Variant report
| Variant | rs2516685 |
|---|---|
| Chromosome Location | chr6:30361608-30361609 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000204590 | Chromatin interaction |
| ENSG00000204576 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs1264570 | 0.86[EUR][1000 genomes] |
| rs2072111 | 0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2516688 | 0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs2524205 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs3094623 | 0.84[AFR][1000 genomes] |
| rs3129825 | 0.84[AFR][1000 genomes] |
| rs3129826 | 0.84[AFR][1000 genomes] |
| rs3129827 | 0.84[AFR][1000 genomes] |
| rs3129828 | 0.84[AFR][1000 genomes] |
| rs3132621 | 0.84[AFR][1000 genomes] |
| rs3132622 | 0.84[AFR][1000 genomes] |
| rs9261700 | 0.84[AFR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1025667 | chr6:30292845-30638066 | Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 825 gene(s) | inside rSNPs | diseases |
| 2 | nsv969293 | chr6:30348821-30368580 | Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription | Chromatin interactive region | 4 gene(s) | inside rSNPs | diseases |
| 3 | esv18372 | chr6:30359622-30363319 | Enhancers Weak transcription Bivalent Enhancer | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 4 | esv16525 | chr6:30361117-30364291 | Bivalent Enhancer Weak transcription Enhancers | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 5 | esv18201 | chr6:30361192-30362471 | Enhancers Bivalent Enhancer Weak transcription | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 6 | esv1841008 | chr6:30361193-30362425 | Bivalent Enhancer Enhancers Weak transcription | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 7 | esv1842534 | chr6:30361193-30362425 | Bivalent Enhancer Weak transcription Enhancers | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2516685 | HCG22 | cis | lymphoblastoid | seeQTL |
| rs2516685 | C6orf227 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:30359800-30364600 | Weak transcription | ES-UCSF4 Cell Line | embryonic stem cell |
