Variant report
| Variant | rs6702913 |
|---|---|
| Chromosome Location | chr1:168837845-168837846 |
| allele | C/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 | chr1:168831234..168833463-chr1:168837204..168838715,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:27)
| rs_ID | r2[population] |
|---|---|
| rs10489364 | 0.91[CHB][hapmap] |
| rs10753780 | 1.00[ASN][1000 genomes] |
| rs10753781 | 0.85[ASN][1000 genomes] |
| rs10800392 | 0.85[ASN][1000 genomes] |
| rs10800393 | 0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes] |
| rs10919006 | 0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs10919011 | 0.91[CHB][hapmap];0.88[CHD][hapmap] |
| rs1407477 | 0.90[JPT][hapmap] |
| rs1575329 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1885557 | 1.00[ASN][1000 genomes] |
| rs2065129 | 0.91[CHB][hapmap] |
| rs34298853 | 0.88[ASN][1000 genomes] |
| rs4656163 | 0.86[ASN][1000 genomes] |
| rs4656622 | 0.88[ASN][1000 genomes] |
| rs4656624 | 0.84[ASN][1000 genomes] |
| rs6427155 | 0.86[ASN][1000 genomes] |
| rs6657987 | 0.91[CHB][hapmap] |
| rs6666564 | 0.87[ASN][1000 genomes] |
| rs6683127 | 0.87[ASN][1000 genomes] |
| rs6683236 | 0.86[ASN][1000 genomes] |
| rs6683991 | 1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes] |
| rs6694810 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs715008 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs7525262 | 0.99[ASN][1000 genomes] |
| rs7550083 | 0.88[ASN][1000 genomes] |
| rs857633 | 0.99[ASN][1000 genomes] |
| rs857635 | 0.99[ASN][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 | nsv869415 | chr1:168467284-169153863 | Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 44 gene(s) | inside rSNPs | diseases |
| 2 | nsv831847 | chr1:168669877-168850129 | Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 3 | nsv437258 | chr1:168824111-168890420 | Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6702913 | SCYL3 | cis | parietal | SCAN |
| rs6702913 | CREG1 | cis | cerebellum | SCAN |
| rs6702913 | XCL1 | cis | parietal | SCAN |
| rs6702913 | CREG1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:168836800-168838000 | Enhancers | Pancreas | Pancrea |
| 2 | chr1:168837000-168838800 | Enhancers | Breast Myoepithelial Primary Cells | Breast |
| 3 | chr1:168837600-168838000 | Enhancers | Psoas Muscle | Psoas |
