Variant report
| Variant | rs3736780 |
|---|---|
| Chromosome Location | chr6:26505135-26505136 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:26504100..26506506-chr6:26521207..26524146,2 | MCF-7 | breast: | |
| 2 | chr6:26505036..26509551-chr6:26513654..26517917,7 | K562 | blood: | |
| 3 | chr6:26498274..26501430-chr6:26504852..26507027,3 | K562 | blood: | |
| 4 | chr6:26504071..26506546-chr6:26568162..26569845,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000228223 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs1535278 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs15580 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs1796524 | 1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes] |
| rs2145319 | 0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs2224379 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3864291 | 1.00[JPT][hapmap] |
| rs4713007 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6905163 | 0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6911330 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6922256 | 0.83[LWK][hapmap] |
| rs6927012 | 1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs6929908 | 0.87[LWK][hapmap];1.00[MKK][hapmap] |
| rs7745632 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes] |
| rs9295697 | 0.86[EUR][1000 genomes] |
| rs9366661 | 0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9379892 | 0.87[MKK][hapmap] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1029920 | chr6:25638507-26585842 | Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 2 | nsv538162 | chr6:25638507-26585842 | Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1215 gene(s) | inside rSNPs | diseases |
| 3 | nsv1023453 | chr6:25853830-26528250 | Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 1201 gene(s) | inside rSNPs | diseases |
| 4 | nsv482836 | chr6:26352883-26520964 | Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 49 gene(s) | inside rSNPs | diseases |
| 5 | nsv482407 | chr6:26369320-26550148 | Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 62 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:9)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3736780 | RP11-457M11.5 | cis | Esophagus Mucosa | GTEx |
| rs3736780 | RP11-457M11.5 | cis | Adipose Subcutaneous | GTEx |
| rs3736780 | ZSCAN23 | cis | cerebellum | SCAN |
| rs3736780 | HIST1H3E | cis | parietal | SCAN |
| rs3736780 | RP11-457M11.5 | cis | Artery Aorta | GTEx |
| rs3736780 | HMGN4 | cis | parietal | SCAN |
| rs3736780 | RP11-457M11.5 | cis | Thyroid | GTEx |
| rs3736780 | RP11-457M11.5 | cis | lung | GTEx |
| rs3736780 | ABT1 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
