Variant report
| Variant | rs6687527 |
|---|---|
| Chromosome Location | chr1:228703641-228703642 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:8)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | RAD21 | chr1:228702623-228703787 | SK-N-SH | brain: | n/a | chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174 |
| No data |
(count:8 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:228638761..228647671-chr1:228695176..228704605,18 | K562 | blood: | |
| 2 | chr1:228696529..228699343-chr1:228702490..228705353,2 | K562 | blood: | |
| 3 | chr1:228191722..228192636-chr1:228703111..228703660,2 | K562 | blood: | |
| 4 | chr1:228452377..228453300-chr1:228702937..228703662,2 | K562 | blood: | |
| 5 | chr1:228392725..228394871-chr1:228701724..228704719,2 | K562 | blood: | |
| 6 | chr1:228528158..228528703-chr1:228703089..228703660,2 | K562 | blood: | |
| 7 | chr1:228414817..228415566-chr1:228702553..228703686,3 | K562 | blood: | |
| 8 | chr1:228645121..228649502-chr1:228703257..228706050,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| BTNL10 | TF binding region |
| ENSG00000196890 | Chromatin interaction |
| ENSG00000181218 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs1011878 | 1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs1011879 | 0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs10916336 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs11586639 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs11588356 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs12025421 | 0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs12028536 | 0.84[ASN][1000 genomes] |
| rs12035781 | 0.83[ASN][1000 genomes] |
| rs1925716 | 0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4147254 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs4653978 | 0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs56709082 | 0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs60733763 | 0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs6426508 | 0.88[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs7539072 | 0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs942851 | 0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs942854 | 0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv32853 | chr1:227880116-228806209 | Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 187 gene(s) | inside rSNPs | diseases |
| 2 | nsv1009891 | chr1:228450763-228742676 | Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 68 gene(s) | inside rSNPs | diseases |
| 3 | nsv1013500 | chr1:228459134-228849601 | Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 98 gene(s) | inside rSNPs | diseases |
| 4 | nsv549296 | chr1:228585837-228720480 | Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 64 gene(s) | inside rSNPs | diseases |
| 5 | nsv549297 | chr1:228681195-228720480 | Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 6 | nsv468305 | chr1:228681195-228731677 | Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 7 | nsv549298 | chr1:228681195-228731677 | Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 8 | nsv947521 | chr1:228698244-228704499 | Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS | TF binding regionCpG islandChromatin interactive region | 10 gene(s) | inside rSNPs | diseases |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
