Variant report

Variant	rs1397729
Chromosome Location	chr4:26324479-26324480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:26322937-26324695	U87	brain:	n/a	n/a
2	SIN3AK20	chr4:26324049-26324479	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr4:26324061-26324489	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26319239..26325766-chr4:26360124..26364446,7	MCF-7	breast:

Variant related genes	Relation type
RBPJ	TF binding region
ENSG00000168214	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1567545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1967281	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2063448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2667064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2725321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2725326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2788855	0.93[AMR][1000 genomes]
rs2788856	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2788859	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2788862	1.00[EUR][1000 genomes]
rs3109831	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3109840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3109846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3109847	1.00[AMR][1000 genomes]
rs3109853	0.93[AMR][1000 genomes]
rs3109854	0.93[AMR][1000 genomes]
rs3113014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3113027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3113028	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3113030	0.86[AMR][1000 genomes]
rs57899161	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6856923	0.86[AMR][1000 genomes]
rs7665261	0.85[AMR][1000 genomes]
rs7689471	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs907273	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829889	chr4:26169954-26338313	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26319800-26324800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:26320200-26324800	Active TSS	HSMMtube	muscle
3	chr4:26320200-26325200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:26320200-26326200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:26320400-26324600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:26320400-26324600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr4:26320400-26324600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr4:26320400-26324600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:26320400-26324800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr4:26320400-26324800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:26320400-26325400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr4:26320400-26325400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:26320400-26326000	Active TSS	Fetal Brain Female	brain
14	chr4:26320600-26324600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:26320600-26324600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:26320600-26324600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:26320600-26324600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr4:26320600-26324600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:26320600-26324600	Active TSS	Right Atrium	heart
20	chr4:26320600-26324800	Active TSS	NHDF-Ad	bronchial
21	chr4:26320600-26325000	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr4:26322000-26324800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr4:26322200-26325000	Active TSS	Fetal Muscle Leg	muscle
24	chr4:26322200-26325800	Active TSS	GM12878-XiMat	blood
25	chr4:26322200-26325800	Active TSS	NHLF	lung
26	chr4:26322200-26326200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:26322600-26326000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:26323400-26325000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:26323800-26324600	Enhancers	Fetal Heart	heart
30	chr4:26323800-26325000	Flanking Active TSS	NHEK	skin
31	chr4:26323800-26325200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:26323800-26326200	Weak transcription	Esophagus	oesophagus
33	chr4:26323800-26330200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:26323800-26332600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:26323800-26333000	Weak transcription	Small Intestine	intestine
36	chr4:26323800-26374400	Weak transcription	Lung	lung
37	chr4:26324000-26324800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr4:26324000-26325000	Enhancers	Primary B cells from cord blood	blood
39	chr4:26324000-26325200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:26324000-26325600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:26324000-26325600	Enhancers	Rectal Smooth Muscle	rectum
42	chr4:26324000-26325800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr4:26324000-26325800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr4:26324000-26325800	Enhancers	Brain Cingulate Gyrus	brain
45	chr4:26324000-26325800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr4:26324000-26326000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr4:26324000-26326000	Enhancers	Liver	Liver
48	chr4:26324000-26326000	Enhancers	Brain Substantia Nigra	brain
49	chr4:26324000-26326000	Enhancers	Colon Smooth Muscle	Colon
50	chr4:26324000-26326800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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