Table 3.
Summary of data on SNPs, closest gene and all genes in 1 MB region for each locus
| Loci | Position of top SNP |
# putatively causal SNPs |
Genes in window of putatively causal SNPs |
# SNPs aligned w/ biofeatures♭ |
Normal eQTL closest gene |
Tumour DNA copy number |
Significant expression difference in tumour vs normal |
Known role of gene in cancer |
# Genes in 1MB region |
Other known cancer genes in 1MB region |
|---|---|---|---|---|---|---|---|---|---|---|
| 1p36 | promoter region of WNT4 |
39 |
WNT4, CDC42, LINC00339 |
11 | NS | loss | Yes | 11 | RAP1GAP, CDC42 | |
| 1p34.3 | intron 3 of RSPO1 |
15 | RSPO1 | 0 | NS | gain | Yes | 22 | C1orf109, FHL3 | |
| 4q26 | intron 3 of SYNPO2 |
4 | SYNPO2 | 2 | NS** | loss | down | Yes | 12 | none |
| 6p22.1 | intron 1 of GPX6 |
22 | GPX6, GPX5 | 1 | N/A | gain | 23 | ZKSCAN3, TRIM27 | ||
| 9q34.2 | 4.3kb upstream of ABO |
18 | ABO, SLC2A6* | 1 | NS | loss | down | Yes | 32 |
TSC1, RALGDS, RPL7A, VAV2 |
| 17q11.2 | intron 6 of ATAD5 |
16 |
ATAD5, TEFM, ADAP2, CRLF3, SUZ12P1 |
0 | NS | loss | up | Yes | 17 | NF1 |
Proximal promoter regions were defined as 1kb upstream of the transcription start site
N/A indicated no expression of GPX6 in normal tissues. NS, not significant.
♭
Biofeatures defined as open chromatin, H3K4me3 or H3K27ac marks detected in normal ovarian and/or fallopian cells
*
There are 16 genes in this region; ABO, SURF6, MED22, RPL7A, SNORD24, SNORD36B, SNORD36A, SNORD36C, SURF1, SURF2, SURF4, C9orf96, REXO4, ADAMTS13, CACFD1, SLC2A6, however all SNPs are within or upstream of ABO or upstream of SLC2A6.
**
Trend p=0.067