Variant report
| Variant | rs16831802 |
|---|---|
| Chromosome Location | chr3:160749981-160749982 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:160748979..160751725-chr3:160821249..160823513,2 | MCF-7 | breast: | |
| 2 | chr3:160749654..160751759-chr3:160753566..160755069,2 | MCF-7 | breast: | |
| 3 | chr3:160746924..160750622-chr3:160787755..160791172,3 | MCF-7 | breast: | |
| 4 | chr3:160717602..160719198-chr3:160748866..160750938,2 | MCF-7 | breast: | |
| 5 | chr3:160748438..160750159-chr3:160785119..160786787,2 | MCF-7 | breast: | |
| 6 | chr3:160747461..160750414-chr3:161128370..161130411,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000169251 | Chromatin interaction |
| ENSG00000169255 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:29)
| rs_ID | r2[population] |
|---|---|
| rs10513557 | 1.00[CEU][hapmap] |
| rs10513563 | 1.00[CEU][hapmap];1.00[EUR][1000 genomes] |
| rs12488403 | 1.00[CEU][hapmap] |
| rs12630250 | 1.00[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs1374792 | 1.00[CEU][hapmap];0.82[EUR][1000 genomes] |
| rs1447613 | 1.00[CEU][hapmap] |
| rs16831546 | 1.00[CEU][hapmap] |
| rs16831549 | 1.00[CEU][hapmap] |
| rs16831552 | 1.00[CEU][hapmap] |
| rs16831555 | 1.00[CEU][hapmap] |
| rs16831581 | 1.00[CEU][hapmap] |
| rs16831611 | 1.00[CEU][hapmap] |
| rs16831760 | 1.00[CEU][hapmap];1.00[EUR][1000 genomes] |
| rs16831771 | 1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs17405707 | 1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs60768391 | 0.96[EUR][1000 genomes] |
| rs62278044 | 0.85[EUR][1000 genomes] |
| rs62278045 | 0.88[EUR][1000 genomes] |
| rs62278046 | 0.88[EUR][1000 genomes] |
| rs62280310 | 0.86[EUR][1000 genomes] |
| rs62280332 | 0.93[EUR][1000 genomes] |
| rs62280340 | 0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs62282270 | 0.87[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs62282271 | 0.82[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs62282275 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs6767132 | 0.80[EUR][1000 genomes] |
| rs6787599 | 0.85[CEU][hapmap] |
| rs6807796 | 1.00[CEU][hapmap] |
| rs935499 | 1.00[CEU][hapmap] |
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 | 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 | nsv965126 | chr3:160748670-160750148 | Weak transcription Enhancers | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs16831802 | B3GALNT1 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:160745200-160782600 | Weak transcription | Skeletal Muscle Female | skeletal muscle |
| 2 | chr3:160749400-160753200 | Weak transcription | Primary hematopoietic stem cells | blood |
| 3 | chr3:160749800-160759000 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
