Variant report
| Variant | rs4554407 |
|---|---|
| Chromosome Location | chr7:129189650-129189651 |
| 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 | chr7:129188028..129191960-chr7:129192887..129197274,4 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs10257409 | 0.95[ASN][1000 genomes] |
| rs1125056 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs11765308 | 0.91[ASN][1000 genomes] |
| rs11765389 | 0.91[ASN][1000 genomes] |
| rs11768713 | 0.91[ASN][1000 genomes] |
| rs12154955 | 1.00[CHB][hapmap] |
| rs12706898 | 1.00[CHB][hapmap] |
| rs13233863 | 1.00[CHB][hapmap] |
| rs13235012 | 0.80[ASN][1000 genomes] |
| rs13239330 | 0.84[ASN][1000 genomes] |
| rs2121265 | 0.83[ASN][1000 genomes] |
| rs2598178 | 0.93[ASN][1000 genomes] |
| rs2896417 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs34780485 | 0.80[ASN][1000 genomes] |
| rs56052358 | 0.90[ASN][1000 genomes] |
| rs56178414 | 0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs612972 | 0.85[AMR][1000 genomes];0.95[ASN][1000 genomes] |
| rs659495 | 0.83[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs875832 | 0.83[AMR][1000 genomes];0.97[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 | nsv831128 | chr7:129063040-129240800 | Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 14 gene(s) | inside rSNPs | diseases |
| 2 | esv3478069 | chr7:129157163-129204221 | Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh | Chromatin interactive region | 4 gene(s) | inside rSNPs | diseases |
| 3 | esv3478070 | chr7:129157177-129204220 | Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS | Chromatin interactive region | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4554407 | CALU | cis | cerebellum | SCAN |
| rs4554407 | IRF5 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr7:129181400-129192600 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
| 2 | chr7:129186400-129201600 | Weak transcription | Right Atrium | heart |
