Variant report
Variant | rs8102707 |
---|---|
Chromosome Location | chr19:52008754-52008755 |
allele | A/G |
Outlinks | Ensembl   UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
No data |
No data |
(count:1 , 50 per page) page:
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No. | Distal block | Cell Line | Cell type | Cell Stage |
---|---|---|---|---|
1 | chr19:51895053..51897765-chr19:52007493..52009642,2 | K562 | blood: |
No data |
No data |
No data |
Variant related genes | Relation type |
---|---|
ENSG00000268889 | Chromatin interaction |
rs_ID | r2[population] |
---|---|
rs10420446 | 0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes] |
rs10420457 | 0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes] |
rs11084083 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
rs1160392 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
rs11668941 | 0.83[EUR][1000 genomes] |
rs13343377 | 0.87[LWK][hapmap];0.86[MEX][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes] |
rs1551555 | 0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes] |
rs1551556 | 1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
rs16982743 | 0.83[ASW][hapmap] |
rs1973095 | 0.97[ASN][1000 genomes] |
rs2009362 | 1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes] |
rs2864097 | 0.96[YRI][hapmap];0.80[AFR][1000 genomes] |
rs2864101 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
rs2864102 | 0.84[CEU][hapmap] |
rs2864104 | 0.84[CEU][hapmap] |
rs3810106 | 0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes] |
rs3810108 | 0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes] |
rs3810109 | 0.81[ASN][1000 genomes] |
rs3810110 | 1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes] |
rs3810113 | 0.81[ASN][1000 genomes] |
rs3829658 | 0.82[ASW][hapmap];0.84[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes] |
rs3976745 | 0.87[CEU][hapmap] |
rs4801873 | 0.87[CEU][hapmap] |
rs7246846 | 0.82[MEX][hapmap] |
rs7253637 | 0.84[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes] |
rs7255948 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
rs9304718 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |

No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
---|---|---|---|---|---|---|---|
1 | nsv1066308 | chr19:51680133-52103974 | Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 71 gene(s) | inside rSNPs | diseases |
2 | nsv544049 | chr19:51680133-52103974 | Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 71 gene(s) | inside rSNPs | diseases |
3 | nsv544051 | chr19:51944903-52147459 | Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 26 gene(s) | inside rSNPs | diseases |
4 | esv2758504 | chr19:51991896-52266700 | Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 542 gene(s) | inside rSNPs | diseases |
5 | esv2758767 | chr19:51991896-52604625 | Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 578 gene(s) | inside rSNPs | diseases |
6 | nsv469584 | chr19:52001381-52151821 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 25 gene(s) | inside rSNPs | diseases |
7 | nsv482654 | chr19:52001381-52151821 | Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 25 gene(s) | inside rSNPs | diseases |
8 | esv33175 | chr19:52002098-52010839 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive region | 6 gene(s) | inside rSNPs | diseases |
SNP | Gene | Cis/trans | Tissue | Source |
---|---|---|---|---|
rs8102707 | NLRP5 | cis | cerebellum | SCAN |
rs8102707 | ZNF137P | cis | cerebellum | SCAN |
rs8102707 | SIGLEC12 | cis | Whole Blood | GTEx |
rs8102707 | SIGLEC12 | cis | Artery Aorta | GTEx |
rs8102707 | SIGLEC12 | cis | Adipose Subcutaneous | GTEx |
rs8102707 | SIGLEC12 | cis | Nerve Tibial | GTEx |
rs8102707 | SIGLEC12 | cis | lung | GTEx |
rs8102707 | SIGLEC12 | cis | Thyroid | GTEx |
rs8102707 | ZNF468 | cis | cerebellum | SCAN |
rs8102707 | ZNF584 | cis | parietal | SCAN |
rs8102707 | SIGLEC12 | cis | Artery Tibial | GTEx |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr19:52002600-52015000 | Enhancers | Primary monocytes fromperipheralblood | blood |
2 | chr19:52005000-52009400 | Weak transcription | Duodenum Mucosa | Duodenum |
3 | chr19:52007000-52010800 | Enhancers | Monocytes-CD14+_RO01746 | blood |
4 | chr19:52007800-52011000 | Weak transcription | Primary neutrophils fromperipheralblood | blood |
5 | chr19:52008200-52010400 | Enhancers | K562 | blood |
6 | chr19:52008400-52010800 | Weak transcription | Primary hematopoietic stem cells short term culture | blood |