Variant report
| Variant | rs3020444 |
|---|---|
| Chromosome Location | chr14:64791013-64791014 |
| 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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr14:64789559..64792915-chr14:64794645..64797859,3 | MCF-7 | breast: | |
| 2 | chr14:64788790..64792892-chr14:64803767..64805586,3 | K562 | blood: | |
| 3 | chr14:64790771..64792766-chr14:64798246..64800317,2 | MCF-7 | breast: | |
| 4 | chr14:64787867..64791213-chr14:64803202..64806273,3 | MCF-7 | breast: | |
| 5 | chr14:64788702..64791071-chr14:64791186..64793425,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000214770 | Chromatin interaction |
| ENSG00000140009 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs12323665 | 0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs17101765 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs17179740 | 1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes] |
| rs2978381 | 0.89[GIH][hapmap] |
| rs2987983 | 1.00[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes] |
| rs3020449 | 0.89[GIH][hapmap] |
| rs3020450 | 1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs3783736 | 1.00[CHB][hapmap];0.85[JPT][hapmap] |
| rs6573553 | 0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap] |
| rs7148637 | 0.80[MEX][hapmap] |
| rs7154455 | 0.96[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes] |
| rs8011682 | 0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs8020356 | 0.90[EUR][1000 genomes] |
| rs867443 | 0.83[CEU][hapmap] |
| rs960070 | 0.80[CHB][hapmap] |
Variant overlapped rSNPs/rCNVs (count:1 , 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 | nsv902019 | chr14:64395569-64882380 | Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 48 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3020444 | MTHFD1 | cis | parietal | SCAN |
| rs3020444 | MTHFD1 | cis | cerebellum | SCAN |
| rs3020444 | MTHFD1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs3020444 | ESR2 | Cis_1M | lymphoblastoid | RTeQTL |
| rs3020444 | KCNH5 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr14:64790800-64792400 | Enhancers | HSMM | muscle |
