Variant report
| Variant | rs41371952 |
|---|---|
| Chromosome Location | chr4:68702568-68702569 |
| allele | C/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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr4:68698345..68700379-chr4:68701901..68703616,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000153802 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs10022268 | 0.87[AFR][1000 genomes] |
| rs10022455 | 0.91[AFR][1000 genomes] |
| rs13114094 | 0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1595933 | 0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1899218 | 1.00[ASN][1000 genomes] |
| rs2165363 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs6552116 | 0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6552118 | 0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6824984 | 1.00[ASN][1000 genomes] |
| rs6831736 | 0.88[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9312189 | 0.81[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv879214 | chr4:68389841-68789778 | Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
| 2 | nsv829960 | chr4:68649237-68809629 | Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 3 | esv3446954 | chr4:68653705-68709553 | Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 4 | nsv1007376 | chr4:68693483-69008202 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 19 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs41371952 | GNRHR | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:68699000-68719000 | Weak transcription | Esophagus | oesophagus |
