Variant report
| Variant | rs12310595 |
|---|---|
| Chromosome Location | chr12:49678835-49678836 |
| allele | A/G |
| 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 | chr12:49677467..49679581-chr12:49679946..49682245,2 | K562 | blood: | |
| 2 | chr12:49677107..49685653-chr12:49686694..49692276,10 | MCF-7 | breast: | |
| 3 | chr12:49678740..49680286-chr12:49680841..49682374,2 | MCF-7 | breast: | |
| 4 | chr12:49676556..49679894-chr12:49730163..49733307,3 | MCF-7 | breast: | |
| 5 | chr12:49665631..49676200-chr12:49678297..49684493,17 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000186897 | Chromatin interaction |
| ENSG00000135406 | Chromatin interaction |
| ENSG00000258232 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs10875946 | 0.82[AMR][1000 genomes] |
| rs10875948 | 0.82[AMR][1000 genomes] |
| rs11168972 | 0.82[AMR][1000 genomes] |
| rs12306969 | 0.98[ASN][1000 genomes] |
| rs12318618 | 0.82[AMR][1000 genomes] |
| rs12322497 | 0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12322501 | 1.00[ASN][1000 genomes] |
| rs12322506 | 0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12580095 | 0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12582651 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12582657 | 1.00[ASN][1000 genomes] |
| rs12582901 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3847764 | 0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4382953 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4898502 | 0.89[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs57755392 | 0.82[AMR][1000 genomes] |
| rs58456199 | 0.85[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1051161 | chr12:49314550-49828473 | Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 322 gene(s) | inside rSNPs | diseases |
| 2 | nsv541489 | chr12:49314550-49828473 | Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 322 gene(s) | inside rSNPs | diseases |
| 3 | nsv1036452 | chr12:49376285-49867760 | Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 315 gene(s) | inside rSNPs | diseases |
| 4 | nsv428801 | chr12:49536659-49744884 | Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 145 gene(s) | inside rSNPs | diseases |
| 5 | esv19135 | chr12:49676002-49690399 | Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 6 | nsv558834 | chr12:49676010-49691567 | Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 7 | nsv1042122 | chr12:49678529-49823168 | Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 54 gene(s) | inside rSNPs | diseases |
| 8 | nsv1039176 | chr12:49678529-49832618 | Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 55 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12310595 | C1QL4 | cis | Thyroid | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:49668600-49682400 | Weak transcription | HMEC | breast |
| 2 | chr12:49678200-49686800 | Weak transcription | HSMM | muscle |
| 3 | chr12:49678800-49681600 | Weak transcription | HSMMtube | muscle |
