Variant report

Variant	rs28542968
Chromosome Location	chr6:27261295-27261296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27260766..27263711-chr6:27659606..27661608,2	K562	blood:
2	chr6:27260999..27263500-chr6:27265988..27267831,3	K562	blood:
3	chr6:27218105..27220281-chr6:27259553..27261970,3	K562	blood:
4	chr6:27261110..27263869-chr6:27440100..27444366,4	K562	blood:
5	chr6:27098205..27100481-chr6:27261214..27263124,2	K562	blood:
6	chr6:27144021..27146883-chr6:27258754..27261461,2	MCF-7	breast:
7	chr6:27218105..27220511-chr6:27260350..27262089,3	K562	blood:

Variant related genes	Relation type
ENSG00000112812	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs61736094	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61736098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61743942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61743950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61746402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73738742	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461361	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9468028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468036	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9468046	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9468059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs956149	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs956150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27258000-27261800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
2	chr6:27259400-27263400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:27259400-27263600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:27260000-27261400	Weak transcription	K562	blood
5	chr6:27261000-27261400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:27261000-27261800	ZNF genes & repeats	Psoas Muscle	Psoas
7	chr6:27261000-27263800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:27261000-27264600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:27261000-27264600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr6:27261000-27265600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:27261000-27266400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:27261000-27266400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr6:27261000-27266800	Active TSS	A549	lung
14	chr6:27261200-27261400	Flanking Bivalent TSS/Enh	ES-WA7 Cell Line	embryonic stem cell
15	chr6:27261200-27261400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
16	chr6:27261200-27261400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:27261200-27261400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
18	chr6:27261200-27261400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:27261200-27261400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
20	chr6:27261200-27261400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:27261200-27261400	Active TSS	HMEC	breast
22	chr6:27261200-27261600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:27261200-27261600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:27261200-27261600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:27261200-27261600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:27261200-27261600	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr6:27261200-27262000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:27261200-27262200	Active TSS	NHEK	skin
29	chr6:27261200-27262400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:27261200-27262400	Active TSS	Osteobl	bone
31	chr6:27261200-27263400	ZNF genes & repeats	GM12878-XiMat	blood
32	chr6:27261200-27263600	Active TSS	HUES48 Cell Line	embryonic stem cell

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