Variant report

Variant	rs56253808
Chromosome Location	chr4:88345977-88345978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88342302..88345638-chr4:88345920..88348886,5	K562	blood:
2	chr4:88345779..88348484-chr4:88376364..88379281,2	K562	blood:
3	chr4:88344098..88346850-chr4:88347399..88349099,3	MCF-7	breast:
4	chr4:88340563..88342774-chr4:88344260..88346848,4	MCF-7	breast:
5	chr4:88342695..88344657-chr4:88345813..88347482,2	MCF-7	breast:
6	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:

Variant related genes	Relation type
ENSG00000170502	Chromatin interaction
ENSG00000198189	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11932891	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11932933	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11935226	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11936273	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11937770	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11940597	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56189054	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58555412	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60350615	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60465726	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60622737	0.97[AFR][1000 genomes]
rs6825532	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6826257	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6833270	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6833835	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6838776	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6839314	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72877349	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72877357	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72877358	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88342600-88346000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:88343400-88346000	Active TSS	H1 Cell Line	embryonic stem cell
3	chr4:88344400-88346000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:88344400-88346200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:88344400-88346200	Weak transcription	Esophagus	oesophagus
6	chr4:88344400-88346200	Weak transcription	Spleen	Spleen
7	chr4:88344400-88398600	Weak transcription	Gastric	stomach
8	chr4:88344600-88346400	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:88344600-88356200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:88344600-88356200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:88344800-88346400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr4:88345000-88346000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:88345000-88346400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr4:88345000-88346600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr4:88345200-88346000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr4:88345200-88346000	Enhancers	Primary B cells from cord blood	blood
17	chr4:88345200-88346000	Enhancers	Primary T cells from cord blood	blood
18	chr4:88345200-88346000	Weak transcription	Aorta	Aorta
19	chr4:88345200-88346000	Enhancers	Fetal Heart	heart
20	chr4:88345200-88346000	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr4:88345200-88346000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr4:88345200-88346200	Enhancers	Colon Smooth Muscle	Colon
23	chr4:88345200-88346200	Enhancers	Thymus	Thymus
24	chr4:88345200-88346400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:88345200-88346400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr4:88345200-88346400	Enhancers	Brain Angular Gyrus	brain
27	chr4:88345200-88346400	Enhancers	Brain Substantia Nigra	brain
28	chr4:88345200-88346400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:88345200-88346400	Enhancers	Fetal Brain Female	brain
30	chr4:88345200-88346400	Enhancers	HepG2	liver
31	chr4:88345200-88346600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:88345200-88346800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:88345200-88346800	Enhancers	Lung	lung
34	chr4:88345200-88347200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr4:88345200-88356200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:88345200-88356200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:88345200-88356800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:88345200-88362800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:88345200-88363000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr4:88345200-88400000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:88345200-88416400	Weak transcription	Colonic Mucosa	Colon
42	chr4:88345400-88346000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:88345400-88346000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:88345400-88346000	Enhancers	Brain Germinal Matrix	brain
45	chr4:88345400-88346200	Enhancers	HSMMtube	muscle
46	chr4:88345400-88346200	Enhancers	K562	blood
47	chr4:88345400-88346200	Enhancers	NHDF-Ad	bronchial
48	chr4:88345400-88346400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:88345400-88346400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:88345400-88346400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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