Variant report

Variant	rs6478021
Chromosome Location	chr9:116316730-116316731
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	chr9:116314955..116316764-chr9:116317777..116320410,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12346476	1.00[EUR][1000 genomes]
rs16908653	1.00[EUR][1000 genomes]
rs60969910	1.00[EUR][1000 genomes]
rs7023224	1.00[EUR][1000 genomes]
rs7027261	1.00[EUR][1000 genomes]
rs7032245	1.00[EUR][1000 genomes]
rs7032414	1.00[EUR][1000 genomes]
rs7033489	1.00[EUR][1000 genomes]
rs7038258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73538901	1.00[EUR][1000 genomes]
rs73544687	1.00[EUR][1000 genomes]
rs73544688	1.00[EUR][1000 genomes]
rs73548441	1.00[EUR][1000 genomes]
rs73655894	1.00[EUR][1000 genomes]
rs7851265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853612	1.00[EUR][1000 genomes]
rs7856713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864169	1.00[EUR][1000 genomes]
rs7865642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7866866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867017	1.00[EUR][1000 genomes]
rs7870008	0.96[AFR][1000 genomes];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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116304400-116323600	Weak transcription	Hela-S3	cervix
2	chr9:116304600-116321000	Weak transcription	A549	lung
3	chr9:116309600-116321000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr9:116310400-116321200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:116310800-116321000	Weak transcription	Fetal Kidney	kidney
6	chr9:116311000-116321000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:116311200-116323000	Weak transcription	Primary T cells from cord blood	blood
8	chr9:116311200-116326600	Weak transcription	Fetal Thymus	thymus
9	chr9:116311400-116317600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:116311400-116319800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:116311400-116321200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:116311400-116321600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:116311400-116321800	Weak transcription	GM12878-XiMat	blood
14	chr9:116311400-116322400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:116311400-116322400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr9:116311400-116326200	Weak transcription	Fetal Intestine Large	intestine
17	chr9:116311600-116317800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:116311600-116318800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr9:116311600-116318800	Weak transcription	Left Ventricle	heart
20	chr9:116311600-116318800	Weak transcription	Right Atrium	heart
21	chr9:116311600-116319600	Weak transcription	Fetal Intestine Small	intestine
22	chr9:116311600-116319600	Weak transcription	Placenta	Placenta
23	chr9:116311600-116319800	Weak transcription	Spleen	Spleen
24	chr9:116311600-116321000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:116311600-116321000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:116311600-116322200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr9:116311600-116322400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:116311600-116326800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:116311600-116331600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:116311800-116318000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:116311800-116320800	Weak transcription	Fetal Stomach	stomach
32	chr9:116311800-116321000	Weak transcription	Brain Anterior Caudate	brain
33	chr9:116311800-116321000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:116311800-116321200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:116311800-116322400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr9:116312000-116320800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:116312000-116320800	Weak transcription	HUVEC	blood vessel
38	chr9:116312400-116318800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:116312400-116319000	Weak transcription	Right Ventricle	heart
40	chr9:116312400-116319200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:116312400-116319600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr9:116312400-116321000	Weak transcription	Brain Angular Gyrus	brain
43	chr9:116312400-116321000	Weak transcription	Stomach Mucosa	stomach
44	chr9:116312600-116319200	Weak transcription	Pancreas	Pancrea
45	chr9:116312600-116321000	Weak transcription	Brain Substantia Nigra	brain
46	chr9:116312600-116321200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr9:116312800-116318200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr9:116312800-116320200	Weak transcription	HepG2	liver
49	chr9:116316600-116318800	Weak transcription	Lung	lung
50	chr9:116316600-116319200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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