Variant report
| Variant | rs10753199 |
|---|---|
| Chromosome Location | chr1:179559632-179559633 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:1)
- 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 | REST | chr1:179559524-179559871 | H1-neurons | neurons: | n/a | chr1:179559808-179559826 |
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-TDRD5-1 | chr1:179559507-179560440 | ENSG00000261060.1 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| TDRD5 | TF binding region |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs12136977 | 0.92[CEU][hapmap] |
| rs12137397 | 0.92[CEU][hapmap] |
| rs12138189 | 0.92[CEU][hapmap] |
| rs12568706 | 0.86[CEU][hapmap] |
| rs12724074 | 0.88[CEU][hapmap] |
| rs1576225 | 0.92[CEU][hapmap] |
| rs4475708 | 0.98[EUR][1000 genomes] |
| rs6425567 | 0.92[CEU][hapmap] |
| rs6668035 | 0.92[CEU][hapmap] |
| rs6672804 | 0.92[CEU][hapmap] |
| rs6674274 | 0.92[CEU][hapmap] |
| rs6691184 | 1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes] |
| rs962429 | 0.92[CEU][hapmap] |
| rs9787089 | 0.92[CEU][hapmap] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv946524 | chr1:179558860-179559970 | Weak transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:12)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10753199 | SOAT1 | cis | cerebellum | SCAN |
| rs10753199 | RASAL2 | cis | parietal | SCAN |
| rs10753199 | TDRD5 | cis | cerebellum | SCAN |
| rs10753199 | TDRD5 | cis | Artery Aorta | GTEx |
| rs10753199 | TDRD5 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs10753199 | TDRD5 | cis | Esophagus Mucosa | GTEx |
| rs10753199 | TDRD5 | cis | parietal | SCAN |
| rs10753199 | TDRD5 | cis | Nerve Tibial | GTEx |
| rs10753199 | TDRD5 | cis | Adipose Subcutaneous | GTEx |
| rs10753199 | RP11-545A16.4 | cis | Artery Tibial | GTEx |
| rs10753199 | TDRD5 | cis | Artery Tibial | GTEx |
| rs10753199 | TDRD5 | cis | Thyroid | 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 |
