Variant report
| Variant | rs41758 |
|---|---|
| Chromosome Location | chr7:116456466-116456467 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:7)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:7 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | 7:116454408-116459849..7:117100350-117112126 | H1-hESC | embryonic stem cell: | embryo |
| 2 | 7:115890993-115892266..7:116454408-116459849 | GM12878 | blood: | |
| 3 | 7:116454408-116459849..7:116754962-116765597 | Hela-S3 | cervix: | |
| 4 | chr7:116310791..116312418-chr7:116455052..116456877,2 | MCF-7 | breast: | |
| 5 | 7:116454408-116459849..7:117432820-117434816 | H1-hESC | embryonic stem cell: | embryo |
| 6 | chr7:116452981..116454622-chr7:116455451..116457556,2 | K562 | blood: | |
| 7 | 7:115847372-115857098..7:116454408-116459849 | GM12878 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000001626 | Chromatin interaction |
| ENSG00000135269 | Chromatin interaction |
| ENSG00000077063 | Chromatin interaction |
| ENSG00000004866 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs1356 | 0.84[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs28167 | 0.87[EUR][1000 genomes] |
| rs28896 | 0.86[EUR][1000 genomes] |
| rs41750 | 0.84[CEU][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes] |
| rs41754 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs41762 | 0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes] |
| rs41770 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs41773 | 0.87[EUR][1000 genomes] |
| rs41776 | 0.84[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs41778 | 0.84[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs41779 | 0.85[EUR][1000 genomes] |
| rs41781 | 0.85[EUR][1000 genomes] |
| rs41783 | 0.85[EUR][1000 genomes] |
| rs41784 | 0.85[EUR][1000 genomes] |
| rs41786 | 0.84[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs41791 | 0.84[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs41792 | 0.85[EUR][1000 genomes] |
| rs41793 | 0.84[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs42230 | 0.81[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs9640774 | 0.85[ASN][1000 genomes] |
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 | nsv831107 | chr7:116414734-116649466 | Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 45 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs41758 | CTTNBP2 | cis | cerebellum | SCAN |
| rs41758 | CASP4 | trans | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr7:116455600-116468400 | Weak transcription | Liver | Liver |
