Variant report
| Variant | rs16833867 |
|---|---|
| Chromosome Location | chr1:152145661-152145662 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:152140753..152142610-chr1:152144905..152147472,2 | MCF-7 | breast: | |
| 2 | chr1:152019081..152021323-chr1:152144362..152146461,2 | MCF-7 | breast: | |
| 3 | chr1:152140466..152143541-chr1:152143958..152146288,4 | MCF-7 | breast: | |
| 4 | chr1:152145123..152147434-chr1:152151128..152152716,2 | MCF-7 | breast: | |
| 5 | chr1:152021638..152025256-chr1:152144689..152147457,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000163191 | Chromatin interaction |
| ENSG00000237975 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10494272 | 0.88[ASW][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs10494273 | 1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11204927 | 1.00[ASN][1000 genomes] |
| rs1390489 | 0.85[CHD][hapmap] |
| rs16833966 | 1.00[CHD][hapmap] |
| rs16833974 | 1.00[MEX][hapmap] |
| rs1858481 | 1.00[CHD][hapmap] |
| rs3120669 | 1.00[MEX][hapmap] |
| rs3134871 | 1.00[CHD][hapmap] |
| rs4559506 | 0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4845735 | 1.00[MEX][hapmap] |
| rs6587655 | 1.00[MEX][hapmap] |
| rs74126341 | 0.84[AMR][1000 genomes] |
| rs7523354 | 1.00[MEX][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 | nsv1007097 | chr1:151832796-152227977 | Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 2 | nsv1012327 | chr1:151835544-152200890 | Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 3 | nsv535159 | chr1:151835544-152200890 | Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 4 | nsv547853 | chr1:152008671-152236760 | Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 83 gene(s) | inside rSNPs | diseases |
| 5 | nsv872442 | chr1:152054120-152187641 | Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 9 gene(s) | inside rSNPs | diseases |
| 6 | nsv1014095 | chr1:152104486-152454591 | Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
| 7 | nsv547854 | chr1:152145661-152165878 | Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:152131400-152145800 | Enhancers | Primary monocytes fromperipheralblood | blood |
| 2 | chr1:152142200-152151800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
