Variant report

Variant	rs17089253
Chromosome Location	chr4:69178117-69178118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:69177090..69179857-chr4:69251602..69253290,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10024896	1.00[EUR][1000 genomes]
rs10027564	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10031034	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11932381	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11940780	1.00[EUR][1000 genomes]
rs11942378	1.00[EUR][1000 genomes]
rs2056802	1.00[EUR][1000 genomes]
rs28633232	1.00[EUR][1000 genomes]
rs28758556	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28866177	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35883654	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7664735	1.00[EUR][1000 genomes]
rs7684922	1.00[EUR][1000 genomes]
rs9998289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS 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 target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69167000-69179400	Weak transcription	HepG2	liver
2	chr4:69173400-69178600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:69174000-69182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:69174000-69182000	Weak transcription	Esophagus	oesophagus
5	chr4:69174000-69182600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:69174400-69179800	Weak transcription	Fetal Intestine Small	intestine
7	chr4:69174400-69179800	Weak transcription	Fetal Stomach	stomach
8	chr4:69174400-69182000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:69174800-69178800	Weak transcription	Lung	lung
10	chr4:69175000-69178200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:69175000-69178800	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:69175000-69179200	Weak transcription	Psoas Muscle	Psoas
13	chr4:69175000-69179200	Weak transcription	NHEK	skin
14	chr4:69175000-69179600	Weak transcription	Fetal Brain Male	brain
15	chr4:69175000-69182000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:69175000-69182000	Weak transcription	Thymus	Thymus
17	chr4:69175000-69182400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:69175200-69178200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:69175200-69178200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:69175200-69178200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:69175200-69178800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:69175200-69178800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:69175200-69180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:69175400-69178200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:69175400-69179000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:69175400-69179400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:69176000-69182400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:69176200-69181600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:69176200-69182000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:69176200-69182000	Weak transcription	Pancreas	Pancrea
31	chr4:69176200-69182200	Weak transcription	Gastric	stomach
32	chr4:69176200-69203600	Strong transcription	Liver	Liver
33	chr4:69176200-69203600	Strong transcription	HSMM	muscle
34	chr4:69176200-69204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:69176200-69204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:69176400-69178800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:69176400-69182000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:69176400-69183600	Strong transcription	Primary hematopoietic stem cells	blood
39	chr4:69176400-69184600	Strong transcription	Fetal Intestine Large	intestine
40	chr4:69176400-69184800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr4:69176400-69185200	Strong transcription	Primary B cells from cord blood	blood
42	chr4:69176400-69185200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr4:69176400-69185400	Strong transcription	Brain Germinal Matrix	brain
44	chr4:69176400-69185400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr4:69176400-69185600	Strong transcription	Brain Anterior Caudate	brain
46	chr4:69176400-69186000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:69176400-69186000	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr4:69176400-69186000	Strong transcription	Adipose Nuclei	Adipose
49	chr4:69176400-69186200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:69176400-69188800	Strong transcription	GM12878-XiMat	blood

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