Variant report
| Variant | rs41272451 |
|---|---|
| Chromosome Location | chr1:169411888-169411889 |
| allele | A/C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:169409746..169412742-chr1:169454228..169456553,2 | MCF-7 | breast: |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-SLC19A2-1 | chr1:169411876-169412646 | ENSG00000234437.1 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000213062 | Chromatin interaction |
| ENSG00000117479 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:6)
| rs_ID | r2[population] |
|---|---|
| rs11581416 | 0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17345412 | 0.81[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs17516734 | 0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17518601 | 0.82[AMR][1000 genomes] |
| rs17576071 | 0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17577345 | 0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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 | esv10418 | chr1:169059628-169621268 | Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 56 gene(s) | inside rSNPs | diseases |
| 2 | nsv831871 | chr1:169320673-169486680 | Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
| 3 | nsv1001454 | chr1:169387381-169465274 | Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 26 gene(s) | inside rSNPs | diseases |
| 4 | nsv1005941 | chr1:169410486-169456393 | Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 26 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs41272451 | KIFAP3 | cis | Artery Tibial | GTEx |
Chromatin state (count:0 , 50 per page) page:
| No data |
