Variant report

Variant	rs16890653
Chromosome Location	chr6:25487525-25487526
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	chr6:25471739..25473870-chr6:25485448..25487878,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10946784	0.83[EUR][1000 genomes]
rs12665641	0.83[EUR][1000 genomes]
rs7760799	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9356979	0.82[EUR][1000 genomes]
rs9358859	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366625	0.82[EUR][1000 genomes]
rs9379770	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9379771	0.87[EUR][1000 genomes]
rs9393647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393648	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	9 gene(s)	inside rSNPs	diseases
2	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv432856	chr6:25468825-25494666	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25446800-25493600	Weak transcription	Left Ventricle	heart
2	chr6:25446800-25504400	Weak transcription	Primary B cells from cord blood	blood
3	chr6:25449400-25515800	Weak transcription	Lung	lung
4	chr6:25450400-25488400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:25456400-25499200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:25456400-25515800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:25456400-25537000	Weak transcription	Esophagus	oesophagus
8	chr6:25463000-25490000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:25463200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:25464000-25498800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:25464200-25518400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:25464800-25490000	Weak transcription	Hela-S3	cervix
13	chr6:25465400-25499000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:25466400-25516000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:25466800-25515800	Weak transcription	Fetal Stomach	stomach
16	chr6:25468400-25488400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:25469800-25490200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:25471200-25490200	Weak transcription	Small Intestine	intestine
19	chr6:25471600-25597200	Weak transcription	Gastric	stomach
20	chr6:25471800-25493200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25473400-25490200	Weak transcription	Ovary	ovary
22	chr6:25473400-25495400	Weak transcription	Pancreas	Pancrea
23	chr6:25473600-25499600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:25473600-25516000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:25474000-25490000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:25474000-25492200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:25474400-25490000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:25475000-25488600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:25475600-25490200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:25476800-25499800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:25477800-25490200	Weak transcription	Placenta	Placenta
32	chr6:25477800-25499600	Weak transcription	NHLF	lung
33	chr6:25477800-25499800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:25478000-25490200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:25478000-25499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:25478000-25499200	Weak transcription	NHEK	skin
37	chr6:25480000-25511400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:25480800-25523600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:25482000-25490200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:25482400-25490600	Weak transcription	Fetal Kidney	kidney
41	chr6:25482600-25490400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:25482800-25490200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:25483000-25532200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr6:25483200-25487600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:25483400-25490200	Weak transcription	Thymus	Thymus
46	chr6:25483800-25488200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:25483800-25490000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:25483800-25491200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:25483800-25499000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:25484000-25500000	Weak transcription	HMEC	breast

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