TABLE 2.
Significant CpG-SNP pairs with region- or phenotype (pheno)-wide cis associations in the AA and EA samples.
| Gene | CpG methylation probe ID | RefGene Group | SNP ID (A1/A2) | SNP position | Distance to CpG | AA (N = 31) |
EA (N = 29) |
||||||
| A1 Freq | R 2 | Region -wide P |
Pheno -wide P |
A1 Freq | R 2 | Region -wide P |
Pheno -wide P |
||||||
| NRXN1 | cg10917619 | 5′-UTR | rs7567632 (C/T) | 51,198,384 | –57,243 | 0.10 | 0.13 | 1 | 1 | 0.19 | 0.51 | 0.033 | 0.054 |
| rs6545187 (C/T) | 51,200,546 | –55,081 | 0.23 | 0.23 | 0.098 | 1 | 0.40 | 0.55 | 0.015 | 0.03 | |||
| rs7574611 (A/C) | 51,214,993 | –40,634 | 0.16 | 0.27 | 0.099 | 1 | 0.34 | 0.70 | 0.001 | 0.002 | |||
| rs7594170 (G/A) | 51,237,767 | –17,860 | 0.35 | 0.20 | 1 | 1 | 0.40 | 0.61 | 0.004 | 0.008 | |||
| rs2163018 (T/C) | 51,304,238 | 48,611 | 0.11 | 0.14 | 1 | 1 | 0.19 | 0.51 | 0.033 | 0.066 | |||
| PDE1C | cg22131691 | Body | rs73303752 (G/A) | 31,495,561 | –615,427 | 0.11 | 0.55 | 0.038 | 0.067 | 0 | NA | 1 | 1 |
| CHRM2 | cg04748704 | TSS1500 | rs35259000 (C/CTA) | 13,715,061 | 599,818 | 0.13 | 0.54 | 0.015 | 0.024 | 0.07 | 0 | 1 | 1 |
| rs1528099 (A/G) | 137,167,984 | 614,741 | 0.26 | 0.50 | 0.038 | 0.07 | 0.07 | 0 | 1 | 1 | |||
| TAS2R38 | cg25481253 | 1st Exon | rs6949261 (G/C) | 141,980,921 | 307,537 | 0.42 | 0.46 | 0.05 | 0.07 | 0.09 | 0.03 | 1 | 1 |
| cg03017475 | rs1110074 (T/C) | 141,210,054 | –464,287 | 0.24 | 0 | 1 | 1 | 0.47 | 0.46 | 0.019 | 0.031 | ||
| rs4726505 (A/C) | 141,949,743 | 275,402 | 0.41 | 0.50 | 0.017 | 0.032 | 0.09 | 0 | 1 | 1 | |||
| CHRNA2 | cg02953306 | 5′-UTR | rs78908411 (T/A) | 27,331,607 | –5,019 | 0.07 | 0.55 | 0.009 | 0.018 | 0 | NA | 1 | 1 |
| DBH | cg25020204 | rs117956167 (G/C) | 136,466,632 | –33,602 | 0.02 | 0 | 1 | 1 | 0.04 | 0.52 | 0.043 | 0.066 | |
| PTEN | cg01228636 | TSS1500 | rs140133143 (AT/A) | 89,751,172 | 129,399 | 0 | NA | 1 | 1 | 0.04 | 0.53 | 0.025 | 0.044 |
| rs118039301 (A/C) | 89,759,243 | 137,470 | 0 | NA | 1 | 1 | 0.04 | 0.53 | 0.025 | 0.05 | |||
| cg16687447 | 5′-UTR | rs185979581 (T/C) | 88,920,089 | –703,247 | 0.04 | 0.83 | 0.007 | 0.014 | 0 | NA | 1 | 1 | |
| CHRM1 | cg13530039 | TSS1500 | rs2736595 (G/A) | 61,720,538 | –969,019 | 0.23 | 0.53 | 0.035 | 0.034 | 0.79 | 0.05 | 1 | 1 |
| rs2524294 (G/A) | 61,721,234 | –968,323 | 0.23 | 0.53 | 0.035 | 0.045 | 0.79 | 0.05 | 1 | 1 | |||
| NRXN3 | cg15572745 | 5′-UTR | rs144623790 (AAT/A) | 78,026,973 | –843,259 | 0.25 | 0.01 | 1 | 1 | 0.05 | 0.46 | 0.044 | 0.066 |
| CYP2A7 | cg25427638 | rs10500282 (C/T) | 41,508,442 | 119,085 | 0.39 | 0.56 | 0.002 | 0.004 | 0.29 | 0.27 | 0.65 | 0.787 | |
| rs11673270 (C/A) | 41,520,844 | 131,487 | 0.48 | 0.49 | 0.009 | 0.018 | 0.26 | 0.32 | 0.38 | 0.505 | |||
| rs3745275 (A/G) | 41,531,705 | 142,348 | 0.42 | 0.59 | 0.0001 | 0.002 | 0.31 | 0.48 | 0.014 | 0.028 | |||
| rs3745277 (A/G) | 41,531,915 | 142,558 | 0.48 | 0.54 | 0.003 | 0.006 | 0.22 | 0.43 | 0.058 | 0.088 | |||
| rs10409701 (A/G) | 41,537,868 | 148,511 | 0.40 | 0.73 | 0.0001 | 0.002 | 0.21 | 0.52 | 0.009 | 0.018 | |||
Genomic positions are based on the NCBI Build 37/hg19 assembly. Significant region- and pheno-wide p-values are given in bold. SNP 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; 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 at this CpG site; Pheno-wide p, region-wide p-value after correcting for the 107 CpG sites tested using augmentation multiple testing procedure.