Variant report
| Variant | rs4657581 |
|---|---|
| Chromosome Location | chr1:166649807-166649808 |
| allele | C/G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:166649321..166652229-chr1:166657244..166659747,3 | K562 | blood: | |
| 2 | chr1:166649643..166651708-chr1:166806859..166808634,2 | MCF-7 | breast: | |
| 3 | chr1:166645312..166647328-chr1:166649340..166651227,2 | K562 | blood: | |
| 4 | chr1:166646941..166649899-chr1:166808639..166811427,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000143157 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs10918549 | 0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap] |
| rs10918565 | 0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs12074945 | 0.94[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs17472904 | 0.84[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs2119900 | 0.84[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs34311259 | 0.84[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs3856217 | 1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs4657570 | 0.85[TSI][hapmap] |
| rs4657571 | 1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs6676923 | 0.80[AFR][1000 genomes] |
| rs7531612 | 0.90[AMR][1000 genomes];0.91[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv916491 | chr1:166000783-166948513 | Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 38 gene(s) | inside rSNPs | diseases |
| 2 | esv2757759 | chr1:166491879-166650985 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | esv2758975 | chr1:166491879-166650985 | ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 4 | esv2752389 | chr1:166625342-166706342 | Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS | TF binding regionChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 5 | nsv947550 | chr1:166647096-166673303 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4657581 | RCSD1 | cis | lymphoblastoid | seeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
