Variant report
| Variant | rs5753425 |
|---|---|
| Chromosome Location | chr22:31410356-31410357 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr22:31364474..31366749-chr22:31408252..31410827,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000253352 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs2285920 | 0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs2286214 | 1.00[YRI][hapmap] |
| rs4820922 | 0.90[ASN][1000 genomes] |
| rs56683450 | 0.92[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs5749190 | 0.92[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs5749196 | 0.88[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs5749205 | 0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs5753371 | 0.92[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs5753375 | 0.88[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs5753380 | 0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs5753391 | 0.92[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs5753409 | 0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes] |
| rs5753416 | 0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62236060 | 0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62238089 | 0.92[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs62238091 | 0.92[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs62238093 | 0.92[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs62238094 | 0.92[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs62238096 | 0.88[EUR][1000 genomes];0.86[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 | nsv9896 | chr22:31369204-31513933 | Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 35 gene(s) | inside rSNPs | diseases |
| 2 | nsv966103 | chr22:31410201-31452981 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS | TF binding regionChromatin interactive region | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs5753425 | UTS2 | trans | lymphoblastoid | seeQTL |
| rs5753425 | CNTN6 | trans | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr22:31409400-31413000 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
