Variant report
| Variant | rs2122527 |
|---|---|
| Chromosome Location | chr3:161091636-161091637 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:4)
- CpG islands (count:0)
- Chromatin interactive region (count:17)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:4 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | EP300 | chr3:161089035-161091712 | MCF-7 | breast: | n/a | chr3:161089801-161089817 |
| 2 | POLR2A | chr3:161091450-161091874 | MCF-7 | breast: | n/a | n/a |
| 3 | POLR2A | chr3:161091394-161091954 | MCF-7 | breast: | n/a | n/a |
| 4 | POLR2A | chr3:161084726-161091997 | MCF-7 | breast: | n/a | n/a |
| No data |
(count:17 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:161089815..161091859-chr5:87970263..87972091,2 | MCF-7 | breast: | |
| 2 | chr3:161038392..161046344-chr3:161085640..161093564,25 | MCF-7 | breast: | |
| 3 | chr3:160934982..160947568-chr3:161079696..161093037,40 | MCF-7 | breast: | |
| 4 | chr3:161090661..161092175-chr9:130953250..130955416,2 | MCF-7 | breast: | |
| 5 | chr3:160936365..160960187-chr3:161078472..161094658,51 | MCF-7 | breast: | |
| 6 | chr11:75061761..75064404-chr3:161090947..161092751,2 | MCF-7 | breast: | |
| 7 | chr3:161090533..161094064-chr8:101963094..101965869,3 | MCF-7 | breast: | |
| 8 | chr17:57916984..57919121-chr3:161089806..161091709,2 | MCF-7 | breast: | |
| 9 | chr3:161089882..161091893-chr9:14313286..14315891,2 | MCF-7 | breast: | |
| 10 | chr3:160282384..160284279-chr3:161090070..161092453,3 | MCF-7 | breast: | |
| 11 | chr11:65265519..65268230-chr3:161089523..161091817,2 | MCF-7 | breast: | |
| 12 | chr3:160813033..160824577-chr3:161083489..161092050,35 | MCF-7 | breast: | |
| 13 | chr3:160472518..160475131-chr3:161089184..161091851,3 | MCF-7 | breast: | |
| 14 | chr14:38061358..38063507-chr3:161089489..161091930,2 | MCF-7 | breast: | |
| 15 | chr22:30683032..30685513-chr3:161089094..161092006,2 | MCF-7 | breast: | |
| 16 | chr20:56282039..56284863-chr3:161089358..161091881,2 | MCF-7 | breast: | |
| 17 | chr3:160166836..160169216-chr3:161090028..161092220,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| SPTSSB | TF binding region |
| ENSG00000129514 | Chromatin interaction |
| ENSG00000213186 | Chromatin interaction |
| ENSG00000229320 | Chromatin interaction |
| ENSG00000270117 | Chromatin interaction |
| ENSG00000251562 | Chromatin interaction |
| ENSG00000124225 | Chromatin interaction |
| ENSG00000260572 | Chromatin interaction |
| ENSG00000199004 | Chromatin interaction |
| ENSG00000169255 | Chromatin interaction |
| ENSG00000169251 | Chromatin interaction |
| ENSG00000163590 | Chromatin interaction |
| ENSG00000239282 | Chromatin interaction |
| ENSG00000271052 | Chromatin interaction |
| ENSG00000147862 | Chromatin interaction |
| ENSG00000137486 | Chromatin interaction |
| ENSG00000148337 | Chromatin interaction |
| ENSG00000164924 | Chromatin interaction |
| ENSG00000240138 | Chromatin interaction |
| ENSG00000245864 | Chromatin interaction |
| ENSG00000186432 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs11710489 | 0.85[EUR][1000 genomes] |
| rs11715591 | 0.81[EUR][1000 genomes] |
| rs13059340 | 0.81[EUR][1000 genomes] |
| rs13076251 | 0.85[EUR][1000 genomes] |
| rs13084731 | 0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs13084746 | 0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs1450519 | 0.98[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs1450521 | 0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1450522 | 0.83[EUR][1000 genomes] |
| rs1450523 | 0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2054710 | 0.85[EUR][1000 genomes] |
| rs2404341 | 0.85[EUR][1000 genomes] |
| rs2404342 | 0.85[EUR][1000 genomes] |
| rs35100811 | 0.83[EUR][1000 genomes] |
| rs60625846 | 0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs67460515 | 0.83[EUR][1000 genomes] |
| rs7610985 | 0.81[EUR][1000 genomes] |
| rs9844862 | 0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv931072 | chr3:160669567-161159779 | Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 98 gene(s) | inside rSNPs | diseases |
| 2 | nsv533237 | chr3:161019834-161804660 | Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 91 gene(s) | inside rSNPs | diseases |
| 3 | nsv829772 | chr3:161047817-161202554 | Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 88 gene(s) | inside rSNPs | diseases |
| 4 | nsv877710 | chr3:161087857-161245414 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 84 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2122527 | SPTSSB | cis | Heart Left Ventricle | GTEx |
| rs2122527 | SPTSSB | cis | Thyroid | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:161091000-161091800 | Bivalent Enhancer | Primary Natural Killer cells fromperipheralblood | blood |
| 2 | chr3:161091200-161092800 | Weak transcription | ES-UCSF4 Cell Line | embryonic stem cell |
| 3 | chr3:161091200-161093200 | Weak transcription | H9 Cell Line | embryonic stem cell |
| 4 | chr3:161091200-161096800 | Weak transcription | Primary T helper naive cells from peripheral blood | blood |
| 5 | chr3:161091400-161093000 | Weak transcription | H1 Cell Line | embryonic stem cell |
| 6 | chr3:161091400-161102800 | Weak transcription | Pancreatic Islets | Pancreatic Islet |
