 kb of the specified SNP, that were also associated with the phenotype with a p-value <10−5. Complete details for these additional SNPs are provided online in the Appendix, Table A. Alleles were identified based on the plus strand of the NCBI build #36. The minor allele was also the coded allele, and minor allele frequency (MAF) is based on allele frequency in meta-analysis sample. The Appendix, Section 8, has details on calculating the population attributable risk (PAR). For SNPs whose minor allele had an inverse association with MRI-infarcts (OR<1.0), the PAR has been calculated using the major allele as the risk allele. The Human Gene Organization (HUGO) Gene Nomenclature System symbols is used for the 2 genes located closest to each SNP, and the distance of the associated SNP from the 5′ end (start) or 3’ end (stop) of the gene (the closest of the 2). Standardized gene annotations for all SNP results were derived programmatically from the UCSC Genome Browser RefSeq gene track (hg18). Distances to genes are given in kilo-base (kb) pairs, based on NCBI build #36.