Variant report
| Variant | rs12660028 |
|---|---|
| Chromosome Location | chr5:74605502-74605503 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:30)
| rs_ID | r2[population] |
|---|---|
| rs1009417 | 0.84[EUR][1000 genomes] |
| rs10515197 | 0.83[CHD][hapmap] |
| rs12654238 | 0.91[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs12659206 | 0.86[EUR][1000 genomes] |
| rs12659221 | 0.86[EUR][1000 genomes] |
| rs1423526 | 0.91[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs17671549 | 0.86[EUR][1000 genomes] |
| rs17739025 | 0.84[EUR][1000 genomes] |
| rs2241402 | 1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap] |
| rs2303151 | 1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap] |
| rs3733907 | 0.83[CHD][hapmap] |
| rs3761739 | 0.83[CHD][hapmap] |
| rs4072112 | 0.86[EUR][1000 genomes] |
| rs4703664 | 0.82[EUR][1000 genomes] |
| rs4703666 | 0.91[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs4704203 | 0.86[EUR][1000 genomes] |
| rs4704205 | 0.86[EUR][1000 genomes] |
| rs4704209 | 1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap] |
| rs57528678 | 0.86[EUR][1000 genomes] |
| rs6870787 | 0.86[EUR][1000 genomes] |
| rs6872197 | 0.86[EUR][1000 genomes] |
| rs6877840 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7700655 | 0.86[EUR][1000 genomes] |
| rs7710120 | 0.86[EUR][1000 genomes] |
| rs7717396 | 1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap] |
| rs7719376 | 0.82[EUR][1000 genomes] |
| rs7731499 | 0.91[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs7731875 | 0.86[EUR][1000 genomes] |
| rs7732958 | 1.00[CEU][hapmap];0.86[EUR][1000 genomes] |
| rs7737008 | 0.86[EUR][1000 genomes] |
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 | nsv1016610 | chr5:74403611-74627654 | Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 2 | esv2758000 | chr5:74433760-74611714 | Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 3 | esv2759350 | chr5:74433760-74611714 | Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12660028 | DNAJB4 | trans | brain | seeQTL |
| rs12660028 | HSPD1 | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:74602400-74606400 | Weak transcription | Rectal Mucosa Donor 31 | rectum |
| 2 | chr5:74602800-74607400 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
| 3 | chr5:74604000-74606400 | Weak transcription | Fetal Adrenal Gland | Adrenal Gland |
