Variant report

Variant	rs17081937
Chromosome Location	chr4:57846553-57846554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:57842395-57846714	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57301138..57303431-chr4:57844871..57846919,2	MCF-7	breast:
2	chr4:57844609..57846562-chr4:57874022..57876813,2	K562	blood:
3	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:
4	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
5	chr4:57332287..57335313-chr4:57842375..57846822,5	K562	blood:
6	chr4:57845155..57847188-chr4:57856587..57858696,2	MCF-7	breast:
7	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:

No data

Variant related genes	Relation type
NOA1	TF binding region
ENSG00000174780	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000269949	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10866440	1.00[JPT][hapmap]
rs10866441	1.00[JPT][hapmap]
rs1105434	1.00[JPT][hapmap]
rs1107675	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11727683	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11730321	0.93[JPT][hapmap]
rs11735158	0.81[ASN][1000 genomes]
rs11932673	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12500454	1.00[JPT][hapmap]
rs12511020	0.84[ASN][1000 genomes]
rs1277287	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1277288	0.90[ASN][1000 genomes]
rs13108245	1.00[JPT][hapmap]
rs13121176	0.85[ASN][1000 genomes]
rs1315005	0.90[ASN][1000 genomes]
rs1625691	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17087307	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17087317	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17087411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs17087414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1713994	0.81[ASN][1000 genomes]
rs1718839	1.00[JPT][hapmap]
rs1877669	1.00[JPT][hapmap]
rs1976780	0.84[ASN][1000 genomes]
rs2228991	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3000	1.00[JPT][hapmap]
rs34659774	0.84[ASN][1000 genomes]
rs3733306	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796528	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3806745	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs41552420	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41556916	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56182208	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56285301	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57469512	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554398	1.00[JPT][hapmap]
rs6838948	1.00[JPT][hapmap]
rs6847086	0.82[JPT][hapmap]
rs6852110	1.00[JPT][hapmap]
rs73242631	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7661194	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7680734	1.00[JPT][hapmap]
rs781666	1.00[JPT][hapmap]
rs781668	1.00[JPT][hapmap]
rs9942208	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57840800-57846800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:57841400-57846600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:57841400-57846600	Active TSS	Hela-S3	cervix
4	chr4:57841600-57846600	Active TSS	NHLF	lung
5	chr4:57842000-57846600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:57842000-57846600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr4:57842000-57846600	Active TSS	HSMM	muscle
8	chr4:57842000-57846600	Active TSS	K562	blood
9	chr4:57842000-57846800	Active TSS	HSMMtube	muscle
10	chr4:57842000-57847000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:57842000-57847000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:57842000-57847000	Active TSS	A549	lung
13	chr4:57842200-57846600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:57842600-57846600	Active TSS	NHDF-Ad	bronchial
15	chr4:57842800-57846800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:57842800-57846800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:57843600-57846600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:57843800-57846600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:57845000-57846800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr4:57845600-57847000	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr4:57845800-57846600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr4:57845800-57847000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:57845800-57847000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr4:57846000-57846600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:57846000-57846600	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr4:57846000-57846600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr4:57846000-57846600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:57846000-57846600	Active TSS	Brain Anterior Caudate	brain
29	chr4:57846000-57846600	Weak transcription	Lung	lung
30	chr4:57846000-57846600	Weak transcription	Pancreas	Pancrea
31	chr4:57846000-57846600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:57846000-57846600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:57846000-57846600	Weak transcription	Small Intestine	intestine
34	chr4:57846000-57846600	Weak transcription	Spleen	Spleen
35	chr4:57846000-57846800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:57846000-57846800	Flanking Active TSS	Thymus	Thymus
37	chr4:57846000-57846800	Active TSS	HepG2	liver
38	chr4:57846000-57847000	Flanking Active TSS	Fetal Brain Female	brain
39	chr4:57846000-57847000	Flanking Active TSS	Dnd41	blood
40	chr4:57846000-57847400	Enhancers	Stomach Mucosa	stomach
41	chr4:57846000-57848000	Enhancers	Brain Substantia Nigra	brain
42	chr4:57846000-57848400	Weak transcription	Gastric	stomach
43	chr4:57846000-57849400	Enhancers	Brain Angular Gyrus	brain
44	chr4:57846000-57852000	Weak transcription	Aorta	Aorta
45	chr4:57846000-57853600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:57846000-57855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr4:57846200-57846600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:57846200-57846600	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr4:57846200-57846600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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