Variant report
| Variant | rs4951457 |
|---|---|
| Chromosome Location | chr1:212879500-212879501 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:212878919..212880536-chr1:212965416..212968390,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000203705 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs10494955 | 0.85[CEU][hapmap] |
| rs11120002 | 0.91[ASN][1000 genomes] |
| rs11120024 | 0.86[YRI][hapmap] |
| rs11120025 | 0.86[YRI][hapmap] |
| rs11120027 | 0.85[CEU][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap] |
| rs12119821 | 0.84[ASN][1000 genomes] |
| rs12239975 | 0.83[ASN][1000 genomes] |
| rs12727790 | 0.91[ASN][1000 genomes] |
| rs12734543 | 0.85[CEU][hapmap] |
| rs12747251 | 0.81[YRI][hapmap] |
| rs3820679 | 0.86[YRI][hapmap] |
| rs4951460 | 0.91[ASN][1000 genomes] |
| rs4951636 | 0.91[ASN][1000 genomes] |
| rs4951637 | 0.89[ASN][1000 genomes] |
| rs6540763 | 0.86[YRI][hapmap] |
| rs6658029 | 0.86[AFR][1000 genomes];0.83[AMR][1000 genomes] |
| rs6679549 | 0.86[YRI][hapmap] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1013110 | chr1:212555764-212948092 | Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 81 gene(s) | inside rSNPs | diseases |
| 2 | nsv535287 | chr1:212555764-212948092 | Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 81 gene(s) | inside rSNPs | diseases |
| 3 | nsv549148 | chr1:212876902-212962207 | Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4951457 | LQK1 | cis | cerebellum | SCAN |
| rs4951457 | LQK1 | cis | parietal | SCAN |
| rs4951457 | C1orf227 | cis | cerebellum | SCAN |
| rs4951457 | SERTAD4 | cis | cerebellum | SCAN |
| rs4951457 | LOC642946 | cis | multi-tissue | Pritchard |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:212877800-212879600 | Enhancers | Primary T helper cells PMA-I stimulated | -- |
