Variant report
Variant | rs12402006 |
---|---|
Chromosome Location | chr1:150869829-150869830 |
allele | A/G |
Outlinks | Ensembl   UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:3)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
No data |
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Variant related genes | Relation type |
---|---|
ENSG00000143437 | Chromatin interaction |
rs_ID | r2[population] |
---|---|
rs1081512 | 0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes] |
rs11204725 | 0.80[EUR][1000 genomes] |
rs11204735 | 0.95[EUR][1000 genomes] |
rs11204737 | 0.94[EUR][1000 genomes] |
rs12125650 | 0.83[EUR][1000 genomes] |
rs12126004 | 0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes] |
rs12404199 | 0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes] |
rs12410050 | 0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes] |
rs12758227 | 0.95[EUR][1000 genomes] |
rs2039590 | 0.91[EUR][1000 genomes] |
rs2089081 | 0.92[EUR][1000 genomes] |
rs3754211 | 0.83[AMR][1000 genomes];0.88[EUR][1000 genomes] |
rs486836 | 0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
rs4970932 | 0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes] |
rs4970976 | 0.88[EUR][1000 genomes] |
rs6587551 | 0.86[EUR][1000 genomes] |
rs7412746 | 0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes] |
rs7534124 | 0.80[EUR][1000 genomes] |

No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
---|---|---|---|---|---|---|---|
1 | esv2829859 | chr1:150608894-150937329 | Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 38 gene(s) | inside rSNPs | diseases |
2 | nsv1001897 | chr1:150743271-151241600 | Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 156 gene(s) | inside rSNPs | diseases |
3 | nsv535158 | chr1:150743271-151241600 | Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 156 gene(s) | inside rSNPs | diseases |
4 | nsv2810 | chr1:150835173-150879869 | Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 21 gene(s) | inside rSNPs | diseases |
5 | nsv1008496 | chr1:150845827-150970656 | Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 62 gene(s) | inside rSNPs | diseases |
SNP | Gene | Cis/trans | Tissue | Source |
---|---|---|---|---|
rs12402006 | HORMAD1 | cis | Adipose Subcutaneous | GTEx |
rs12402006 | RP11-316M1.12 | cis | Adipose Subcutaneous | GTEx |
rs12402006 | RP11-316M1.12 | cis | Nerve Tibial | GTEx |
rs12402006 | HORMAD1 | cis | Esophagus Mucosa | GTEx |
rs12402006 | CTSS | Cis_1M | lymphoblastoid | RTeQTL |
rs12402006 | RP11-316M1.12 | cis | Esophagus Muscularis | GTEx |
rs12402006 | CTSK | cis | multi-tissue | Pritchard |
rs12402006 | HORMAD1 | cis | Skin Sun Exposed Lower leg | GTEx |
rs12402006 | RP11-316M1.12 | cis | Artery Tibial | GTEx |
rs12402006 | HORMAD1 | cis | Nerve Tibial | GTEx |
rs12402006 | RP11-316M1.12 | cis | Muscle Skeletal | GTEx |
rs12402006 | RNU6-1042P | cis | Esophagus Mucosa | GTEx |
rs12402006 | CTSK | Cis_1M | lymphoblastoid | RTeQTL |
rs12402006 | RP11-316M1.12 | cis | Thyroid | GTEx |
rs12402006 | RP11-316M1.12 | cis | lung | GTEx |
rs12402006 | ARNT | Cis_1M | lymphoblastoid | RTeQTL |
rs12402006 | RP11-316M1.12 | cis | Whole Blood | GTEx |
rs12402006 | RP11-316M1.12 | cis | Skin Sun Exposed Lower leg | GTEx |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr1:150868600-150874000 | Weak transcription | Placenta | Placenta |
2 | chr1:150869000-150870000 | Enhancers | Skeletal Muscle Female | skeletal muscle |