Variant report
| Variant | rs1623375 |
|---|---|
| Chromosome Location | chr6:38698113-38698114 |
| allele | A/C/G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:16)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:16 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | EP300 | chr6:38697596-38699623 | SK-N-SH | brain: | n/a | chr6:38698620-38698634 chr6:38697653-38697667 |
| 2 | TCF12 | chr6:38697834-38698799 | SK-N-SH | brain: | n/a | n/a |
| 3 | REST | chr6:38697949-38698588 | SK-N-SH | brain: | n/a | n/a |
| 4 | GATA2 | chr6:38697876-38698963 | SH-SY5Y | brain: | n/a | chr6:38698931-38698944 chr6:38698766-38698774 |
| 5 | GATA3 | chr6:38697904-38698770 | SK-N-SH | brain: | n/a | n/a |
| 6 | RAD21 | chr6:38697858-38698156 | SK-N-SH_RA | brain: | n/a | chr6:38697983-38698002 chr6:38697986-38697999 chr6:38698091-38698104 |
| 7 | EP300 | chr6:38697859-38698764 | SK-N-SH_RA | brain: | n/a | chr6:38698620-38698634 |
| 8 | EP300 | chr6:38697916-38698684 | SK-N-SH_RA | brain: | n/a | chr6:38698620-38698634 |
| 9 | YY1 | chr6:38697915-38698223 | SK-N-SH_RA | brain: | n/a | chr6:38698052-38698060 |
| 10 | POLR2A | chr6:38697889-38698271 | SK-N-SH | brain: | n/a | n/a |
| 11 | TCF12 | chr6:38697871-38698716 | SK-N-SH | brain: | n/a | n/a |
| 12 | RAD21 | chr6:38697896-38698206 | SK-N-SH_RA | brain: | n/a | chr6:38697983-38698002 chr6:38697986-38697999 chr6:38698091-38698104 |
| 13 | GATA3 | chr6:38697855-38698768 | SK-N-SH | brain: | n/a | n/a |
| 14 | CTCF | chr6:38697980-38698130 | SK-N-SH_RA | brain: | n/a | chr6:38697987-38698000 |
| 15 | GATA3 | chr6:38697854-38698972 | SH-SY5Y | brain: | n/a | chr6:38698931-38698944 chr6:38698766-38698774 |
| 16 | YY1 | chr6:38697839-38698260 | SK-N-SH_RA | brain: | n/a | chr6:38698052-38698060 |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| DNAH8 | TF binding region |
rSNPs within LD-proxies of this variant (count:3)
| rs_ID | r2[population] |
|---|---|
| rs13209417 | 0.82[CHB][hapmap] |
| rs2654447 | 0.82[JPT][hapmap] |
| rs6458067 | 0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1021991 | chr6:37893949-38738720 | Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
| 2 | nsv885817 | chr6:38036420-39019503 | Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 26 gene(s) | inside rSNPs | diseases |
| 3 | esv2758049 | chr6:38588969-38711085 | Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 4 | esv2759421 | chr6:38588969-38711085 | Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 5 | nsv427754 | chr6:38588969-38711085 | Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 6 | nsv428144 | chr6:38588969-38711085 | Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 11 gene(s) | inside rSNPs | diseases |
| 7 | nsv830642 | chr6:38645056-38800657 | Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 8 | esv3474723 | chr6:38696177-38701061 | Active TSS Enhancers | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 9 | esv3486100 | chr6:38696187-38701063 | Enhancers Active TSS | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 10 | esv3474724 | chr6:38696191-38701061 | Enhancers Active TSS | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 11 | esv3486101 | chr6:38696191-38701061 | Enhancers Active TSS | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:7)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1623375 | MAPK13 | cis | parietal | SCAN |
| rs1623375 | TREM2 | cis | parietal | SCAN |
| rs1623375 | KIAA0240 | cis | parietal | SCAN |
| rs1623375 | ZFAND3 | cis | cerebellum | SCAN |
| rs1623375 | ANKS1A | cis | cerebellum | SCAN |
| rs1623375 | LHFPL5 | cis | cerebellum | SCAN |
| rs1623375 | FANCE | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:38698000-38698600 | Enhancers | Colon Smooth Muscle | Colon |
| 2 | chr6:38698000-38698800 | Enhancers | Fetal Stomach | stomach |
