Variant report
| Variant | rs6904071 |
|---|---|
| Chromosome Location | chr6:27047256-27047257 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:6)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:6 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | GATA2 | chr6:27046583-27047335 | SH-SY5Y | brain: | n/a | chr6:27047224-27047231 |
| 2 | CTCF | chr6:27046239-27047362 | SK-N-SH | brain: | n/a | n/a |
| 3 | RAD21 | chr6:27046234-27047513 | SK-N-SH | brain: | n/a | n/a |
| 4 | CTCF | chr6:27047140-27047290 | AG09319 | gingival: | n/a | n/a |
| 5 | SMC3 | chr6:27046285-27047300 | SK-N-SH | brain: | n/a | chr6:27046846-27046860 chr6:27046848-27046862 |
| 6 | GATA3 | chr6:27046805-27047317 | SH-SY5Y | brain: | n/a | chr6:27047224-27047231 |
| No data |
(count:6 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:26596507..26599265-chr6:27045244..27047262,3 | K562 | blood: | |
| 2 | chr6:27043192..27047825-chr6:27099036..27106055,7 | K562 | blood: | |
| 3 | chr6:27045716..27047825-chr6:27099036..27103328,4 | K562 | blood: | |
| 4 | chr6:26985450..26988105-chr6:27045850..27047500,2 | MCF-7 | breast: | |
| 5 | chr6:27038557..27041239-chr6:27046359..27048606,2 | K562 | blood: | |
| 6 | chr6:26053749..26055733-chr6:27045370..27048111,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| VN1R11P | TF binding region |
| ENSG00000196787 | Chromatin interaction |
| ENSG00000146109 | Chromatin interaction |
| ENSG00000124635 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs13194053 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes] |
| rs13219181 | 1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes] |
| rs34569203 | 1.00[ASN][1000 genomes] |
| rs4452638 | 0.85[CEU][hapmap] |
| rs4713074 | 0.81[YRI][hapmap] |
| rs5030956 | 0.81[YRI][hapmap] |
| rs61240102 | 1.00[ASN][1000 genomes] |
| rs67330695 | 0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs67540232 | 1.00[ASN][1000 genomes] |
| rs6913660 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6914824 | 1.00[ASN][1000 genomes] |
| rs72842197 | 0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7757148 | 1.00[CHD][hapmap] |
| rs926300 | 1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs9468015 | 0.81[YRI][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv948921 | chr6:26556890-27443957 | Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 472 gene(s) | inside rSNPs | diseases |
| 2 | esv2758038 | chr6:26695219-27095714 | Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 67 gene(s) | inside rSNPs | diseases |
| 3 | esv2759410 | chr6:26695219-27095714 | Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 67 gene(s) | inside rSNPs | diseases |
| 4 | nsv1029124 | chr6:26825468-27109774 | Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 244 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:7)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6904071 | BTN3A2 | cis | lymphoblastoid | seeQTL |
| rs6904071 | BTN3A2 | Cis_1M | lymphoblastoid | RTeQTL |
| rs6904071 | HIST1H2BH | cis | cerebellum | SCAN |
| rs6904071 | BTN3A3 | cis | lymphoblastoid | seeQTL |
| rs6904071 | BTN2A1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs6904071 | SLC17A3 | cis | parietal | SCAN |
| rs6904071 | BTN3A2///BTN3A3 | Cis_1M | lymphoblastoid | RTeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
