Variant report

Variant	rs28706592
Chromosome Location	chr4:3873464-3873465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3868448..3872127-chr4:3872488..3876782,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs28416806	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28435291	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28449795	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484568	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28489239	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505188	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28514729	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28521923	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28522536	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28523451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28525038	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28539438	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28544923	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28553551	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28565417	0.90[ASN][1000 genomes]
rs28612119	0.94[ASN][1000 genomes]
rs28664793	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28689771	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34679937	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3979	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58523725	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933265	chr4:3392824-4283640	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv2757918	chr4:3394344-4350986	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2759219	chr4:3394344-4350986	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv878471	chr4:3413209-3884998	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	esv1816543	chr4:3414654-3942867	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1011554	chr4:3436478-3975772	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv537002	chr4:3436478-3975772	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1012371	chr4:3450810-3878976	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv537003	chr4:3450810-3878976	Active TSS Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv998670	chr4:3453787-3909535	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv432549	chr4:3487321-3975048	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv1002558	chr4:3505290-3878976	Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv878508	chr4:3737883-3884998	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv593473	chr4:3792209-3875234	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3872800-3873600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
2	chr4:3872800-3873800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr4:3872800-3873800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr4:3872800-3874000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr4:3872800-3874200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:3872800-3874200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr4:3872800-3874200	Bivalent Enhancer	Fetal Thymus	thymus
8	chr4:3872800-3874400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr4:3872800-3874400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:3872800-3875600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:3873000-3873600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:3873000-3873600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:3873000-3873600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:3873000-3873800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:3873000-3873800	Enhancers	Liver	Liver
16	chr4:3873000-3873800	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr4:3873000-3874000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:3873000-3874000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr4:3873000-3874200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:3873000-3874200	Bivalent Enhancer	Spleen	Spleen
21	chr4:3873000-3874400	Enhancers	Pancreas	Pancrea
22	chr4:3873000-3875600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr4:3873200-3873600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:3873200-3873600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr4:3873200-3873600	Bivalent Enhancer	Fetal Stomach	stomach
26	chr4:3873200-3873600	Bivalent Enhancer	Ovary	ovary
27	chr4:3873200-3873600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
28	chr4:3873200-3873800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
29	chr4:3873200-3873800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:3873200-3873800	Bivalent Enhancer	Lung	lung
31	chr4:3873200-3873800	Bivalent/Poised TSS	Right Ventricle	heart
32	chr4:3873200-3873800	Bivalent/Poised TSS	Thymus	Thymus
33	chr4:3873200-3874000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:3873200-3874000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
35	chr4:3873200-3874000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:3873400-3873600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:3873400-3873600	Bivalent/Poised TSS	Primary B cells from peripheral blood	blood
38	chr4:3873400-3873600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:3873400-3873600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
40	chr4:3873400-3873600	Active TSS	HSMM	muscle
41	chr4:3873400-3873800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:3873400-3873800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr4:3873400-3874000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:3873400-3874000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr4:3873400-3874200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr4:3873400-3874400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr4:3873400-3874600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
48	chr4:3873400-3875200	Weak transcription	Right Atrium	heart

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