Variant report
| Variant | rs17113889 |
|---|---|
| Chromosome Location | chr12:74989236-74989237 |
| allele | C/T |
| 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 | chr12:74985828..74988147-chr12:74988930..74991203,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:35)
| rs_ID | r2[population] |
|---|---|
| rs10506698 | 0.91[CEU][hapmap];0.82[CHB][hapmap] |
| rs1353155 | 0.88[ASN][1000 genomes] |
| rs1353156 | 0.97[EUR][1000 genomes] |
| rs1353157 | 0.97[EUR][1000 genomes] |
| rs1389494 | 0.88[ASN][1000 genomes] |
| rs1493819 | 0.88[ASN][1000 genomes] |
| rs17113906 | 1.00[EUR][1000 genomes] |
| rs17114035 | 0.91[CEU][hapmap];0.82[CHB][hapmap] |
| rs17183486 | 0.95[EUR][1000 genomes] |
| rs17786699 | 1.00[EUR][1000 genomes] |
| rs17787103 | 0.95[EUR][1000 genomes] |
| rs17787309 | 0.97[EUR][1000 genomes] |
| rs2201343 | 0.88[ASN][1000 genomes] |
| rs2605351 | 0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes] |
| rs2605355 | 0.80[ASN][1000 genomes] |
| rs2605363 | 0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2641493 | 0.88[ASN][1000 genomes] |
| rs2641495 | 0.88[ASN][1000 genomes] |
| rs2641497 | 0.88[ASN][1000 genomes] |
| rs2641498 | 0.88[ASN][1000 genomes] |
| rs2641500 | 0.88[ASN][1000 genomes] |
| rs2641501 | 0.88[ASN][1000 genomes] |
| rs2661714 | 0.88[ASN][1000 genomes] |
| rs2661717 | 0.91[ASN][1000 genomes] |
| rs4475988 | 0.88[ASN][1000 genomes] |
| rs55987711 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs56147955 | 0.97[EUR][1000 genomes] |
| rs7295394 | 0.91[CEU][hapmap];0.82[CHB][hapmap] |
| rs7302481 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs748378 | 1.00[JPT][hapmap];0.80[ASN][1000 genomes] |
| rs7962067 | 0.97[EUR][1000 genomes] |
| rs7965242 | 0.82[CEU][hapmap] |
| rs7967033 | 0.97[EUR][1000 genomes] |
| rs822801 | 0.91[ASN][1000 genomes] |
| rs822802 | 0.91[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1039468 | chr12:74080586-75000246 | Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 31 gene(s) | inside rSNPs | diseases |
| 2 | nsv899293 | chr12:74835107-74995760 | Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionmiRNA target site | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17113889 | LRRC10 | cis | cerebellum | SCAN |
| rs17113889 | CPSF6 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:74988800-74989400 | Active TSS | Hela-S3 | cervix |
| 2 | chr12:74988800-74990000 | Enhancers | Fetal Intestine Small | intestine |
| 3 | chr12:74989200-74990000 | Enhancers | Stomach Mucosa | stomach |
