Variant report
| Variant | rs2305549 |
|---|---|
| Chromosome Location | chr1:75055419-75055420 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:2)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 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 | chr1:75055348-75058691 | SK-N-SH | brain: | n/a | chr1:75057601-75057615 chr1:75058488-75058502 chr1:75058562-75058576 |
| No data |
| No data |
(count:2 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-FPGT-TNNI3K-1 | chr1:75055419-75055591 | ENSG00000234497.1 |
| 2 | lnc-FPGT-TNNI3K-1 | chr1:75055018-75055591 | NONHSAT003967 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000234497 | TF binding region |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs12567936 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap] |
| rs12567994 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap] |
| rs17095579 | 0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs17095629 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs17095663 | 0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap] |
| rs61646994 | 0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs696686 | 0.87[CHB][hapmap] |
| rs696687 | 0.87[CHB][hapmap] |
| rs696688 | 0.87[CHB][hapmap] |
| rs696689 | 0.84[CHB][hapmap] |
| rs696694 | 0.87[CHB][hapmap] |
| rs696699 | 0.87[CHB][hapmap] |
| rs696700 | 0.87[CHB][hapmap] |
| rs696702 | 0.87[CHB][hapmap] |
| rs72984909 | 0.84[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs9661135 | 1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 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 | nsv1003171 | chr1:74407468-75122270 | Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 18 gene(s) | inside rSNPs | diseases |
| 2 | nsv535000 | chr1:74407468-75122270 | Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 18 gene(s) | inside rSNPs | diseases |
| 3 | nsv1011745 | chr1:74730942-75477618 | Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 23 gene(s) | inside rSNPs | diseases |
| 4 | nsv535003 | chr1:74730942-75477618 | Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 23 gene(s) | inside rSNPs | diseases |
| 5 | nsv830248 | chr1:74962391-75144458 | Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 6 | nsv870824 | chr1:75019390-75125581 | Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:75054000-75058200 | Weak transcription | Liver | Liver |
