Table 3.
Top results LEO analysis, Results for top SNPs
| Gene symbol | M&E | CGI | LEO model | LEO score | P-value | Top SNP | Chr | Bp | Full name |
|---|---|---|---|---|---|---|---|---|---|
|
BTN3A2
|
- |
Outside |
S → M → E |
6.90 |
0.15 |
rs2093169 |
6 |
26,603,078 |
butyrophilin, subfamily 3, member A2 |
|
HP
|
- |
Outside |
S → M → E |
4.24 |
0.82 |
rs8044555 |
16 |
70,710,256 |
haptoglobin |
|
CTSW
|
- |
Outside |
S → M → E |
2.73 |
0.13 |
rs11227306 |
11 |
65,335,248 |
cathepsin W |
|
NAPRT1
|
- |
Shore |
S → M → E |
2.69 |
0.11 |
rs4874159 |
8 |
144,742,093 |
nicotinate phosphoribosyltransferase domain containing 1 |
|
PHACS
|
- |
Shore |
S → M → E |
1.50 |
2.9e-03 |
rs4755227 |
11 |
44,078,659 |
1-aminocyclopropane-1-carboxylate synthase homolog |
|
PNMA3
|
+ |
Shore |
S → M → E |
1.36 |
0.16 |
rs6627737 |
X |
151,971,610 |
nicotinate phosphoribosyltransferase domain containing 1 |
|
CDC16
|
- |
Island |
S → M → E |
1.09 |
0.01 |
rs11147317 |
13 |
113,957,498 |
cell division cycle 16 homolog (S. cerevisiae) |
|
HRASLS3
|
- |
Shore |
S → E → M |
2.42 |
7.2e-04 |
rs2030731 |
11 |
63,130,224 |
phospholipase A2, group XVI |
|
TACSTD2
|
- |
Island |
S → E → M |
2.08 |
9.5e-03 |
rs11207272 |
1 |
58,846,018 |
tumor-associated calcium signal transducer 2 |
|
SRXN1
|
- |
Shore |
S → E → M |
1.87 |
5.4e-03 |
rs6076864 |
20 |
569,825 |
sulfiredoxin 1 homolog (S. cerevisiae) |
|
C21orf56
|
- |
Outside |
S → E → M |
1.30 |
2.8e-03 |
rs8133866 |
21 |
46,423,604 |
chromosome 21 open reading frame 56 |
|
BTN3A2
|
- |
Outside |
S → E → M |
1.14 |
6.4e-05 |
rs12199613 |
6 |
26,475,197 |
butyrophilin, subfamily 3, member A2 |
|
WBSCR27
|
- |
Shore |
S → E → M |
0.95 |
8.6e-04 |
rs11763011 |
7 |
72,922,084 |
Williams Beuren syndrome chromosome region 27 |
| GSTM3 | - | Island | S → E → M | 0.88 | 1.4e-03 | rs11807 | 1 | 110,062,265 | glutathione S-transferase mu 3 (brain) |
This table contains top probes resulting from causality analysis (LEO scores > 0.8). The top seven genes fit the causal scenario SNP → Methylation → Expression (S→M→E), while the bottom seven genes fit the reverse model in which DNA methylation is regulated by gene expression that is under genetic control (S→E→M). The Gene Symbol is given in the first column. The second column indicates whether the methylation and expression levels are associated negatively (−) or positively (+). The third column indicates whether the methylation probe is located in a CpG island (CGI), in the shore, or outside both. The columns “LEO model”, “LEO score” and “P-value” indicate which causal model fits best with the corresponding LEO score and P-value. This model fitting p-value is calculated using the model chi-square statistic statistic. The chi-square statistic tests the null hypothesis that the model is correct, thus a p-value > 0.01 indicates good fit. The next column indicates the SNP most significantly associated. The last three columns contain chromosome number and base pair location (NCBI build 36) of the SNP and full name of the gene.