Variant report
| Variant | rs10183113 |
|---|---|
| Chromosome Location | chr2:73154613-73154614 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:73113462..73116046-chr2:73153242..73156114,3 | MCF-7 | breast: | |
| 2 | chr2:73152139..73154940-chr21:43795140..43797048,2 | MCF-7 | breast: | |
| 3 | chr2:73154403..73156745-chr2:73162341..73165045,2 | K562 | blood: | |
| 4 | chr2:73151599..73154763-chr2:73155312..73159264,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000116096 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs10185826 | 0.85[JPT][hapmap] |
| rs10195562 | 0.85[CEU][hapmap] |
| rs10196456 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs10196568 | 0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs1048704 | 0.95[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs11686652 | 0.95[ASN][1000 genomes] |
| rs12473812 | 0.85[JPT][hapmap] |
| rs17008501 | 1.00[JPT][hapmap];0.95[ASN][1000 genomes] |
| rs1898442 | 0.85[JPT][hapmap] |
| rs2077586 | 0.91[YRI][hapmap] |
| rs2164733 | 0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes] |
| rs59833760 | 0.92[ASN][1000 genomes] |
| rs59924850 | 0.95[ASN][1000 genomes] |
| rs6728203 | 0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs6745468 | 0.94[ASW][hapmap];0.90[CEU][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes] |
| rs6748324 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs6757051 | 0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs73945638 | 0.95[ASN][1000 genomes] |
| rs755409 | 0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes] |
| rs999494 | 0.85[JPT][hapmap] |
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 | nsv532723 | chr2:73088191-73219259 | Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 13 gene(s) | inside rSNPs | diseases |
| 2 | nsv874266 | chr2:73137991-73220138 | Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionmiRNA target site | 8 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10183113 | SFXN5 | cis | parietal | SCAN |
| rs10183113 | SPR | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:73154000-73158200 | Weak transcription | Fetal Brain Female | brain |
