Variant report
| Variant | rs60621219 |
|---|---|
| Chromosome Location | chr2:57744559-57744560 |
| allele | A/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 | chr2:56409714..56412670-chr2:57741960..57744837,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000233251 | Chromatin interaction |
| ENSG00000055813 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:2)
| rs_ID | r2[population] |
|---|---|
| rs10496068 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1518683 | 0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv999898 | chr2:57193127-57901238 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv535729 | chr2:57193127-57901238 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 3 | nsv1012285 | chr2:57453353-57760750 | Enhancers Weak transcription Active TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 4 | nsv1007118 | chr2:57562051-58147588 | Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 5 | nsv1001176 | chr2:57618795-57770261 | Enhancers Weak transcription Active TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 6 | nsv834137 | chr2:57683649-57913898 | Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 7 | nsv1013212 | chr2:57687436-57760750 | Enhancers Active TSS Weak transcription | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 8 | nsv535732 | chr2:57687436-57760750 | Enhancers Weak transcription Active TSS | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs60621219 | TCEA2 | trans | lymphoblastoid | RTeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
