Variant report
| Variant | rs500565 |
|---|---|
| Chromosome Location | chr1:84861403-84861404 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:3)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:3 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | MAFK | chr1:84861296-84861531 | IMR90 | lung: | n/a | n/a |
| 2 | MAFK | chr1:84861237-84861505 | HepG2 | liver: | n/a | n/a |
| 3 | STAT3 | chr1:84861368-84861532 | MCF10A-Er-Src | breast: | n/a | chr1:84861442-84861453 |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:84859668..84862400-chr1:84868271..84869833,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| DNASE2B | TF binding region |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs10493747 | 0.89[EUR][1000 genomes] |
| rs10874438 | 0.95[EUR][1000 genomes] |
| rs11163962 | 0.93[EUR][1000 genomes] |
| rs12049602 | 0.92[EUR][1000 genomes] |
| rs12118984 | 0.89[EUR][1000 genomes] |
| rs12406723 | 0.93[EUR][1000 genomes] |
| rs1246330 | 0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs1246331 | 0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs1588037 | 0.95[EUR][1000 genomes] |
| rs558268 | 0.91[EUR][1000 genomes] |
| rs646681 | 0.88[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs6576704 | 0.91[EUR][1000 genomes] |
| rs6661172 | 1.00[CEU][hapmap];0.95[EUR][1000 genomes] |
| rs667923 | 1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes] |
| rs679152 | 1.00[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs7511984 | 1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes] |
| rs7512262 | 0.93[EUR][1000 genomes] |
| rs7514601 | 0.93[CEU][hapmap];0.89[EUR][1000 genomes] |
| rs7515964 | 0.89[EUR][1000 genomes] |
| rs7516125 | 0.81[EUR][1000 genomes] |
| rs7523888 | 0.83[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes] |
| rs7541465 | 0.92[EUR][1000 genomes] |
| rs7547088 | 0.89[EUR][1000 genomes] |
| rs7548231 | 0.92[EUR][1000 genomes] |
| rs9433225 | 0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv830437 | chr1:84837524-85001269 | Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 40 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs500565 | HS2ST1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:84858000-84863200 | Weak transcription | Cortex derived primary cultured neurospheres | brain |
