Variant report
| Variant | rs6508750 |
|---|---|
| Chromosome Location | chr19:38379446-38379447 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr19:38378406..38380093-chr19:38396646..38398156,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000171804 | Chromatin interaction |
| ENSG00000105738 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs10406856 | 0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs10418133 | 0.86[EUR][1000 genomes] |
| rs10421572 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs10426553 | 0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs10426712 | 0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs17306795 | 1.00[CEU][hapmap] |
| rs2382622 | 0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs241951 | 1.00[CEU][hapmap] |
| rs4802132 | 0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs4802133 | 0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs4802137 | 0.86[EUR][1000 genomes] |
| rs56851463 | 0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs57268445 | 0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs59489006 | 0.80[EUR][1000 genomes] |
| rs6508747 | 0.86[EUR][1000 genomes] |
| rs7245957 | 0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs7253870 | 0.89[ASN][1000 genomes] |
| rs8100684 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs8101131 | 0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs953370 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv949296 | chr19:38034722-38763140 | Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 58 gene(s) | inside rSNPs | diseases |
| 2 | nsv833820 | chr19:38190721-38414049 | Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 27 gene(s) | inside rSNPs | diseases |
| 3 | esv3338745 | chr19:38376812-38381510 | Enhancers | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6508750 | AC012309.5 | cis | Heart Left Ventricle | GTEx |
| rs6508750 | AC012309.5 | cis | Artery Tibial | GTEx |
| rs6508750 | AC012309.5 | cis | Thyroid | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr19:38379200-38379600 | Enhancers | Primary neutrophils fromperipheralblood | blood |
