Variant report
| Variant | rs1233493 |
|---|---|
| Chromosome Location | chr6:29458241-29458242 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:6)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:6 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | GATA3 | chr6:29458207-29459194 | MCF-7 | breast: | n/a | chr6:29458615-29458631 chr6:29458615-29458631 chr6:29458620-29458637 chr6:29458618-29458628 chr6:29458502-29458509 chr6:29458502-29458509 chr6:29458502-29458509 chr6:29458501-29458511 |
| 2 | GATA2 | chr6:29458230-29458945 | K562 | blood: | n/a | chr6:29458615-29458631 chr6:29458615-29458631 chr6:29458620-29458637 chr6:29458618-29458628 chr6:29458502-29458509 chr6:29458502-29458509 chr6:29458502-29458509 chr6:29458501-29458511 |
| 3 | GATA3 | chr6:29458213-29458467 | MCF-7 | breast: | n/a | n/a |
| 4 | CCNT2 | chr6:29458160-29458786 | K562 | blood: | n/a | n/a |
| 5 | GATA1 | chr6:29457892-29458925 | K562 | blood: | n/a | chr6:29458615-29458631 chr6:29458615-29458631 chr6:29458067-29458076 chr6:29458620-29458637 chr6:29458618-29458628 chr6:29458502-29458509 chr6:29458502-29458509 chr6:29458502-29458509 chr6:29458501-29458511 |
| 6 | TEAD4 | chr6:29457925-29458971 | K562 | blood: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:29457898..29460263-chr6:29462415..29464583,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| RPS17P1 | TF binding region |
| MAS1L | TF binding region |
rSNPs within LD-proxies of this variant (count:46)
| rs_ID | r2[population] |
|---|---|
| rs11968213 | 1.00[ASN][1000 genomes] |
| rs1233480 | 0.84[EUR][1000 genomes] |
| rs1233494 | 1.00[EUR][1000 genomes] |
| rs1234844 | 1.00[EUR][1000 genomes] |
| rs2023463 | 1.00[EUR][1000 genomes] |
| rs2143668 | 0.98[EUR][1000 genomes] |
| rs2523431 | 0.98[EUR][1000 genomes] |
| rs2523432 | 0.90[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2523443 | 0.98[EUR][1000 genomes] |
| rs2535247 | 1.00[ASN][1000 genomes] |
| rs2535248 | 1.00[ASN][1000 genomes] |
| rs2535250 | 1.00[ASN][1000 genomes] |
| rs2535251 | 1.00[ASN][1000 genomes] |
| rs2535252 | 1.00[ASN][1000 genomes] |
| rs2535255 | 1.00[ASN][1000 genomes] |
| rs2535256 | 1.00[ASN][1000 genomes] |
| rs2535257 | 1.00[ASN][1000 genomes] |
| rs2535259 | 1.00[ASN][1000 genomes] |
| rs2746149 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2746150 | 0.98[EUR][1000 genomes] |
| rs2747417 | 1.00[ASN][1000 genomes] |
| rs2747418 | 1.00[ASN][1000 genomes] |
| rs2747419 | 1.00[ASN][1000 genomes] |
| rs2857767 | 1.00[ASN][1000 genomes] |
| rs2857768 | 1.00[ASN][1000 genomes] |
| rs2857770 | 1.00[ASN][1000 genomes] |
| rs2857780 | 1.00[ASN][1000 genomes] |
| rs2857783 | 1.00[ASN][1000 genomes] |
| rs2857784 | 1.00[ASN][1000 genomes] |
| rs2907893 | 1.00[ASN][1000 genomes] |
| rs2907895 | 1.00[ASN][1000 genomes] |
| rs2907896 | 1.00[ASN][1000 genomes] |
| rs2982834 | 1.00[ASN][1000 genomes] |
| rs2982835 | 1.00[ASN][1000 genomes] |
| rs3094569 | 0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3117286 | 1.00[ASN][1000 genomes] |
| rs3117287 | 1.00[ASN][1000 genomes] |
| rs387603 | 1.00[ASN][1000 genomes] |
| rs404240 | 0.89[EUR][1000 genomes] |
| rs406424 | 1.00[ASN][1000 genomes] |
| rs408623 | 0.89[EUR][1000 genomes] |
| rs416560 | 1.00[ASN][1000 genomes] |
| rs61730667 | 1.00[ASN][1000 genomes] |
| rs9468579 | 1.00[ASN][1000 genomes] |
| rs9468581 | 1.00[ASN][1000 genomes] |
| rs9500953 | 1.00[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 | esv3424039 | chr6:29439297-29504564 | Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv883528 | chr6:29447724-29494897 | Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive region | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:10)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1233493 | HIST1H2BC | cis | parietal | SCAN |
| rs1233493 | HLA-C | cis | multi-tissue | Pritchard |
| rs1233493 | BTN2A1 | cis | parietal | SCAN |
| rs1233493 | HLA-H | cis | multi-tissue | Pritchard |
| rs1233493 | BTN3A2 | cis | multi-tissue | Pritchard |
| rs1233493 | HIST1H2BM | cis | cerebellum | SCAN |
| rs1233493 | ZNF323 | cis | parietal | SCAN |
| rs1233493 | HLA-A | cis | multi-tissue | Pritchard |
| rs1233493 | ZFP57 | cis | multi-tissue | Pritchard |
| rs1233493 | HLA-G | cis | multi-tissue | Pritchard |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:29457200-29459400 | Enhancers | Primary hematopoietic stem cells short term culture | blood |
| 2 | chr6:29457200-29461200 | Enhancers | Primary hematopoietic stem cells G-CSF-mobilized Female | -- |
| 3 | chr6:29457800-29458600 | Enhancers | Primary neutrophils fromperipheralblood | blood |
| 4 | chr6:29457800-29459800 | Enhancers | Primary hematopoietic stem cells | blood |
| 5 | chr6:29457800-29459800 | Enhancers | K562 | blood |
| 6 | chr6:29458000-29459000 | Flanking Active TSS | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
