Variant report
| Variant | rs11123206 |
|---|---|
| Chromosome Location | chr2:114541696-114541697 |
| allele | A/G |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:114512154..114515195-chr2:114539066..114542535,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000115084 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs10167730 | 0.85[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs10177576 | 0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes] |
| rs10179657 | 0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs10209330 | 0.84[AFR][1000 genomes];0.83[ASN][1000 genomes] |
| rs11123207 | 0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs11686297 | 0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs11694130 | 0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs12711788 | 0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs2122097 | 0.85[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs2442136 | 0.85[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs2687627 | 0.85[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs28451366 | 0.85[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs4848349 | 0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs4849275 | 0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs4849277 | 0.85[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs4849278 | 0.86[AMR][1000 genomes] |
| rs4849279 | 0.84[AMR][1000 genomes];0.81[ASN][1000 genomes] |
| rs6711542 | 0.85[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs7600228 | 0.85[AMR][1000 genomes];0.85[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 | nsv1009509 | chr2:114432965-114557306 | Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
| 2 | nsv535896 | chr2:114432965-114557306 | Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11123206 | RPL23AP7 | cis | lung | GTEx |
| rs11123206 | SLC35F5 | Cis_1M | lymphoblastoid | RTeQTL |
| rs11123206 | RPL23AP7 | cis | Whole Blood | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:114541200-114542400 | Weak transcription | Psoas Muscle | Psoas |
