Variant report
| Variant | rs2823121 |
|---|---|
| Chromosome Location | chr21:16551257-16551258 |
| 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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr21:16435581..16439206-chr21:16548873..16552756,4 | MCF-7 | breast: | |
| 2 | chr21:16444369..16446485-chr21:16550996..16553338,2 | MCF-7 | breast: | |
| 3 | chr21:16436485..16439041-chr21:16550508..16552632,3 | MCF-7 | breast: | |
| 4 | chr21:16549985..16551510-chr21:16570529..16573382,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000180530 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs1009576 | 0.91[JPT][hapmap] |
| rs1014526 | 0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs11088299 | 0.82[EUR][1000 genomes] |
| rs2223128 | 0.84[CEU][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs2823097 | 0.87[YRI][hapmap] |
| rs2823107 | 0.80[EUR][1000 genomes] |
| rs2823109 | 0.86[JPT][hapmap] |
| rs2823114 | 0.91[JPT][hapmap] |
| rs2823118 | 0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2823124 | 0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7275196 | 1.00[JPT][hapmap];0.87[YRI][hapmap] |
| rs7279893 | 0.84[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs7282135 | 0.85[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs965098 | 1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs9974193 | 0.84[CEU][hapmap] |
| rs9976384 | 0.91[JPT][hapmap] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1063385 | chr21:16521617-16926212 | Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers | TF binding regionChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 2 | nsv913413 | chr21:16537728-16621859 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | Chromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2823121 | SAMSN1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr21:16551200-16555200 | Weak transcription | Fetal Heart | heart |
