Variant report
| Variant | rs2999562 |
|---|---|
| Chromosome Location | chr1:152046032-152046033 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:152043416..152046211-chr1:152074806..152077684,2 | MCF-7 | breast: | |
| 2 | chr1:152043433..152046409-chr1:152058160..152060472,2 | MCF-7 | breast: | |
| 3 | chr1:152042308..152047029-chr1:152081777..152083465,4 | MCF-7 | breast: | |
| 4 | chr1:152043286..152045269-chr1:152045806..152047940,2 | MCF-7 | breast: | |
| 5 | chr1:151964883..151966894-chr1:152045649..152048031,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000197747 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs1496037 | 0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2999547 | 0.87[ASN][1000 genomes] |
| rs2999551 | 1.00[ASN][1000 genomes] |
| rs2999553 | 1.00[ASN][1000 genomes] |
| rs2999554 | 1.00[ASN][1000 genomes] |
| rs3007672 | 1.00[ASN][1000 genomes] |
| rs3007673 | 1.00[ASN][1000 genomes] |
| rs3007678 | 1.00[ASN][1000 genomes] |
| rs3104205 | 0.91[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs3122301 | 0.95[ASN][1000 genomes] |
| rs3122303 | 1.00[ASN][1000 genomes] |
| rs3122304 | 0.95[ASN][1000 genomes] |
| rs3134814 | 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 | nsv1007097 | chr1:151832796-152227977 | Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 2 | nsv1012327 | chr1:151835544-152200890 | Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 3 | nsv535159 | chr1:151835544-152200890 | Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 196 gene(s) | inside rSNPs | diseases |
| 4 | nsv547853 | chr1:152008671-152236760 | Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 83 gene(s) | inside rSNPs | diseases |
| 5 | nsv535160 | chr1:152031280-152050179 | Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive region | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2999562 | S100A11 | Cis_1M | lymphoblastoid | RTeQTL |
| rs2999562 | S100A11 | cis | Artery Tibial | GTEx |
Chromatin state (count:0 , 50 per page) page:
| No data |
