Variant report
| Variant | rs2638330 |
|---|---|
| Chromosome Location | chr12:56895629-56895630 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000257576 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:21)
| rs_ID | r2[population] |
|---|---|
| rs10876895 | 0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs11171862 | 0.82[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs11171863 | 0.83[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs11171865 | 0.84[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs11171870 | 0.87[AMR][1000 genomes] |
| rs12304519 | 0.82[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs12316930 | 0.84[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs12809550 | 0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs12813881 | 0.84[ASN][1000 genomes] |
| rs2638285 | 0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2638318 | 0.82[EUR][1000 genomes] |
| rs2638319 | 0.82[EUR][1000 genomes] |
| rs2638334 | 0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2638335 | 0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2657909 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs3809122 | 0.91[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs58252713 | 0.81[ASN][1000 genomes] |
| rs6581096 | 0.81[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs71459375 | 0.82[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs71459376 | 0.86[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7314242 | 0.90[EUR][1000 genomes];0.91[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1043622 | chr12:56571476-56974448 | Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 95 gene(s) | inside rSNPs | diseases |
| 2 | nsv541500 | chr12:56571476-56974448 | Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 95 gene(s) | inside rSNPs | diseases |
| 3 | nsv1052713 | chr12:56848036-56917602 | Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionmiRNA target site | 35 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2638330 | FUT1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs2638330 | RBMS2 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:56894600-56900400 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
