Variant report
| Variant | rs17148600 |
|---|---|
| Chromosome Location | chr11:85628827-85628828 |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr11:85627451..85630538-chr11:85632565..85635879,3 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000255005 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:44)
| rs_ID | r2[population] |
|---|---|
| rs1002405 | 1.00[CEU][hapmap];1.00[LWK][hapmap] |
| rs10501603 | 1.00[ASN][1000 genomes] |
| rs10898431 | 1.00[ASN][1000 genomes] |
| rs11234441 | 1.00[ASN][1000 genomes] |
| rs11234489 | 1.00[ASN][1000 genomes] |
| rs11234492 | 1.00[ASN][1000 genomes] |
| rs11234496 | 1.00[ASN][1000 genomes] |
| rs11234502 | 1.00[ASN][1000 genomes] |
| rs11234512 | 1.00[ASN][1000 genomes] |
| rs11234513 | 1.00[ASN][1000 genomes] |
| rs11234517 | 1.00[ASN][1000 genomes] |
| rs11234522 | 1.00[ASN][1000 genomes] |
| rs11825378 | 0.85[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11825912 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11828161 | 1.00[CEU][hapmap];1.00[ASN][1000 genomes] |
| rs12278260 | 1.00[ASN][1000 genomes] |
| rs12279581 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12281958 | 1.00[ASN][1000 genomes] |
| rs12287170 | 1.00[ASN][1000 genomes] |
| rs12790645 | 0.88[MKK][hapmap] |
| rs17745153 | 1.00[ASN][1000 genomes] |
| rs17745236 | 1.00[ASN][1000 genomes] |
| rs17817588 | 1.00[ASN][1000 genomes] |
| rs17817919 | 1.00[ASN][1000 genomes] |
| rs2509347 | 1.00[EUR][1000 genomes] |
| rs3213934 | 0.88[MKK][hapmap] |
| rs41381550 | 1.00[ASN][1000 genomes] |
| rs4944552 | 1.00[ASN][1000 genomes] |
| rs56944537 | 1.00[ASN][1000 genomes] |
| rs57125313 | 1.00[ASN][1000 genomes] |
| rs58515881 | 1.00[ASN][1000 genomes] |
| rs59019168 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs59104711 | 1.00[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs60253048 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs60264644 | 1.00[ASN][1000 genomes] |
| rs60737637 | 1.00[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs61535933 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs72951268 | 1.00[ASN][1000 genomes] |
| rs72959177 | 1.00[ASN][1000 genomes] |
| rs72959197 | 1.00[ASN][1000 genomes] |
| rs72963077 | 1.00[ASN][1000 genomes] |
| rs72965157 | 1.00[ASN][1000 genomes] |
| rs7939690 | 1.00[EUR][1000 genomes] |
| rs7950710 | 1.00[CEU][hapmap] |
Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1051155 | chr11:85006564-85721261 | Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 64 gene(s) | inside rSNPs | diseases |
| 2 | nsv541110 | chr11:85006564-85721261 | Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 64 gene(s) | inside rSNPs | diseases |
| 3 | nsv1035489 | chr11:85502953-85778229 | ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 21 gene(s) | inside rSNPs | diseases |
| 4 | nsv1048818 | chr11:85524635-85746473 | Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 18 gene(s) | inside rSNPs | diseases |
| 5 | nsv541116 | chr11:85524635-85746473 | Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 18 gene(s) | inside rSNPs | diseases |
| 6 | nsv898053 | chr11:85579304-85634425 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 7 | nsv1053808 | chr11:85588919-85757693 | Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 12 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17148600 | GUCA1C | trans | brain | seeQTL |
| rs17148600 | FABP4 | trans | brain | seeQTL |
| rs17148600 | SH2D2A | trans | brain | seeQTL |
| rs17148600 | CRX | trans | brain | seeQTL |
| rs17148600 | LRTM1 | trans | brain | seeQTL |
| rs17148600 | SLC5A7 | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr11:85615800-85630200 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
