Variant report
| Variant | rs175954 |
|---|---|
| Chromosome Location | chr6:28011585-28011586 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
1
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:28004584..28007238-chr6:28010224..28013138,2 | K562 | blood: | |
| 2 | chr6:27861805..27863822-chr6:28010938..28012589,2 | MCF-7 | breast: | |
| 3 | chr6:27797828..27799356-chr6:28009972..28012647,2 | K562 | blood: | |
| 4 | chr6:28010916..28013781-chr6:28060247..28062544,2 | K562 | blood: | |
| 5 | chr6:28004519..28007774-chr6:28009594..28013138,4 | K562 | blood: | |
| 6 | chr6:28011209..28013344-chr6:28013937..28015849,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| OR2B7P | TF binding region |
| ENSG00000187763 | Chromatin interaction |
| ENSG00000197914 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs149899 | 0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs149946 | 0.85[EUR][1000 genomes] |
| rs149947 | 0.85[EUR][1000 genomes] |
| rs149961 | 0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs149964 | 0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs149968 | 0.87[EUR][1000 genomes] |
| rs149969 | 0.87[EUR][1000 genomes] |
| rs156736 | 0.80[EUR][1000 genomes] |
| rs156744 | 0.85[EUR][1000 genomes] |
| rs169431 | 0.85[AFR][1000 genomes] |
| rs172166 | 0.85[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs202908 | 0.84[AFR][1000 genomes] |
| rs203890 | 0.80[AFR][1000 genomes];0.88[EUR][1000 genomes] |
| rs9348789 | 0.82[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9357060 | 0.82[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9380045 | 0.83[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9393881 | 0.82[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9468271 | 0.82[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9468274 | 0.81[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9468275 | 0.82[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9468277 | 0.82[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9468278 | 0.82[AFR][1000 genomes];0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv432858 | chr6:27719375-28011652 | Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 387 gene(s) | inside rSNPs | diseases |
| 2 | nsv1022651 | chr6:27864217-28017997 | Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 50 gene(s) | inside rSNPs | diseases |
| 3 | nsv830619 | chr6:27872302-28062544 | Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 38 gene(s) | inside rSNPs | diseases |
| 4 | nsv883513 | chr6:27982152-28033087 | Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 5 | nsv981052 | chr6:27987196-28024382 | Bivalent Enhancer | TF binding regionCpG islandChromatin interactive region | 12 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:8)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs175954 | RP1-265C24.5 | cis | Muscle Skeletal | GTEx |
| rs175954 | BTN3A2 | Cis_chr | lymphoblastoid | RTeQTL |
| rs175954 | BTN3A2///BTN3A3 | Cis_chr | lymphoblastoid | RTeQTL |
| rs175954 | AL022393.7 | cis | Muscle Skeletal | GTEx |
| rs175954 | RP1-265C24.5 | cis | Heart Left Ventricle | GTEx |
| rs175954 | OR2B7P | cis | Thyroid | GTEx |
| rs175954 | OR2B8P | cis | Thyroid | GTEx |
| rs175954 | AL022393.7 | cis | Nerve Tibial | GTEx |
Chromatin state (count:0 , 50 per page) page:
| No data |
