Variant report
| Variant | rs7544863 |
|---|---|
| Chromosome Location | chr1:168752298-168752299 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:9)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:9 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | CEBPB | chr1:168751737-168753683 | Hela-S3 | cervix: | n/a | chr1:168751980-168751989 chr1:168751979-168751990 chr1:168751980-168751989 chr1:168751980-168751989 chr1:168751978-168751991 chr1:168751980-168751989 chr1:168753652-168753661 |
| 2 | PRDM1 | chr1:168752020-168752476 | Hela-S3 | cervix: | n/a | n/a |
| 3 | RCOR1 | chr1:168751822-168752313 | Hela-S3 | cervix: | n/a | n/a |
| 4 | TCF7L2 | chr1:168751707-168752406 | Hela-S3 | cervix: | n/a | n/a |
| 5 | FOS | chr1:168751869-168752319 | Hela-S3 | cervix: | n/a | n/a |
| 6 | EP300 | chr1:168751853-168752420 | Hela-S3 | cervix: | n/a | n/a |
| 7 | STAT3 | chr1:168752166-168752606 | MCF10A-Er-Src | breast: | n/a | n/a |
| 8 | BRCA1 | chr1:168751705-168752454 | Hela-S3 | cervix: | n/a | n/a |
| 9 | STAT1 | chr1:168751792-168752321 | Hela-S3 | cervix: | n/a | chr1:168751981-168751989 |
| No data |
(count:5 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:168750443..168753211-chr1:169074233..169077019,2 | MCF-7 | breast: | |
| 2 | chr1:168745044..168747432-chr1:168750860..168753701,2 | K562 | blood: | |
| 3 | chr1:168745883..168748242-chr1:168750356..168753264,2 | MCF-7 | breast: | |
| 4 | chr1:168742365..168745315-chr1:168750346..168752707,2 | MCF-7 | breast: | |
| 5 | chr1:168742907..168744935-chr1:168749748..168752648,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| LINC00626 | TF binding region |
| ENSG00000143153 | Chromatin interaction |
| ENSG00000235736 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs1008483 | 0.94[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs10918994 | 0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs11582358 | 0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11583049 | 0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12059023 | 0.94[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs12067471 | 0.93[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs12564363 | 0.93[ASN][1000 genomes] |
| rs12567397 | 0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12569208 | 0.95[ASN][1000 genomes] |
| rs17570453 | 0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap] |
| rs2066895 | 0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3738241 | 0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3738242 | 0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56032568 | 0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs59454169 | 0.93[ASN][1000 genomes] |
| rs6686124 | 0.93[ASN][1000 genomes] |
| rs6699777 | 0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs72703566 | 0.93[ASN][1000 genomes] |
| rs926432 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
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| 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 |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7544863 | POU2F1 | cis | parietal | SCAN |
| rs7544863 | C1orf156 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:168751600-168754200 | Enhancers | Hela-S3 | cervix |
| 2 | chr1:168752000-168754400 | Enhancers | Fetal Lung | lung |
| 3 | chr1:168752200-168753400 | Enhancers | Colon Smooth Muscle | Colon |
