Variant report
| Variant | rs992078 |
|---|---|
| Chromosome Location | chr12:68380506-68380507 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:14)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:14 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | PBX3 | chr12:68380321-68380756 | SK-N-SH | brain: | n/a | n/a |
| 2 | EP300 | chr12:68380302-68380957 | SK-N-SH | brain: | n/a | n/a |
| 3 | POLR2A | chr12:68380492-68380690 | SK-N-SH | brain: | n/a | n/a |
| 4 | NFIC | chr12:68380324-68380908 | SK-N-SH | brain: | n/a | n/a |
| 5 | TCF12 | chr12:68380293-68380936 | SK-N-SH | brain: | n/a | n/a |
| 6 | EP300 | chr12:68380446-68380739 | SK-N-SH_RA | brain: | n/a | n/a |
| 7 | GATA3 | chr12:68380259-68380890 | SK-N-SH | brain: | n/a | chr12:68380710-68380717 chr12:68380703-68380724 chr12:68380264-68380273 chr12:68380266-68380273 chr12:68380264-68380274 chr12:68380710-68380717 chr12:68380261-68380277 chr12:68380705-68380721 chr12:68380705-68380721 chr12:68380266-68380273 chr12:68380710-68380717 chr12:68380266-68380273 |
| 8 | EP300 | chr12:68380497-68380701 | SK-N-SH_RA | brain: | n/a | n/a |
| 9 | JUND | chr12:68380361-68380879 | SK-N-SH | brain: | n/a | chr12:68380863-68380877 |
| 10 | POLR2A | chr12:68380349-68380528 | MCF10A-Er-Src | breast: | n/a | n/a |
| 11 | GATA3 | chr12:68380300-68380989 | SK-N-SH | brain: | n/a | chr12:68380710-68380717 chr12:68380703-68380724 chr12:68380710-68380717 chr12:68380705-68380721 chr12:68380705-68380721 chr12:68380710-68380717 |
| 12 | TCF12 | chr12:68380206-68380998 | SK-N-SH | brain: | n/a | n/a |
| 13 | PBX3 | chr12:68380274-68380820 | SK-N-SH | brain: | n/a | n/a |
| 14 | POLR2A | chr12:68380416-68380714 | SK-N-SH | brain: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:68379962..68383054-chr12:68386184..68387987,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| IFNG-AS1 | TF binding region |
rSNPs within LD-proxies of this variant (count:3)
| rs_ID | r2[population] |
|---|---|
| rs2906848 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2906852 | 0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap] |
| rs56236103 | 0.85[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3411149 | chr12:68066948-68435533 | Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 24 gene(s) | inside rSNPs | diseases |
| 2 | nsv1039638 | chr12:68293351-68399871 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs992078 | C12orf56 | cis | cerebellum | SCAN |
| rs992078 | TBK1 | cis | parietal | SCAN |
| rs992078 | IFNG-AS1 | cis | Artery Tibial | GTEx |
Chromatin state (count:0 , 50 per page) page:
| No data |
