Variant report
| Variant | rs10196452 |
|---|---|
| Chromosome Location | chr2:38991193-38991194 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:38974221..38979921-chr2:38986851..38994572,21 | K562 | blood: | |
| 2 | chr2:38973025..38976072-chr2:38989424..38992491,3 | MCF-7 | breast: | |
| 3 | chr2:38976319..38979796-chr2:38988969..38996616,16 | MCF-7 | breast: | |
| 4 | chr2:38973912..38980240-chr2:38989822..38999883,17 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000152147 | Chromatin interaction |
| ENSG00000115875 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs13015612 | 0.81[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap] |
| rs13390845 | 0.88[AFR][1000 genomes] |
| rs13412656 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs13425948 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs1541877 | 1.00[CHD][hapmap];0.85[TSI][hapmap] |
| rs1897327 | 1.00[YRI][hapmap] |
| rs2888570 | 0.83[AFR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3099969 | 0.83[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs3108662 | 0.90[AFR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3112187 | 0.80[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs3112190 | 0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs6746931 | 0.88[TSI][hapmap] |
| rs72797312 | 0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv916059 | chr2:38332341-39119398 | Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 143 gene(s) | inside rSNPs | diseases |
| 2 | nsv9646 | chr2:38358311-39082189 | Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 141 gene(s) | inside rSNPs | diseases |
| 3 | esv1798055 | chr2:38955865-39039504 | Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 111 gene(s) | inside rSNPs | diseases |
| 4 | nsv1014616 | chr2:38985472-39022893 | Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10196452 | DHX57 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:38979200-39005000 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
| 2 | chr2:38990400-38991200 | Enhancers | HepG2 | liver |
