Variant report
| Variant | rs3899017 |
|---|---|
| Chromosome Location | chr8:19669198-19669199 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr8:19664721..19666469-chr8:19669172..19670993,2 | K562 | blood: | |
| 2 | chr8:19656532..19659284-chr8:19668673..19672507,3 | K562 | blood: | |
| 3 | chr8:19668752..19670633-chr8:19673215..19675993,4 | MCF-7 | breast: | |
| 4 | chr8:19668951..19670842-chr8:19672716..19674665,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000104613 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs17091534 | 0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs57462676 | 0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs57837509 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs59259846 | 0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs59565447 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs60329942 | 0.81[EUR][1000 genomes] |
| rs60369789 | 0.95[ASN][1000 genomes] |
| rs61180388 | 0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs62496731 | 0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs67989257 | 0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs6981306 | 0.86[ASN][1000 genomes] |
| rs6981674 | 0.94[ASN][1000 genomes] |
| rs6993525 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs7005767 | 0.92[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs7012358 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7461774 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs7822495 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes] |
| rs7832638 | 0.94[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 | nsv890625 | chr8:19368697-19799641 | Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 19 gene(s) | inside rSNPs | diseases |
| 2 | nsv610759 | chr8:19561997-20068842 | Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 21 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3899017 | INTS10 | cis | multi-tissue | Pritchard |
Chromatin state (count:0 , 50 per page) page:
| No data |
