Variant report
Variant | rs6454504 |
---|---|
Chromosome Location | chr6:86580330-86580331 |
allele | C/G |
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 |
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No data |
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No data |
rs_ID | r2[population] |
---|---|
rs1059307 | 0.82[CHB][hapmap] |
rs10944137 | 0.90[CEU][hapmap] |
rs1173418 | 0.83[CHB][hapmap] |
rs11752180 | 0.81[ASN][1000 genomes] |
rs11752223 | 0.81[ASN][1000 genomes] |
rs11755642 | 0.90[CEU][hapmap] |
rs11758508 | 0.90[CEU][hapmap] |
rs12055653 | 0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes] |
rs12190603 | 0.94[CEU][hapmap] |
rs12192546 | 0.90[CEU][hapmap] |
rs12193904 | 0.90[CEU][hapmap] |
rs12202712 | 0.82[ASN][1000 genomes] |
rs12209668 | 0.80[ASN][1000 genomes] |
rs12212480 | 0.90[CEU][hapmap] |
rs12216103 | 0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
rs12660846 | 0.81[ASN][1000 genomes] |
rs12661231 | 0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes] |
rs12661611 | 0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes] |
rs12664634 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
rs12665464 | 0.90[CEU][hapmap];0.81[ASN][1000 genomes] |
rs13207173 | 0.90[CEU][hapmap] |
rs13212415 | 0.85[AFR][1000 genomes];0.83[ASN][1000 genomes] |
rs1335442 | 0.90[CEU][hapmap] |
rs1447159 | 0.85[AFR][1000 genomes];0.84[ASN][1000 genomes] |
rs1470531 | 0.90[CEU][hapmap];0.84[CHB][hapmap] |
rs1838954 | 0.80[ASN][1000 genomes] |
rs1838955 | 0.80[ASN][1000 genomes] |
rs1838956 | 0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes] |
rs1838957 | 0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes] |
rs1838958 | 0.80[ASN][1000 genomes] |
rs1838959 | 0.80[ASN][1000 genomes] |
rs1995688 | 0.81[CEU][hapmap] |
rs2084293 | 0.80[ASN][1000 genomes] |
rs2084294 | 0.80[ASN][1000 genomes] |
rs2121594 | 0.90[CEU][hapmap] |
rs2121595 | 0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs2225754 | 0.90[CEU][hapmap] |
rs3087978 | 0.82[CHB][hapmap] |
rs36035797 | 0.80[ASN][1000 genomes] |
rs4706252 | 0.80[ASN][1000 genomes] |
rs4706253 | 0.80[ASN][1000 genomes] |
rs4707235 | 0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs6454487 | 0.90[CEU][hapmap] |
rs6454492 | 0.85[ASN][1000 genomes] |
rs6929514 | 0.85[EUR][1000 genomes];0.92[ASN][1000 genomes] |
rs7739241 | 0.90[CEU][hapmap];0.83[CHB][hapmap];0.82[ASN][1000 genomes] |
rs7755730 | 0.80[ASN][1000 genomes] |
rs7755790 | 0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
rs7770835 | 0.84[ASN][1000 genomes] |
rs9647601 | 0.90[CEU][hapmap] |

No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
---|---|---|---|---|---|---|---|
1 | nsv1028293 | chr6:86353958-86778912 | Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 100 gene(s) | inside rSNPs | diseases |
2 | nsv538350 | chr6:86353958-86778912 | Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 100 gene(s) | inside rSNPs | diseases |
3 | nsv886335 | chr6:86445651-86669361 | Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
4 | nsv1022618 | chr6:86465365-87432069 | Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
5 | nsv538352 | chr6:86465365-87432069 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
6 | nsv1033637 | chr6:86482045-86701733 | Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
7 | nsv538353 | chr6:86482045-86701733 | Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
8 | esv1802672 | chr6:86546123-86662267 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
9 | nsv1018453 | chr6:86555984-86761120 | Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
10 | nsv463940 | chr6:86576854-86648436 | Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS | TF binding regionChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
11 | nsv604095 | chr6:86576854-86648436 | Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS | TF binding regionChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
12 | nsv604096 | chr6:86576854-86649705 | Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS | TF binding regionChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
SNP | Gene | Cis/trans | Tissue | Source |
---|---|---|---|---|
rs6454504 | SNHG5 | cis | multi-tissue | Pritchard |
rs6454504 | SNHG5 | cis | Artery Tibial | GTEx |
rs6454504 | SNHG5 | cis | lung | GTEx |
rs6454504 | SNHG5 | cis | Skin Sun Exposed Lower leg | GTEx |
rs6454504 | SNHG5 | cis | Artery Aorta | GTEx |
rs6454504 | SNHG5 | cis | Esophagus Muscularis | GTEx |
rs6454504 | SNHG5 | cis | Whole Blood | GTEx |
rs6454504 | SNHG5 | cis | Esophagus Mucosa | GTEx |
rs6454504 | SNHG5 | cis | Nerve Tibial | GTEx |
rs6454504 | C6orf160 | cis | normal skin | skin_eQTL |
rs6454504 | SNHG5 | cis | Heart Left Ventricle | GTEx |
rs6454504 | SNHG5 | cis | Thyroid | GTEx |
rs6454504 | NT5E | cis | Thyroid | GTEx |
rs6454504 | C6orf160 | cis | lesional skin | skin_eQTL |
rs6454504 | SNHG5 | Cis_1M | lymphoblastoid | RTeQTL |
rs6454504 | SNHG5 | cis | Adipose Subcutaneous | GTEx |
rs6454504 | SNHG5 | cis | Muscle Skeletal | GTEx |
rs6454504 | C6orf160 | cis | uninvolved skin | skin_eQTL |
rs6454504 | SNHG5 | cis | Stomach | GTEx |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr6:86575200-86583400 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
2 | chr6:86579200-86584000 | Weak transcription | Ovary | ovary |