Variant report
| Variant | rs12419197 |
|---|---|
| Chromosome Location | chr11:74449220-74449221 |
| allele | A/G |
| 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 | chr11:74446620..74450203-chr11:74457573..74461764,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000166439 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs10899041 | 0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs10899042 | 0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs11236236 | 0.83[ASN][1000 genomes] |
| rs11236244 | 0.84[ASN][1000 genomes] |
| rs12223076 | 0.98[ASN][1000 genomes] |
| rs12223417 | 0.98[ASN][1000 genomes] |
| rs12421899 | 0.84[ASN][1000 genomes] |
| rs12576129 | 0.84[ASN][1000 genomes] |
| rs12576444 | 0.90[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs1433771 | 0.86[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs4944061 | 0.84[ASN][1000 genomes] |
| rs4944944 | 0.80[ASN][1000 genomes] |
| rs4944947 | 0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4944950 | 0.84[ASN][1000 genomes] |
| rs61734374 | 0.85[ASN][1000 genomes] |
| rs61897000 | 0.83[ASN][1000 genomes] |
| rs6592594 | 0.99[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv2757451 | chr11:73842609-74545888 | Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 87 gene(s) | inside rSNPs | diseases |
| 2 | esv2759837 | chr11:73842609-74557597 | Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 88 gene(s) | inside rSNPs | diseases |
| 3 | esv34979 | chr11:73878688-74533452 | Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 85 gene(s) | inside rSNPs | diseases |
| 4 | esv2758277 | chr11:73887567-74557597 | Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 85 gene(s) | inside rSNPs | diseases |
| 5 | nsv825994 | chr11:73936667-74534455 | Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 83 gene(s) | inside rSNPs | diseases |
| 6 | nsv932190 | chr11:74359867-74618935 | Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 41 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:11)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12419197 | XRRA1 | cis | Whole Blood | GTEx |
| rs12419197 | XRRA1 | cis | Artery Tibial | GTEx |
| rs12419197 | XRRA1 | cis | Esophagus Muscularis | GTEx |
| rs12419197 | XRRA1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs12419197 | XRRA1 | cis | Thyroid | GTEx |
| rs12419197 | XRRA1 | cis | Esophagus Mucosa | GTEx |
| rs12419197 | RP11-147I3.1 | cis | Thyroid | GTEx |
| rs12419197 | XRRA1 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs12419197 | XRRA1 | cis | Adipose Subcutaneous | GTEx |
| rs12419197 | XRRA1 | cis | Nerve Tibial | GTEx |
| rs12419197 | XRRA1 | cis | Muscle Skeletal | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr11:74445600-74459000 | Weak transcription | A549 | lung |
