Variant report

Variant	rs17583593
Chromosome Location	chr4:106113683-106113684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106064689..106068216-chr4:106113083..106116896,4	MCF-7	breast:
2	chr4:106065192..106067810-chr4:106113392..106115229,2	MCF-7	breast:
3	chr4:106112171..106113904-chr4:106125859..106128359,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1114718	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11933960	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12498609	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12506006	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12511800	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12640842	0.83[EUR][1000 genomes]
rs12647779	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12647884	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1391442	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17583579	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17616993	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2023841	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2866774	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6533180	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs949681	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9637601	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
2	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
3	chr4:106099000-106114200	Weak transcription	Gastric	stomach
4	chr4:106101000-106146600	Weak transcription	Spleen	Spleen
5	chr4:106102800-106127400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:106104800-106117400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:106105200-106117800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:106106000-106135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:106106200-106114000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:106106200-106114200	Weak transcription	Small Intestine	intestine
11	chr4:106106200-106118600	Weak transcription	Thymus	Thymus
12	chr4:106106200-106155000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:106106600-106125800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:106108000-106115400	Weak transcription	HMEC	breast
15	chr4:106108000-106123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:106108400-106114200	Weak transcription	Pancreas	Pancrea
17	chr4:106110200-106114600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr4:106110600-106118600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:106110800-106114400	Enhancers	Colon Smooth Muscle	Colon
20	chr4:106110800-106114600	Enhancers	Rectal Smooth Muscle	rectum
21	chr4:106111000-106118800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:106111200-106117200	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr4:106111400-106114600	Enhancers	Adipose Nuclei	Adipose
24	chr4:106111800-106127400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:106112200-106114200	Weak transcription	Liver	Liver
26	chr4:106112200-106127200	Weak transcription	Primary T cells from cord blood	blood
27	chr4:106112400-106114000	Enhancers	Primary B cells from cord blood	blood
28	chr4:106112400-106114000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:106112400-106114200	Weak transcription	Aorta	Aorta
30	chr4:106112400-106114400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:106112400-106114600	Enhancers	Fetal Heart	heart
32	chr4:106112400-106115400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:106112400-106115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:106112400-106116600	Enhancers	Osteobl	bone
35	chr4:106112400-106127000	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:106112600-106113800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:106112600-106114000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:106112600-106114200	Enhancers	A549	lung
39	chr4:106112600-106114200	Enhancers	NHLF	lung
40	chr4:106112600-106114400	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr4:106112600-106114400	Genic enhancers	Fetal Lung	lung
42	chr4:106112600-106114600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr4:106112600-106114800	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr4:106112600-106117000	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr4:106112800-106114000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:106112800-106114000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:106112800-106114400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:106112800-106114400	Enhancers	HSMMtube	muscle
49	chr4:106112800-106114600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr4:106112800-106114600	Enhancers	HSMM	muscle

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