Variant report
Variant | rs13207173 |
---|---|
Chromosome Location | chr6:86457522-86457523 |
allele | C/T |
Outlinks | Ensembl   UCSC |
- TF binding region (count:25)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:25 , 50 per page) page:
1
No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
---|---|---|---|---|---|---|
1 | FOXA2 | chr6:86457431-86457708 | HepG2 | liver: | n/a | n/a |
2 | JUND | chr6:86457449-86457681 | HepG2 | liver: | n/a | chr6:86457576-86457587 |
3 | JUND | chr6:86457304-86457819 | MCF-7 | breast: | n/a | chr6:86457576-86457587 |
4 | CEBPB | chr6:86457496-86457774 | MCF-7 | breast: | n/a | n/a |
5 | NFIC | chr6:86457461-86457789 | HepG2 | liver: | n/a | n/a |
6 | HDAC2 | chr6:86457361-86457883 | MCF-7 | breast: | n/a | n/a |
7 | ARID3A | chr6:86457410-86457713 | HepG2 | liver: | n/a | n/a |
8 | NR2F2 | chr6:86457267-86457727 | MCF-7 | breast: | n/a | n/a |
9 | FOSL2 | chr6:86457375-86457810 | MCF-7 | breast: | n/a | n/a |
10 | GATA3 | chr6:86457283-86457861 | MCF-7 | breast: | n/a | n/a |
11 | JUND | chr6:86457448-86457729 | MCF-7 | breast: | n/a | chr6:86457576-86457587 |
12 | GATA3 | chr6:86457025-86457975 | MCF-7 | breast: | n/a | n/a |
13 | FOXA1 | chr6:86457311-86457808 | HepG2 | liver: | n/a | n/a |
14 | FOS | chr6:86457509-86457713 | MCF10A-Er-Src | breast: | n/a | chr6:86457576-86457587 |
15 | FOS | chr6:86457489-86457734 | MCF10A-Er-Src | breast: | n/a | chr6:86457576-86457587 |
16 | CEBPB | chr6:86457468-86457806 | MCF-7 | breast: | n/a | n/a |
17 | FOSL2 | chr6:86457434-86457629 | A549 | lung: | n/a | n/a |
18 | FOS | chr6:86457445-86457676 | MCF10A-Er-Src | breast: | n/a | chr6:86457576-86457587 |
19 | FOS | chr6:86457504-86457722 | MCF10A-Er-Src | breast: | n/a | chr6:86457576-86457587 |
20 | EP300 | chr6:86457414-86457813 | MCF-7 | breast: | n/a | n/a |
21 | FOSL2 | chr6:86457441-86457855 | MCF-7 | breast: | n/a | n/a |
22 | FOXA1 | chr6:86457380-86457776 | HepG2 | liver: | n/a | n/a |
23 | FOSL2 | chr6:86457430-86457725 | HepG2 | liver: | n/a | n/a |
24 | FOS | chr6:86457461-86457730 | HUVEC | blood vessel: | n/a | chr6:86457576-86457587 |
25 | FOSL2 | chr6:86457441-86457808 | A549 | lung: | n/a | n/a |
No data |
(count:5 , 50 per page) page:
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No. | Distal block | Cell Line | Cell type | Cell Stage |
---|---|---|---|---|
1 | chr6:86452591..86454803-chr6:86455984..86458666,2 | K562 | blood: | |
2 | chr6:86385780..86390752-chr6:86454284..86460508,14 | MCF-7 | breast: | |
3 | chr6:86457332..86459007-chr6:86460736..86462827,2 | MCF-7 | breast: | |
4 | chr6:86383135..86386189-chr6:86457468..86460297,4 | MCF-7 | breast: | |
5 | chr6:86351009..86353966-chr6:86455070..86459127,4 | MCF-7 | breast: |
No data |
No data |
No data |
Variant related genes | Relation type |
---|---|
RNU4-72P | TF binding region |
ENSG00000222686 | Chromatin interaction |
ENSG00000135316 | Chromatin interaction |
ENSG00000203875 | Chromatin interaction |
rs_ID | r2[population] |
---|---|
rs1059306 | 0.82[CEU][hapmap] |
rs10806334 | 0.86[ASN][1000 genomes] |
rs10806337 | 0.97[EUR][1000 genomes] |
rs10944136 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
rs10944137 | 1.00[CEU][hapmap];0.99[EUR][1000 genomes] |
rs10944138 | 0.94[EUR][1000 genomes] |
rs10944144 | 0.81[EUR][1000 genomes] |
rs10944145 | 0.81[EUR][1000 genomes] |
rs1173417 | 0.86[CHB][hapmap] |
rs11752180 | 0.81[ASN][1000 genomes] |
rs11752223 | 0.81[ASN][1000 genomes] |
rs11754330 | 0.99[EUR][1000 genomes] |
rs11755642 | 1.00[CEU][hapmap];0.99[EUR][1000 genomes] |
rs11758508 | 1.00[CEU][hapmap];0.91[EUR][1000 genomes] |
rs12153887 | 0.82[EUR][1000 genomes];0.85[ASN][1000 genomes] |
rs12190603 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
rs12192546 | 1.00[CEU][hapmap];0.97[EUR][1000 genomes] |
rs12193904 | 1.00[CEU][hapmap];0.99[EUR][1000 genomes] |
rs12198061 | 0.81[AMR][1000 genomes];0.86[ASN][1000 genomes] |
rs12198557 | 0.85[EUR][1000 genomes] |
rs12199329 | 0.81[EUR][1000 genomes] |
rs12199873 | 0.82[CEU][hapmap] |
rs12202712 | 0.81[ASN][1000 genomes] |
rs12205492 | 0.96[EUR][1000 genomes] |
rs12209668 | 0.83[ASN][1000 genomes] |
rs12211216 | 0.81[EUR][1000 genomes];0.82[ASN][1000 genomes] |
rs12212151 | 0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes] |
rs12212480 | 1.00[CEU][hapmap];0.99[EUR][1000 genomes] |
rs12660846 | 0.82[ASN][1000 genomes] |
rs12665464 | 1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes] |
rs12665516 | 0.81[EUR][1000 genomes] |
rs12665542 | 0.81[EUR][1000 genomes] |
rs13203309 | 0.81[EUR][1000 genomes] |
rs13207537 | 0.83[AMR][1000 genomes];0.83[ASN][1000 genomes] |
rs13213603 | 0.87[ASN][1000 genomes] |
rs1335442 | 1.00[CEU][hapmap];0.97[EUR][1000 genomes] |
rs1447160 | 0.81[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs1470531 | 1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes] |
rs1813001 | 0.82[EUR][1000 genomes];0.85[ASN][1000 genomes] |
rs1838954 | 0.83[ASN][1000 genomes] |
rs1838955 | 0.83[ASN][1000 genomes] |
rs1838958 | 0.83[ASN][1000 genomes] |
rs1838959 | 0.83[AMR][1000 genomes];0.83[ASN][1000 genomes] |
rs1932225 | 0.85[ASN][1000 genomes] |
rs1995688 | 0.90[CEU][hapmap] |
rs2084293 | 0.83[ASN][1000 genomes] |
rs2084294 | 0.83[ASN][1000 genomes] |
rs2084296 | 0.82[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs2084297 | 0.81[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs2100109 | 0.82[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs2121594 | 1.00[CEU][hapmap] |
rs2166665 | 0.82[EUR][1000 genomes];0.82[ASN][1000 genomes] |
rs2197648 | 0.82[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs2218594 | 0.82[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs2225754 | 1.00[CEU][hapmap];0.99[EUR][1000 genomes] |
rs2324817 | 0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
rs2475790 | 0.82[CEU][hapmap] |
rs2475792 | 0.86[CHB][hapmap] |
rs2758840 | 0.82[CEU][hapmap] |
rs2758847 | 0.82[CEU][hapmap] |
rs2783171 | 0.82[CEU][hapmap] |
rs2842601 | 0.82[CEU][hapmap] |
rs2842607 | 0.82[CEU][hapmap] |
rs2842608 | 0.82[CEU][hapmap] |
rs2842609 | 0.82[CEU][hapmap] |
rs2842612 | 0.85[CEU][hapmap] |
rs2842613 | 0.82[CEU][hapmap] |
rs34522955 | 0.85[AFR][1000 genomes];0.86[AMR][1000 genomes] |
rs34622605 | 0.99[EUR][1000 genomes] |
rs34765423 | 0.94[EUR][1000 genomes] |
rs34795473 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
rs35874630 | 0.80[ASN][1000 genomes] |
rs36035797 | 0.83[AMR][1000 genomes];0.83[ASN][1000 genomes] |
rs3966881 | 0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes] |
rs4098044 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
rs4383777 | 0.86[ASN][1000 genomes] |
rs4706248 | 0.81[EUR][1000 genomes];0.82[ASN][1000 genomes] |
rs4706252 | 0.81[AMR][1000 genomes];0.83[ASN][1000 genomes] |
rs4706253 | 0.83[AMR][1000 genomes];0.83[ASN][1000 genomes] |
rs4707223 | 0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes] |
rs4707229 | 0.82[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs57016132 | 0.83[AMR][1000 genomes] |
rs61119084 | 0.80[ASN][1000 genomes] |
rs6454486 | 0.88[ASN][1000 genomes] |
rs6454487 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes] |
rs6454488 | 0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
rs66807489 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes] |
rs6900436 | 0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes] |
rs72907388 | 0.96[EUR][1000 genomes] |
rs7450035 | 0.81[AMR][1000 genomes];0.83[ASN][1000 genomes] |
rs7739241 | 1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes] |
rs7742201 | 0.85[CEU][hapmap] |
rs7755730 | 0.81[ASN][1000 genomes] |
rs806529 | 0.80[EUR][1000 genomes] |
rs9294338 | 0.82[AFR][1000 genomes] |
rs9342046 | 0.86[ASN][1000 genomes] |
rs9344542 | 0.86[CHB][hapmap] |
rs9351065 | 0.82[CEU][hapmap] |
rs9353327 | 0.86[CHB][hapmap] |
rs9362230 | 0.82[CEU][hapmap] |
rs9362239 | 0.88[ASN][1000 genomes] |
rs9450318 | 0.86[ASN][1000 genomes] |
rs9450319 | 0.87[ASN][1000 genomes] |
rs9647601 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |

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 |
SNP | Gene | Cis/trans | Tissue | Source |
---|---|---|---|---|
rs13207173 | SNHG5 | cis | multi-tissue | Pritchard |
rs13207173 | SNHG5 | cis | Heart Left Ventricle | GTEx |
rs13207173 | SNHG5 | cis | Artery Tibial | GTEx |
rs13207173 | SNHG5 | Cis_1M | lymphoblastoid | RTeQTL |
rs13207173 | SNHG5 | cis | Muscle Skeletal | GTEx |
rs13207173 | SNHG5 | cis | Skin Sun Exposed Lower leg | GTEx |
rs13207173 | SNHG5 | cis | Whole Blood | GTEx |
rs13207173 | C6orf160 | cis | uninvolved skin | skin_eQTL |
rs13207173 | SNHG5 | cis | Nerve Tibial | GTEx |
rs13207173 | SNHG5 | cis | lung | GTEx |
rs13207173 | SNHG5 | cis | Thyroid | GTEx |
rs13207173 | SNHG5 | cis | Adipose Subcutaneous | GTEx |
rs13207173 | SNHG5 | cis | Esophagus Mucosa | GTEx |
rs13207173 | SNHG5 | cis | Artery Aorta | GTEx |
rs13207173 | SNHG5 | cis | Esophagus Muscularis | GTEx |
rs13207173 | C6orf160 | cis | lesional skin | skin_eQTL |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr6:86455600-86458800 | Weak transcription | Fetal Intestine Large | intestine |
2 | chr6:86455600-86460800 | Weak transcription | Fetal Intestine Small | intestine |
3 | chr6:86456400-86457600 | Enhancers | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
4 | chr6:86456400-86457800 | Enhancers | Osteobl | bone |
5 | chr6:86457000-86457800 | Flanking Active TSS | Mesenchymal Stem Cell Derived Adipocyte Cultured Cells | ES cell derived |
6 | chr6:86457000-86457800 | Enhancers | Bone Marrow Derived Cultured Mesenchymal Stem Cells | Bone marrow |
7 | chr6:86457400-86457800 | Enhancers | HepG2 | liver |