Variant report
| Variant | rs2420505 |
|---|---|
| Chromosome Location | chr1:169728137-169728138 |
| 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 | chr1:169727288..169729561-chr1:169762076..169765859,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000171806 | Chromatin interaction |
| ENSG00000000460 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:26)
| rs_ID | r2[population] |
|---|---|
| rs10489181 | 0.86[AFR][1000 genomes];0.93[ASN][1000 genomes] |
| rs10489182 | 0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1051091 | 0.83[CEU][hapmap] |
| rs1076637 | 0.91[CHB][hapmap] |
| rs10919232 | 0.92[ASN][1000 genomes] |
| rs10919233 | 0.92[ASN][1000 genomes] |
| rs12023614 | 0.93[ASN][1000 genomes] |
| rs12027035 | 0.91[CHB][hapmap] |
| rs12044082 | 0.86[AFR][1000 genomes];0.92[ASN][1000 genomes] |
| rs16862663 | 0.86[AFR][1000 genomes];0.93[ASN][1000 genomes] |
| rs1883228 | 0.83[CEU][hapmap] |
| rs2205847 | 0.83[CEU][hapmap] |
| rs2272818 | 0.95[AFR][1000 genomes];0.92[ASN][1000 genomes] |
| rs28469136 | 0.81[AFR][1000 genomes] |
| rs34990593 | 0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs3766129 | 0.83[CEU][hapmap] |
| rs3917406 | 0.83[CEU][hapmap];0.95[CHB][hapmap] |
| rs3917423 | 0.91[CHB][hapmap] |
| rs4265482 | 0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs4656192 | 0.93[ASN][1000 genomes] |
| rs4786 | 0.83[MEX][hapmap] |
| rs5353 | 0.87[MEX][hapmap] |
| rs7520701 | 0.95[ASN][1000 genomes] |
| rs7523319 | 0.95[ASN][1000 genomes] |
| rs7543268 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs932307 | 0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[MEX][hapmap] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3451367 | chr1:169630075-169976964 | Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 37 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:11)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2420505 | C1orf156 | cis | cerebellum | SCAN |
| rs2420505 | METTL18 | cis | Artery Tibial | GTEx |
| rs2420505 | METTL18 | cis | lung | GTEx |
| rs2420505 | METTL18 | cis | Esophagus Mucosa | GTEx |
| rs2420505 | METTL18 | cis | Thyroid | GTEx |
| rs2420505 | C1orf156 | cis | lymphoblastoid | seeQTL |
| rs2420505 | SELL | cis | multi-tissue | Pritchard |
| rs2420505 | KIFAP3 | cis | cerebellum | SCAN |
| rs2420505 | ILDR2 | cis | cerebellum | SCAN |
| rs2420505 | C1orf156 | cis | parietal | SCAN |
| rs2420505 | KIFAP3 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:169728000-169728400 | ZNF genes & repeats | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
| 2 | chr1:169728000-169732800 | Weak transcription | Adipose Nuclei | Adipose |
