Variant report
| Variant | rs1450524 |
|---|---|
| Chromosome Location | chr3:161151534-161151535 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:161129149..161131196-chr3:161149547..161152393,3 | MCF-7 | breast: | |
| 2 | chr3:161149987..161152257-chr3:161152281..161153980,2 | MCF-7 | breast: | |
| 3 | chr3:161085159..161090097-chr3:161151244..161155377,5 | MCF-7 | breast: | |
| 4 | chr3:161149348..161152131-chr3:161159932..161161916,2 | MCF-7 | breast: | |
| 5 | chr3:161144496..161147090-chr3:161151361..161154232,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000196542 | Chromatin interaction |
| ENSG00000269888 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:9)
| rs_ID | r2[population] |
|---|---|
| rs1905533 | 0.92[CEU][hapmap];0.83[CHB][hapmap] |
| rs7625210 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap] |
| rs7627320 | 0.91[CHB][hapmap] |
| rs7651540 | 0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap] |
| rs971515 | 0.92[CEU][hapmap];0.83[CHB][hapmap] |
| rs9816665 | 0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap] |
| rs9836881 | 0.95[CHB][hapmap] |
| rs9836887 | 0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap] |
| rs9858921 | 0.92[CEU][hapmap] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv931072 | chr3:160669567-161159779 | Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 98 gene(s) | inside rSNPs | diseases |
| 2 | nsv533237 | chr3:161019834-161804660 | Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 91 gene(s) | inside rSNPs | diseases |
| 3 | nsv829772 | chr3:161047817-161202554 | Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 88 gene(s) | inside rSNPs | diseases |
| 4 | nsv877710 | chr3:161087857-161245414 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 84 gene(s) | inside rSNPs | diseases |
| 5 | nsv829773 | chr3:161150422-161315189 | Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1450524 | B3GALNT1 | cis | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:161149000-161152000 | Weak transcription | HepG2 | liver |
