Variant report
| Variant | rs17179337 |
|---|---|
| Chromosome Location | chr14:38174359-38174360 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr14:38049420..38072812-chr14:38163892..38186188,147 | MCF-7 | breast: | |
| 2 | chr14:38052270..38073748-chr14:38165681..38186607,118 | MCF-7 | breast: | |
| 3 | chr14:38169631..38171972-chr14:38174267..38176002,2 | MCF-7 | breast: | |
| 4 | chr14:38168671..38173549-chr14:38173725..38178675,7 | MCF-7 | breast: | |
| 5 | chr14:38171586..38175426-chr14:38177253..38179138,3 | K562 | blood: | |
| 6 | chr14:38036372..38038975-chr14:38173852..38175710,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000129514 | Chromatin interaction |
| ENSG00000139865 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs10139826 | 1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11156965 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11844358 | 0.92[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes] |
| rs12431417 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12433850 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs12435334 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs177829 | 0.92[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes] |
| rs177835 | 0.85[EUR][1000 genomes] |
| rs177848 | 0.92[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes] |
| rs177869 | 0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs177871 | 0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs177888 | 0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs177899 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs1951647 | 0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1957588 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1957589 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1998124 | 0.85[EUR][1000 genomes] |
| rs1998125 | 0.92[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes] |
| rs466255 | 0.85[EUR][1000 genomes] |
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 | nsv530038 | chr14:37590543-38336191 | Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 58 gene(s) | inside rSNPs | diseases |
| 2 | nsv832772 | chr14:38030300-38225921 | Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 49 gene(s) | inside rSNPs | diseases |
| 3 | nsv916985 | chr14:38052347-38838551 | Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 59 gene(s) | inside rSNPs | diseases |
| 4 | nsv1036606 | chr14:38156757-38216156 | Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17179337 | FAM177A1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr14:38171800-38177800 | Weak transcription | Liver | Liver |
| 2 | chr14:38172000-38178000 | Weak transcription | HepG2 | liver |
| 3 | chr14:38174200-38174400 | Enhancers | H1 Derived Mesenchymal Stem Cells | ES cell derived |
