Variant report
| Variant | rs10240053 |
|---|---|
| Chromosome Location | chr7:25605725-25605726 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:240)
- CpG islands (count:0)
- Chromatin interactive region (count:16)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
(count:16 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr7:25433474..25434141-chr7:25605268..25606353,4 | K562 | blood: | |
| 2 | chr7:25428818..25429573-chr7:25605415..25606098,2 | K562 | blood: | |
| 3 | chr7:25596711..25599628-chr7:25603188..25605911,2 | K562 | blood: | |
| 4 | chr7:25298973..25299854-chr7:25605283..25606167,4 | MCF-7 | breast: | |
| 5 | chr7:25429055..25432240-chr7:25604579..25606349,45 | MCF-7 | breast: | |
| 6 | chr7:25605406..25606179-chr7:25890948..25891905,5 | K562 | blood: | |
| 7 | chr7:25432296..25432868-chr7:25605222..25605812,2 | MCF-7 | breast: | |
| 8 | chr7:25430622..25431559-chr7:25605393..25606130,7 | MCF-7 | breast: | |
| 9 | chr7:25605314..25606102-chr7:25891008..25891805,3 | MCF-7 | breast: | |
| 10 | chr7:25428848..25430407-chr7:25605173..25606452,6 | MCF-7 | breast: | |
| 11 | chr7:25433157..25433791-chr7:25605378..25606157,2 | MCF-7 | breast: | |
| 12 | chr7:25298951..25300126-chr7:25605192..25606795,18 | K562 | blood: | |
| 13 | chr7:25298470..25299852-chr7:25605228..25606576,11 | MCF-7 | breast: | |
| 14 | chr7:25605147..25606187-chr7:25890189..25892015,14 | MCF-7 | breast: | |
| 15 | chr7:25605629..25606130-chr7:26404535..26405453,2 | K562 | blood: | |
| 16 | chr7:25430463..25431643-chr7:25605112..25606187,14 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000222101 | TF binding region |
rSNPs within LD-proxies of this variant (count:29)
| rs_ID | r2[population] |
|---|---|
| rs10235801 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs12531920 | 0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12534642 | 0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12700650 | 0.82[ASN][1000 genomes] |
| rs169642 | 0.88[ASN][1000 genomes] |
| rs208544 | 0.88[ASN][1000 genomes] |
| rs208545 | 0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs208546 | 0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs208549 | 0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs208555 | 0.88[ASN][1000 genomes] |
| rs208557 | 0.88[ASN][1000 genomes] |
| rs2134480 | 0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2158059 | 0.82[ASN][1000 genomes] |
| rs2188860 | 0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2521745 | 0.82[ASN][1000 genomes] |
| rs2521748 | 0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2521750 | 0.82[ASN][1000 genomes] |
| rs2521751 | 0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2653941 | 0.86[CHB][hapmap] |
| rs2813890 | 0.86[CHB][hapmap] |
| rs2813891 | 0.95[ASN][1000 genomes] |
| rs2813894 | 0.97[ASN][1000 genomes] |
| rs2813895 | 0.89[ASN][1000 genomes] |
| rs28394819 | 0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs739623 | 0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs967864 | 0.86[CHB][hapmap] |
| rs975370 | 0.85[CHB][hapmap] |
| rs980358 | 0.86[CHB][hapmap] |
| rs980359 | 0.86[CHB][hapmap] |
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 | nsv606426 | chr7:25254125-25621579 | Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | nsv1016813 | chr7:25405859-26150509 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 108 gene(s) | inside rSNPs | diseases |
| 3 | nsv538803 | chr7:25405859-26150509 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 108 gene(s) | inside rSNPs | diseases |
| 4 | nsv522815 | chr7:25599858-25606120 | Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | n/a |
| 5 | nsv523322 | chr7:25601480-25606120 | Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | n/a |
| 6 | nsv525378 | chr7:25605725-25615221 | Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10240053 | NPVF | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr7:25604000-25606000 | Enhancers | Colon Smooth Muscle | Colon |
| 2 | chr7:25604000-25606200 | Enhancers | Fetal Lung | lung |
| 3 | chr7:25604600-25608200 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
| 4 | chr7:25604800-25608200 | Weak transcription | Rectal Mucosa Donor 29 | rectum |
| 5 | chr7:25605200-25606400 | Weak transcription | Fetal Stomach | stomach |
| 6 | chr7:25605200-25606800 | Enhancers | Fetal Kidney | kidney |
| 7 | chr7:25605400-25606000 | Enhancers | Pancreatic Islets | Pancreatic Islet |
| 8 | chr7:25605400-25606000 | Enhancers | Rectal Mucosa Donor 31 | rectum |
| 9 | chr7:25605400-25607000 | Enhancers | Stomach Mucosa | stomach |
| 10 | chr7:25605600-25606800 | Weak transcription | Rectal Smooth Muscle | rectum |
