Variant report
| Variant | rs189664 |
|---|---|
| Chromosome Location | chr6:49675544-49675545 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:7)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:7 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:49672074..49677551-chr6:49678532..49683707,8 | K562 | blood: | |
| 2 | chr6:49617885..49620394-chr6:49675007..49676797,2 | K562 | blood: | |
| 3 | chr6:49602506..49604943-chr6:49674658..49678128,4 | K562 | blood: | |
| 4 | chr6:49602506..49604622-chr6:49673985..49676942,2 | K562 | blood: | |
| 5 | chr6:49674727..49677077-chr6:49726981..49728882,2 | K562 | blood: | |
| 6 | chr6:49674713..49678350-chr6:49679075..49681593,3 | K562 | blood: | |
| 7 | chr6:49671946..49673936-chr6:49674455..49676625,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000112077 | Chromatin interaction |
| ENSG00000124490 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs187360 | 0.86[ASN][1000 genomes] |
| rs360549 | 1.00[JPT][hapmap] |
| rs360550 | 1.00[JPT][hapmap] |
| rs360552 | 0.85[EUR][1000 genomes] |
| rs360554 | 0.83[CHB][hapmap];0.95[JPT][hapmap] |
| rs360557 | 0.86[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs495335 | 0.90[JPT][hapmap] |
| rs500423 | 0.86[ASN][1000 genomes] |
| rs508949 | 0.91[JPT][hapmap] |
| rs509699 | 0.83[CHB][hapmap];0.95[JPT][hapmap] |
| rs517705 | 0.86[ASN][1000 genomes] |
| rs547848 | 0.91[JPT][hapmap];0.86[ASN][1000 genomes] |
| rs547972 | 1.00[JPT][hapmap];0.83[ASN][1000 genomes] |
| rs553723 | 0.83[ASN][1000 genomes] |
| rs662874 | 0.83[ASN][1000 genomes] |
| rs669500 | 0.91[JPT][hapmap];0.86[YRI][hapmap] |
| rs696718 | 0.86[JPT][hapmap] |
| rs699954 | 0.86[ASN][1000 genomes] |
| rs699955 | 1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs699957 | 0.86[ASN][1000 genomes] |
| rs699958 | 1.00[JPT][hapmap];0.86[ASN][1000 genomes] |
| rs699966 | 0.85[ASN][1000 genomes] |
| rs699983 | 1.00[JPT][hapmap] |
| rs780442 | 1.00[JPT][hapmap] |
| rs780447 | 0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[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 | nsv933942 | chr6:49480550-50004231 | Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 25 gene(s) | inside rSNPs | diseases |
| 2 | nsv933833 | chr6:49515134-49961765 | Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 23 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs189664 | TMEM14A | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:49672600-49681800 | Strong transcription | Primary neutrophils fromperipheralblood | blood |
