Variant report
| Variant | rs3128365 |
|---|---|
| Chromosome Location | chr1:112841203-112841204 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:7)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:7 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:112840939..112841965-chr1:112911561..112912931,5 | K562 | blood: | |
| 2 | chr1:112840911..112841667-chr1:112879308..112880254,3 | K562 | blood: | |
| 3 | chr1:112840708..112841508-chr1:112911801..112912878,3 | MCF-7 | breast: | |
| 4 | chr1:112841087..112842929-chr1:112901842..112903363,2 | MCF-7 | breast: | |
| 5 | chr1:112840908..112843685-chr1:112848640..112850927,2 | K562 | blood: | |
| 6 | chr1:112840899..112841842-chr1:112879297..112880319,11 | MCF-7 | breast: | |
| 7 | chr1:112840855..112841876-chr1:112879569..112880172,4 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000231246 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs10857952 | 0.83[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs12127798 | 0.81[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2998335 | 0.93[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs3005799 | 0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs3121989 | 0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs3124030 | 0.81[ASN][1000 genomes] |
| rs3128364 | 0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3128366 | 0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3128367 | 0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs3128371 | 0.86[ASN][1000 genomes] |
| rs3128373 | 0.81[ASN][1000 genomes] |
| rs4294408 | 0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs4433390 | 0.81[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs5021965 | 0.87[ASN][1000 genomes] |
| rs6676747 | 0.91[ASN][1000 genomes] |
| rs9429470 | 0.82[EUR][1000 genomes];0.91[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv13370 | chr1:112693290-113246263 | Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 87 gene(s) | inside rSNPs | diseases |
| 2 | nsv2454 | chr1:112813849-112858259 | Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 3 | nsv508526 | chr1:112839396-112915215 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3128365 | NGF | cis | parietal | SCAN |
| rs3128365 | AHCYL1 | cis | cerebellum | SCAN |
| rs3128365 | KCND3 | cis | cerebellum | SCAN |
| rs3128365 | CEPT1 | cis | cerebellum | SCAN |
| rs3128365 | CSDE1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:112840400-112841400 | Weak transcription | HSMMtube | muscle |
| 2 | chr1:112841200-112841600 | Bivalent Enhancer | Fetal Muscle Leg | muscle |
