Variant report
| Variant | rs16959168 |
|---|---|
| Chromosome Location | chr19:45025465-45025466 |
| allele | A/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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr19:45025124..45028007-chr19:45394431..45397224,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000130204 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:6)
| rs_ID | r2[population] |
|---|---|
| rs10408058 | 0.83[MEX][hapmap] |
| rs10408247 | 1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs10409769 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap] |
| rs10414398 | 0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1881042 | 1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap] |
| rs55903102 | 0.88[AMR][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 | nsv1061350 | chr19:44869075-45035469 | Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 18 gene(s) | inside rSNPs | diseases |
| 2 | esv3358964 | chr19:45023012-45027410 | Bivalent/Poised TSS | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 3 | esv3359491 | chr19:45023612-45027010 | Bivalent/Poised TSS | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs16959168 | LOC390940 | cis | lymphoblastoid | seeQTL |
| rs16959168 | NCRNA00099 | trans | lymphoblastoid | seeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
