Variant report
| Variant | rs4643180 |
|---|---|
| Chromosome Location | chr13:39793468-39793469 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr13:39788555..39790778-chr13:39791862..39793526,2 | MCF-7 | breast: |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-LHFP-2 | chr13:39790914-39793642 | XLOC_010575 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs11147758 | 0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11147759 | 0.93[ASN][1000 genomes] |
| rs11147760 | 0.92[ASN][1000 genomes] |
| rs1333449 | 0.97[ASN][1000 genomes] |
| rs59964775 | 0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs7335044 | 0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs9566413 | 0.87[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs9566417 | 0.89[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs9576760 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9576761 | 0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs9576762 | 0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs9576763 | 0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs9576766 | 0.89[EUR][1000 genomes];0.91[ASN][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 | esv2754118 | chr13:39347702-40222644 | Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 22 gene(s) | inside rSNPs | diseases |
| 2 | nsv1048391 | chr13:39735088-39832358 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv1036124 | chr13:39735088-39837566 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 4 | nsv1047276 | chr13:39735088-39839257 | Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4643180 | LHFP | cis | lymphoblastoid | seeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
