Variant report

Variant	rs3800025
Chromosome Location	chr6:56891128-56891129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56819331..56822345-chr6:56888159..56891969,4	K562	blood:
2	chr6:56882958..56887865-chr6:56889010..56894345,6	K562	blood:
3	chr6:56824548..56826799-chr6:56889091..56892083,2	K562	blood:
4	chr6:56881940..56886581-chr6:56889010..56894702,6	K562	blood:
5	chr6:56890706..56893193-chr6:56903389..56905342,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1020550	1.00[ASN][1000 genomes]
rs10484410	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12190575	0.90[ASN][1000 genomes]
rs12192222	0.90[ASN][1000 genomes]
rs12194288	0.80[ASN][1000 genomes]
rs12194407	0.90[ASN][1000 genomes]
rs12198801	0.90[ASN][1000 genomes]
rs12201039	0.80[ASN][1000 genomes]
rs12211901	0.80[ASN][1000 genomes]
rs12214882	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1411578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1547226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16888392	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17619360	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3800018	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3800023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3996934	1.00[ASN][1000 genomes]
rs3996935	1.00[ASN][1000 genomes]
rs3996936	1.00[ASN][1000 genomes]
rs4523090	1.00[ASN][1000 genomes]
rs4631287	1.00[ASN][1000 genomes]
rs6459178	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6936506	0.90[ASN][1000 genomes]
rs72868608	0.80[ASN][1000 genomes]
rs73463742	0.90[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7748120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7753547	1.00[ASN][1000 genomes]
rs7756421	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7771115	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9349841	0.95[ASN][1000 genomes]
rs9396247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9396256	1.00[ASN][1000 genomes]
rs986245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56878600-56905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:56879000-56891600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:56886000-56894000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:56886400-56893200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:56887400-56891400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:56888200-56892000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:56888800-56891400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:56889600-56891400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr6:56889800-56891200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:56890000-56892000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:56890200-56891200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:56890200-56891200	ZNF genes & repeats	Aorta	Aorta
13	chr6:56890400-56891200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:56890400-56891400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr6:56890600-56891400	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:56890600-56893800	Weak transcription	Brain Substantia Nigra	brain
17	chr6:56890600-56894800	Weak transcription	NHDF-Ad	bronchial
18	chr6:56890800-56891800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:56890800-56893400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:56891000-56893200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:56891000-56894000	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links