Variant report
| Variant | rs13155597 |
|---|---|
| Chromosome Location | chr5:154493531-154493532 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | MAFK | chr5:154493324-154493545 | HepG2 | liver: | n/a | chr5:154493392-154493403 chr5:154493424-154493433 chr5:154493423-154493433 chr5:154493351-154493360 |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:155228044..155228643-chr5:154493315..154494007,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000253646 | TF binding region |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs10037186 | 0.89[ASN][1000 genomes] |
| rs10050521 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10050836 | 0.88[ASN][1000 genomes] |
| rs1005789 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs10066196 | 0.88[ASN][1000 genomes] |
| rs10066219 | 0.88[ASN][1000 genomes] |
| rs10066223 | 0.88[ASN][1000 genomes] |
| rs10078699 | 0.94[ASN][1000 genomes] |
| rs1008795 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs10476812 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11167712 | 0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1564885 | 0.88[AMR][1000 genomes];0.94[ASN][1000 genomes] |
| rs17572520 | 0.90[JPT][hapmap] |
| rs17573136 | 0.92[ASN][1000 genomes] |
| rs35161960 | 0.89[ASN][1000 genomes] |
| rs4958779 | 0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs6580136 | 0.84[ASN][1000 genomes] |
| rs6897414 | 0.95[ASN][1000 genomes] |
| rs7703459 | 0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7703759 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs9324804 | 0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs9324805 | 0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv883059 | chr5:154457905-154556230 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 2 | nsv462492 | chr5:154489393-154523910 | Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 3 | nsv600091 | chr5:154489393-154523910 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs13155597 | CLINT1 | cis | parietal | SCAN |
| rs13155597 | SAP30L | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:154490600-154494200 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
| 2 | chr5:154492200-154495800 | Weak transcription | Placenta Amnion | Placenta Amnion |
