Variant report
| Variant | rs913514 |
|---|---|
| Chromosome Location | chr1:179558801-179558802 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:3)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:3 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | POLR2A | chr1:179558469-179559081 | H1-neurons | neurons: | n/a | n/a |
| 2 | POLR2A | chr1:179558615-179559058 | H1-neurons | neurons: | n/a | n/a |
| 3 | REST | chr1:179558504-179559033 | H1-neurons | neurons: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:179553040..179558877-chr1:179559940..179564416,7 | MCF-7 | breast: |
(count:1 , 50 per page) page:
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| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-NPHS2-2 | chr1:179558479-179559134 | NONHSAT007869 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| TDRD5 | TF binding region |
| ENSG00000261060 | TF binding region |
| ENSG00000162782 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:32)
| rs_ID | r2[population] |
|---|---|
| rs10494516 | 0.80[CHB][hapmap] |
| rs10494517 | 0.83[JPT][hapmap] |
| rs10494518 | 0.83[JPT][hapmap] |
| rs1079291 | 0.82[EUR][1000 genomes] |
| rs10913815 | 0.89[CHB][hapmap];0.82[JPT][hapmap] |
| rs11577538 | 0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes] |
| rs11586725 | 0.95[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes] |
| rs11808258 | 0.83[JPT][hapmap] |
| rs12021675 | 0.83[JPT][hapmap] |
| rs1410587 | 0.89[CHB][hapmap];0.82[JPT][hapmap] |
| rs1410588 | 0.89[CHB][hapmap];0.82[JPT][hapmap] |
| rs1410592 | 0.84[CHB][hapmap] |
| rs1999068 | 0.96[EUR][1000 genomes] |
| rs2209922 | 0.83[JPT][hapmap] |
| rs2274622 | 0.83[EUR][1000 genomes] |
| rs2274626 | 0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes] |
| rs2296960 | 0.91[JPT][hapmap] |
| rs3829795 | 0.80[CHB][hapmap] |
| rs4652406 | 0.83[JPT][hapmap] |
| rs4652412 | 0.83[JPT][hapmap] |
| rs6425574 | 0.83[JPT][hapmap] |
| rs6662262 | 0.90[CHB][hapmap];0.83[JPT][hapmap] |
| rs6666456 | 0.84[CHB][hapmap] |
| rs6679542 | 0.84[JPT][hapmap] |
| rs744446 | 0.98[EUR][1000 genomes];0.80[ASN][1000 genomes] |
| rs7519700 | 0.83[EUR][1000 genomes] |
| rs7541890 | 0.95[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes] |
| rs7541899 | 0.83[EUR][1000 genomes] |
| rs928017 | 0.89[CHB][hapmap];0.82[JPT][hapmap] |
| rs9286930 | 0.90[CHB][hapmap];0.81[ASN][1000 genomes] |
| rs964983 | 0.83[JPT][hapmap] |
| rs964984 | 0.83[JPT][hapmap] |
mRNA abundance (count:9)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs913514 | TDRD5 | cis | lung | GTEx |
| rs913514 | TDRD5 | cis | Esophagus Mucosa | GTEx |
| rs913514 | TDRD5 | cis | Adipose Subcutaneous | GTEx |
| rs913514 | TDRD5 | cis | Artery Aorta | GTEx |
| rs913514 | TDRD5 | cis | Thyroid | GTEx |
| rs913514 | RP11-545A16.3 | cis | Artery Aorta | GTEx |
| rs913514 | TDRD5 | cis | Nerve Tibial | GTEx |
| rs913514 | TDRD5 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs913514 | TDRD5 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:179556000-179560600 | Weak transcription | Right Atrium | heart |
| 2 | chr1:179558200-179560600 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
