Variant report
Variant | rs10417909 |
---|---|
Chromosome Location | chr19:55921579-55921580 |
allele | C/T |
Outlinks | Ensembl   UCSC |
- TF binding region (count:3)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:3 , 50 per page) page:
1
No data |
(count:6 , 50 per page) page:
1
No. | Distal block | Cell Line | Cell type | Cell Stage |
---|---|---|---|---|
1 | chr19:55918951..55921734-chr19:55969699..55972371,2 | MCF-7 | breast: | |
2 | chr19:55919243..55921969-chr19:56150138..56152279,2 | K562 | blood: | |
3 | chr19:55919210..55922859-chr19:55979173..55982922,4 | K562 | blood: | |
4 | chr19:55916326..55922315-chr19:55969733..55974780,9 | MCF-7 | breast: | |
5 | chr19:55772423..55775018-chr19:55921452..55924002,2 | MCF-7 | breast: | |
6 | chr19:55669904..55673815-chr19:55917688..55921815,5 | K562 | blood: |
(count:1 , 50 per page) page:
1
No. | lncRNA name | Chromosome Location | lncRNA alias |
---|---|---|---|
1 | lnc-RPL28-1 | chr19:55921579-55921685 | NONHSAT068035 |
No data |
No data |
Variant related genes | Relation type |
---|---|
UBE2S | TF binding region |
ENSG00000167646 | Chromatin interaction |
ENSG00000267577 | Chromatin interaction |
ENSG00000267110 | Chromatin interaction |
ENSG00000063241 | Chromatin interaction |
ENSG00000213015 | Chromatin interaction |
rs_ID | r2[population] |
---|---|
rs10425929 | 0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes] |
rs10853877 | 0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes] |
rs11668142 | 0.87[CHB][hapmap];1.00[YRI][hapmap] |
rs12709950 | 0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes] |
rs8102125 | 0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes] |
rs8113179 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |

No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
---|---|---|---|---|---|---|---|
1 | nsv1065760 | chr19:55721521-55929740 | Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 212 gene(s) | inside rSNPs | diseases |
2 | nsv912456 | chr19:55725410-55925500 | Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 212 gene(s) | inside rSNPs | diseases |
3 | nsv912457 | chr19:55725410-56019597 | Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 228 gene(s) | inside rSNPs | diseases |
4 | nsv432086 | chr19:55807586-56050844 | Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 220 gene(s) | inside rSNPs | diseases |
5 | nsv912462 | chr19:55845386-55925500 | Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 203 gene(s) | inside rSNPs | diseases |
6 | nsv912463 | chr19:55845386-56004901 | Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 219 gene(s) | inside rSNPs | diseases |
7 | nsv912465 | chr19:55854313-55935184 | Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
8 | nsv912473 | chr19:55874642-56145428 | Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 233 gene(s) | inside rSNPs | diseases |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr19:55920000-55922200 | ZNF genes & repeats | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
2 | chr19:55920200-55922200 | Weak transcription | Foreskin Melanocyte Primary Cells skin03 | Skin |
3 | chr19:55920400-55924200 | Weak transcription | hESC Derived CD56+ Ectoderm Cultured Cells | ES cell derived |