Variant report
| Variant | rs17431961 |
|---|---|
| Chromosome Location | chr1:102355357-102355358 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | STAT3 | chr1:102355221-102355518 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| DNAJA1P5 | TF binding region |
rSNPs within LD-proxies of this variant (count:23)
| rs_ID | r2[population] |
|---|---|
| rs10493972 | 1.00[JPT][hapmap] |
| rs12130645 | 1.00[YRI][hapmap] |
| rs12144932 | 1.00[AFR][1000 genomes] |
| rs12731963 | 1.00[AFR][1000 genomes] |
| rs1415099 | 1.00[ASN][1000 genomes] |
| rs1415107 | 1.00[YRI][hapmap];1.00[AFR][1000 genomes] |
| rs1539091 | 0.95[CEU][hapmap] |
| rs1577717 | 1.00[ASN][1000 genomes] |
| rs17125616 | 1.00[ASN][1000 genomes] |
| rs17430580 | 1.00[ASN][1000 genomes] |
| rs17432141 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17470860 | 1.00[ASN][1000 genomes] |
| rs1856037 | 0.82[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1981158 | 1.00[ASN][1000 genomes] |
| rs4907956 | 1.00[ASW][hapmap];1.00[LWK][hapmap] |
| rs58587209 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs6682150 | 0.80[MEX][hapmap];1.00[ASN][1000 genomes] |
| rs6694948 | 1.00[ASN][1000 genomes] |
| rs6695052 | 0.80[MEX][hapmap];1.00[ASN][1000 genomes] |
| rs72729689 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7536632 | 0.90[CEU][hapmap];0.96[GIH][hapmap] |
| rs9943151 | 1.00[ASN][1000 genomes] |
| rs9943277 | 1.00[ASN][1000 genomes] |
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 | nsv522921 | chr1:102170295-102876392 | Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 2 | nsv522156 | chr1:102309649-102421714 | Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17431961 | AMY2B | cis | cerebellum | SCAN |
| rs17431961 | NIN | trans | parietal | SCAN |
| rs17431961 | OLFM3 | cis | cerebellum | SCAN |
| rs17431961 | PALMD | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
