Variant report

Variant	rs28519438
Chromosome Location	chr7:5800161-5800162
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5798985..5801479-chr7:5819651..5822590,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000011275	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2345938	0.89[ASN][1000 genomes]
rs34865088	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3801012	0.82[ASN][1000 genomes]
rs3807580	0.84[ASN][1000 genomes]
rs57309152	0.84[ASN][1000 genomes]
rs58364611	1.00[ASN][1000 genomes]
rs58503972	0.85[ASN][1000 genomes]
rs60181616	0.84[ASN][1000 genomes]
rs60372872	1.00[ASN][1000 genomes]
rs60442234	0.87[ASN][1000 genomes]
rs61033429	0.89[ASN][1000 genomes]
rs61210914	0.87[ASN][1000 genomes]
rs61260366	0.89[ASN][1000 genomes]
rs6463513	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6944627	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951438	0.89[ASN][1000 genomes]
rs6956564	0.92[ASN][1000 genomes]
rs6959871	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6969585	0.92[ASN][1000 genomes]
rs73339903	0.82[ASN][1000 genomes]
rs73341604	0.82[ASN][1000 genomes]
rs7795879	0.89[ASN][1000 genomes]
rs7806110	0.89[ASN][1000 genomes]
rs7809733	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
2	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
3	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
4	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
5	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
6	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
7	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
8	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
10	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
11	nsv887419	chr7:5703669-5820383	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv830891	chr7:5726301-5895460	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1028601	chr7:5748982-5919098	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
15	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
16	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
17	nsv464293	chr7:5778796-5891221	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv464294	chr7:5778796-5891221	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv605987	chr7:5778796-5891221	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	esv2764038	chr7:5785999-5893967	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	nsv464296	chr7:5792745-5850642	Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv605988	chr7:5792745-5850642	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv471315	chr7:5792745-5891221	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	nsv605989	chr7:5794220-5891221	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
25	nsv1020103	chr7:5794220-5893955	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	esv3326694	chr7:5795518-5852599	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
27	esv3375120	chr7:5795699-5852633	Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5762000-5820400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:5774200-5800600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:5781400-5816800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:5784000-5819600	Weak transcription	Fetal Heart	heart
5	chr7:5785200-5807000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:5790400-5800600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:5790400-5804600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:5790800-5820400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:5792600-5816600	Weak transcription	Right Ventricle	heart
10	chr7:5792800-5813400	Weak transcription	Small Intestine	intestine
11	chr7:5792800-5813600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:5792800-5820000	Weak transcription	Fetal Kidney	kidney
13	chr7:5792800-5820200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr7:5792800-5820200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:5792800-5820200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:5793800-5800200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:5794200-5806800	Weak transcription	Pancreas	Pancrea
18	chr7:5794400-5807400	Weak transcription	Gastric	stomach
19	chr7:5794600-5800400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:5795200-5800600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:5795200-5800800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr7:5795200-5800800	Strong transcription	Dnd41	blood
23	chr7:5795200-5812800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:5795400-5800400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:5795400-5813200	Weak transcription	HMEC	breast
26	chr7:5795600-5800400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:5795600-5800400	Strong transcription	Fetal Intestine Large	intestine
28	chr7:5795600-5805800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:5795600-5806400	Weak transcription	Hela-S3	cervix
30	chr7:5795600-5806800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:5795600-5807000	Weak transcription	Psoas Muscle	Psoas
32	chr7:5795800-5800400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr7:5796000-5800400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr7:5796200-5800200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr7:5796200-5800400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:5796200-5800400	Strong transcription	HSMM	muscle
37	chr7:5796200-5800600	Strong transcription	Primary T cells from cord blood	blood
38	chr7:5796400-5800200	Strong transcription	NHEK	skin
39	chr7:5796400-5800400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:5796400-5800400	Strong transcription	GM12878-XiMat	blood
41	chr7:5796600-5800400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:5796600-5800400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:5796600-5800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:5796800-5800200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr7:5796800-5800400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:5797000-5800400	Strong transcription	Fetal Thymus	thymus
47	chr7:5797000-5800600	Strong transcription	Fetal Lung	lung
48	chr7:5797000-5801000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:5797000-5807200	Weak transcription	K562	blood
50	chr7:5797200-5800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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