Variant report
| Variant | rs1004819 |
|---|---|
| Chromosome Location | chr1:67670213-67670214 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:5)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:5 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | MAFK | chr1:67670009-67670261 | HepG2 | liver: | n/a | n/a |
| 2 | RCOR1 | chr1:67670066-67670256 | K562 | blood: | n/a | n/a |
| 3 | MAFF | chr1:67670014-67670274 | HepG2 | liver: | n/a | n/a |
| 4 | MAFK | chr1:67670017-67670263 | HepG2 | liver: | n/a | n/a |
| 5 | MAFF | chr1:67670042-67670262 | K562 | blood: | n/a | n/a |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| IL23R | TF binding region |
| ENSG00000253074 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs1004820 | 0.84[ASN][1000 genomes] |
| rs10489630 | 0.81[CHD][hapmap];0.86[JPT][hapmap] |
| rs10889669 | 0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes] |
| rs11209018 | 0.88[CHD][hapmap];0.95[JPT][hapmap] |
| rs11465817 | 0.91[CHB][hapmap];0.83[CHD][hapmap] |
| rs11580078 | 0.80[ASN][1000 genomes] |
| rs11805303 | 0.93[ASW][hapmap];0.91[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes] |
| rs12075103 | 0.92[AFR][1000 genomes];0.96[EUR][1000 genomes] |
| rs12564022 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1569922 | 0.82[JPT][hapmap] |
| rs1966176 | 0.82[ASN][1000 genomes] |
| rs2863210 | 0.83[ASN][1000 genomes] |
| rs2902440 | 0.83[ASN][1000 genomes] |
| rs6588249 | 0.82[ASN][1000 genomes] |
| rs7539625 | 1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes] |
| rs7539643 | 0.97[EUR][1000 genomes] |
| rs7542066 | 0.96[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 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 | nsv461751 | chr1:67479598-67689036 | Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 2 | nsv546445 | chr1:67479598-67689036 | Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
Variant related diseases (count:1)
| Disease | PMID | Source |
|---|---|---|
| Crohn's disease | 17804789 | GWAS catalog |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1004819 | STRA6 | trans | cerebellum | SCAN |
| rs1004819 | SNAI2 | trans | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:67663400-67677000 | Weak transcription | Primary T helper 17 cells PMA-I stimulated | -- |
| 2 | chr1:67669200-67677200 | Weak transcription | Primary T helper memory cells from peripheral blood 2 | blood |
