TABLE 3.
Significant expression probe-SNP pairs with region- or phenotype (pheno)-wide cis associations in the AA and EA samples.
| Ethnicity | Gene | Expression Probe Oligo ID | SNP ID (A1/A2) | Variant Position | Distance to TSS | A1 Freq | R 2 | Region-wide P | Pheno-wide P |
| AA (N = 94) | DRD1 | hHC010798 | rs147731662 (T/C) | 175600872 | 729,709 | 0.01 | 0.21 | 0.046 | 0.092 |
| CACNA2D1 | hHC009943 | rs73386029 (C/A) | 82036439 | –36,592 | 0.02 | 0.25 | 0.017 | 0.034 | |
| CHRM2 | hHC005116 | rs324650 (A/T) | 136693661 | 140,262 | 0.67 | 0.17 | 0.042 | 0.084 | |
| HTR5A | hHC008651 | rs139998364 (A/G) | 155628744 | 766,134 | 0.01 | 0.46 | 0.018 | 0.036 | |
| DNM1 | hHC021993 | rs3824415 (A/G) | 130145624 | –820,039 | 0.22 | 0.19 | 0.034 | 0.068 | |
| C14orf28 | hHR004782 | rs78410784 (G/C) | 45639985 | 273,478 | 0.08 | 0.18 | 0.036 | 0.072 | |
| EA (N = 84) | BDNF | hHC017923 | rs72887755 (A/G) | 27801789 | 58,493 | 0.02 | 0.22 | 0.035 | 0.062 |
| rs116860953 (G/A) | 27930226 | 186,930 | 0.02 | 0.21 | 0.031 | 0.037 | |||
| EGLN2 | hHC023008 | rs4802088 (T/C) | 41255768 | –49,377 | 0.03 | 0.30 | 0.002 | 0.004 | |
| rs34406232 (A/C) | 41305530 | 385 | 0.02 | 0.29 | 0.003 | 0.006 |
Genomic positions are based on the NCBI Build 37/hg19 assembly. Significant region- and pheno-wide p-values are in bold. Variant annotations were obtained from HaploReg v4.1 (http://www.broadinstitute.org/mammals/haploreg/haploreg.php).
SNP, single nucleotide polymorphism; AA, African American; EA, European American; TSS, transcriptional start site; A1 Freq, allele frequency of A1; R2, regression r-squared; Region-wide p, corrected empirical p-value based on 103 max (T) permutations with correction for the number of variants tested for cis associations with this expression probe; Pheno-wide p, region-wide p-value after correcting for the 51 expression probes tested using augmentation multiple testing procedure.