Variant report
| Variant | rs17139063 |
|---|---|
| Chromosome Location | chr7:116456139-116456140 |
| allele | G/T |
| 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 |
|---|---|
| ENSG00000135269 | Chromatin interaction |
| ENSG00000001626 | Chromatin interaction |
| ENSG00000077063 | Chromatin interaction |
| ENSG00000004866 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:18)
| rs_ID | r2[population] |
|---|---|
| rs12540703 | 0.87[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs16870030 | 0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap] |
| rs17138978 | 0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap] |
| rs17138980 | 0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap] |
| rs17138983 | 0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap] |
| rs17139068 | 1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17139140 | 1.00[TSI][hapmap] |
| rs2237716 | 0.82[JPT][hapmap] |
| rs2237718 | 0.90[CHB][hapmap];0.83[CHD][hapmap] |
| rs28607430 | 0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3807996 | 0.82[JPT][hapmap] |
| rs58430291 | 0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs61657532 | 1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6978257 | 0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap] |
| rs73471137 | 0.87[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs73471159 | 1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73471162 | 0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7779694 | 1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 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 |
| 2 | esv3446627 | chr7:116455962-116456391 | Weak transcription Enhancers | Chromatin interactive region | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17139063 | SDC1 | trans | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr7:116455600-116456200 | Enhancers | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
| 2 | chr7:116455600-116468400 | Weak transcription | Liver | Liver |
