Variant report
| Variant | rs13280085 |
|---|---|
| Chromosome Location | chr8:19669959-19669960 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr8:19669332..19671786-chr8:19673916..19676517,3 | MCF-7 | breast: | |
| 2 | chr8:19664721..19666469-chr8:19669172..19670993,2 | K562 | blood: | |
| 3 | chr8:19656532..19659284-chr8:19668673..19672507,3 | K562 | blood: | |
| 4 | chr8:19668752..19670633-chr8:19673215..19675993,4 | MCF-7 | breast: | |
| 5 | chr8:19664969..19667659-chr8:19669257..19670993,2 | K562 | blood: | |
| 6 | 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:16)
| rs_ID | r2[population] |
|---|---|
| rs10090638 | 1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs10092840 | 0.90[ASN][1000 genomes] |
| rs11204077 | 0.82[CEU][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs12547934 | 0.82[EUR][1000 genomes] |
| rs2083640 | 0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2083641 | 0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs3758061 | 0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs3855754 | 0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs3866469 | 0.82[AFR][1000 genomes];0.82[EUR][1000 genomes] |
| rs4392917 | 0.82[EUR][1000 genomes] |
| rs4464983 | 0.81[EUR][1000 genomes] |
| rs58556504 | 0.80[EUR][1000 genomes] |
| rs6982084 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6986456 | 1.00[CEU][hapmap];0.81[EUR][1000 genomes] |
| rs7012694 | 0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs7823457 | 0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs13280085 | INTS10 | cis | multi-tissue | Pritchard |
| rs13280085 | INTS10 | Cis_1M | lymphoblastoid | RTeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
