Variant report

Variant	rs28679698
Chromosome Location	chr7:5680711-5680712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5631718..5635207-chr7:5679773..5683291,5	MCF-7	breast:
2	chr7:5602390..5604842-chr7:5680680..5682890,2	MCF-7	breast:
3	chr7:5631675..5634644-chr7:5680116..5683516,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075618	Chromatin interaction
ENSG00000075624	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10247769	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10254311	1.00[AMR][1000 genomes]
rs10256234	0.89[AFR][1000 genomes]
rs10265842	1.00[AMR][1000 genomes]
rs10276198	1.00[AMR][1000 genomes]
rs11556570	1.00[AMR][1000 genomes]
rs11976654	1.00[AMR][1000 genomes]
rs57806146	1.00[AMR][1000 genomes]
rs60073378	1.00[AMR][1000 genomes]
rs6975359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73334490	1.00[AMR][1000 genomes]
rs73334491	1.00[AMR][1000 genomes]
rs73334493	1.00[AMR][1000 genomes]
rs73338077	1.00[AMR][1000 genomes]
rs73338095	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
7	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
8	nsv1025434	chr7:5537571-5705283	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
9	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv887416	chr7:5584934-5695259	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv1034883	chr7:5651680-5696147	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv887417	chr7:5667645-5760860	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
18	nsv887418	chr7:5675305-5772551	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5660600-5693800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:5671800-5682800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:5672000-5681200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:5673200-5681000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:5673800-5681800	Strong transcription	Primary T cells from cord blood	blood
6	chr7:5674200-5681200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:5674400-5681400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:5674600-5681000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:5674600-5688800	Weak transcription	Aorta	Aorta
10	chr7:5674800-5681200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:5674800-5681400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr7:5674800-5683000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr7:5674800-5693600	Strong transcription	Dnd41	blood
14	chr7:5674800-5728200	Weak transcription	Small Intestine	intestine
15	chr7:5675000-5681000	Strong transcription	Primary B cells from cord blood	blood
16	chr7:5675000-5688000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr7:5675200-5681400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:5675400-5681400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr7:5675400-5683000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr7:5675400-5684200	Strong transcription	Fetal Intestine Large	intestine
21	chr7:5675400-5689400	Weak transcription	Psoas Muscle	Psoas
22	chr7:5675800-5682200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr7:5676000-5681000	Strong transcription	GM12878-XiMat	blood
24	chr7:5676000-5693800	Strong transcription	Fetal Intestine Small	intestine
25	chr7:5676200-5681200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:5676200-5689000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr7:5676800-5681000	Strong transcription	Thymus	Thymus
28	chr7:5677000-5689200	Weak transcription	Ovary	ovary
29	chr7:5677000-5693400	Weak transcription	Right Atrium	heart
30	chr7:5677000-5701400	Weak transcription	Fetal Brain Male	brain
31	chr7:5677200-5683200	Strong transcription	A549	lung
32	chr7:5677200-5689000	Weak transcription	Fetal Kidney	kidney
33	chr7:5677200-5689200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr7:5677200-5690600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr7:5677200-5707200	Weak transcription	Stomach Mucosa	stomach
36	chr7:5677400-5681000	Strong transcription	Fetal Thymus	thymus
37	chr7:5677400-5681200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:5677400-5681400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:5677400-5681600	Strong transcription	Left Ventricle	heart
40	chr7:5677400-5683400	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:5677400-5686400	Weak transcription	NHDF-Ad	bronchial
42	chr7:5677400-5687600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr7:5677400-5689000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:5677400-5689200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:5677400-5689400	Weak transcription	Brain Substantia Nigra	brain
46	chr7:5677400-5690000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr7:5677400-5706200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr7:5677600-5681000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:5677600-5681000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:5677600-5681000	Strong transcription	Rectal Smooth Muscle	rectum

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