Variant report
| Variant | rs6665804 |
|---|---|
| Chromosome Location | chr1:146501300-146501301 |
| allele | C/T |
| 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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:144889740..144892703-chr1:146500075..146502138,3 | MCF-7 | breast: | |
| 2 | chr1:146500274..146502846-chr1:146563478..146565211,2 | MCF-7 | breast: | |
| 3 | chr1:144890884..144894068-chr1:146500995..146504405,3 | K562 | blood: | |
| 4 | chr1:146500874..146503757-chr1:146554554..146557584,3 | K562 | blood: | |
| 5 | chr1:146500894..146503604-chr1:146505375..146507725,2 | MCF-7 | breast: | |
| 6 | chr1:146500715..146505145-chr1:146554885..146558544,5 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000230832 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs10900384 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs11240094 | 0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes] |
| rs11808402 | 0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs11809158 | 0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs12122453 | 0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes] |
| rs12122534 | 0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs12139768 | 0.82[AMR][1000 genomes];0.89[ASN][1000 genomes] |
| rs12141387 | 0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes] |
| rs12142744 | 0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes] |
| rs12742988 | 0.96[ASN][1000 genomes] |
| rs1925343 | 0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs1984615 | 0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs3862922 | 0.82[AFR][1000 genomes] |
| rs4950330 | 0.98[AFR][1000 genomes];0.89[ASN][1000 genomes] |
| rs4950332 | 0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 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 | nsv428224 | chr1:145613243-146553918 | Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 43 gene(s) | inside rSNPs | diseases |
| 2 | esv2757753 | chr1:145883119-146697542 | Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 96 gene(s) | inside rSNPs | diseases |
| 3 | nsv872251 | chr1:146152553-146803630 | Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 95 gene(s) | inside rSNPs | diseases |
| 4 | nsv946295 | chr1:146471863-146507583 | Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 5 | nsv872252 | chr1:146471863-147398135 | Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 112 gene(s) | inside rSNPs | diseases |
| 6 | nsv872253 | chr1:146494246-146548549 | Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6665804 | RP11-94I2.1 | cis | lung | GTEx |
| rs6665804 | NBPF13P | cis | lung | GTEx |
| rs6665804 | RP11-325P15.1 | cis | lung | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:146494800-146504200 | Weak transcription | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
| 2 | chr1:146501000-146502600 | Enhancers | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
