Variant report
| Variant | rs11718449 |
|---|---|
| Chromosome Location | chr3:112761553-112761554 |
| allele | A/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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:112737944..112740909-chr3:112760087..112762982,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000163608 | Chromatin interaction |
| ENSG00000240057 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs10934211 | 1.00[MEX][hapmap] |
| rs10934213 | 0.80[AMR][1000 genomes] |
| rs12495569 | 0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs1488189 | 1.00[MEX][hapmap];0.82[TSI][hapmap] |
| rs2399460 | 0.82[CEU][hapmap] |
| rs34671634 | 0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs3868879 | 1.00[CEU][hapmap];0.92[EUR][1000 genomes] |
| rs3872610 | 0.83[MEX][hapmap] |
| rs3872611 | 0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs3901416 | 0.84[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs4082467 | 0.80[AMR][1000 genomes] |
| rs6438125 | 0.95[EUR][1000 genomes] |
| rs7620940 | 0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7642680 | 1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7650483 | 0.91[CEU][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes] |
| rs7650656 | 1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs9288967 | 1.00[MEX][hapmap];0.82[TSI][hapmap] |
| rs9874803 | 0.94[MEX][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 | esv3431441 | chr3:112453467-113213252 | Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 43 gene(s) | inside rSNPs | diseases |
| 2 | nsv3951 | chr3:112759554-112800236 | Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11718449 | ZNF346 | trans | cerebellum | SCAN |
| rs11718449 | C3orf17 | cis | cerebellum | SCAN |
| rs11718449 | GTPBP8 | cis | multi-tissue | Pritchard |
| rs11718449 | SIDT1 | cis | cerebellum | SCAN |
| rs11718449 | GTPBP8 | Cis_1M | lymphoblastoid | RTeQTL |
| rs11718449 | GTPBP8 | cis | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:112740800-112770200 | Weak transcription | Primary T cells from cord blood | blood |
| 2 | chr3:112749800-112762800 | Weak transcription | Primary B cells from cord blood | blood |
