Variant report
| Variant | rs10843399 |
|---|---|
| Chromosome Location | chr12:29539069-29539070 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:29534214..29536521-chr12:29538492..29540922,3 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs1006410 | 0.93[JPT][hapmap];0.81[ASN][1000 genomes] |
| rs1072724 | 0.85[ASN][1000 genomes] |
| rs10771520 | 0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs10771521 | 0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs10843376 | 0.90[ASN][1000 genomes] |
| rs10843385 | 0.81[ASN][1000 genomes] |
| rs10843401 | 0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs11050168 | 0.93[JPT][hapmap];0.81[ASN][1000 genomes] |
| rs12578931 | 0.84[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs12581107 | 0.80[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs17715086 | 0.93[JPT][hapmap];0.84[ASN][1000 genomes] |
| rs1836861 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2288128 | 0.93[JPT][hapmap];0.85[ASN][1000 genomes] |
| rs2288129 | 0.93[JPT][hapmap];0.85[ASN][1000 genomes] |
| rs2350315 | 0.81[ASN][1000 genomes] |
| rs3782505 | 0.93[JPT][hapmap];0.85[ASN][1000 genomes] |
| rs3782510 | 0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes] |
| rs3948497 | 0.93[JPT][hapmap] |
| rs4277150 | 0.81[ASN][1000 genomes] |
| rs7299283 | 0.93[JPT][hapmap];0.81[ASN][1000 genomes] |
| rs7302986 | 0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7313552 | 0.81[ASN][1000 genomes] |
| rs7358667 | 0.83[ASN][1000 genomes] |
| rs7964831 | 0.93[JPT][hapmap];0.85[ASN][1000 genomes] |
| rs986072 | 0.85[ASN][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 | nsv995123 | chr12:29095272-29571558 | Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 35 gene(s) | inside rSNPs | diseases |
| 2 | nsv1053641 | chr12:29268813-29854413 | Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 40 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10843399 | RP11-996F15.2 | cis | Thyroid | GTEx |
| rs10843399 | RP11-996F15.2 | cis | lung | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:29535600-29542600 | Weak transcription | Hela-S3 | cervix |
| 2 | chr12:29535600-29543400 | Weak transcription | Primary T cells effector/memory enriched fromperipheralblood | blood |
