Variant report

Variant	rs11945709
Chromosome Location	chr4:56858450-56858451
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	chr4:56857985..56860799-chr4:56861315..56863156,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10212814	0.82[EUR][1000 genomes]
rs10866430	0.82[EUR][1000 genomes]
rs11133419	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724411	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11726419	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11731842	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11732545	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11734217	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11933720	0.82[EUR][1000 genomes]
rs11934142	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11937929	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12642567	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12645491	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13121634	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13127483	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13129197	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290014	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28472524	0.81[EUR][1000 genomes]
rs28507080	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28610174	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3214045	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34285861	0.82[EUR][1000 genomes]
rs35003282	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35123416	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35814086	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806749	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4499751	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59511278	0.93[ASN][1000 genomes]
rs62308565	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62308614	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62308617	0.93[ASN][1000 genomes]
rs62308621	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6814923	0.93[EUR][1000 genomes]
rs6815354	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6823178	0.93[ASN][1000 genomes]
rs6830668	0.93[EUR][1000 genomes]
rs6849999	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7670026	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9312668	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv2653807	chr4:56858322-56859755	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56815800-56875000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56816200-56873400	Weak transcription	Pancreas	Pancrea
3	chr4:56816200-56884200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:56816200-56887800	Weak transcription	Gastric	stomach
5	chr4:56816400-56866000	Weak transcription	Spleen	Spleen
6	chr4:56816400-56890800	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:56816600-56865800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:56816600-56890600	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:56816600-56896400	Weak transcription	Fetal Heart	heart
10	chr4:56816800-56865800	Weak transcription	Small Intestine	intestine
11	chr4:56816800-56869800	Weak transcription	HepG2	liver
12	chr4:56817400-56885400	Weak transcription	NHDF-Ad	bronchial
13	chr4:56819000-56897400	Weak transcription	HSMMtube	muscle
14	chr4:56819200-56859600	Weak transcription	Fetal Kidney	kidney
15	chr4:56819200-56890600	Weak transcription	NHLF	lung
16	chr4:56820600-56892400	Weak transcription	Hela-S3	cervix
17	chr4:56822200-56873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:56822400-56865800	Weak transcription	Psoas Muscle	Psoas
19	chr4:56823600-56893800	Weak transcription	HMEC	breast
20	chr4:56825200-56865800	Weak transcription	Aorta	Aorta
21	chr4:56825600-56870000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:56828200-56884200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:56829200-56881400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:56829400-56865600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:56829600-56890600	Weak transcription	A549	lung
26	chr4:56832400-56865800	Weak transcription	Liver	Liver
27	chr4:56833000-56877200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:56835400-56904800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:56837200-56905000	Weak transcription	Brain Substantia Nigra	brain
30	chr4:56838200-56865400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:56839800-56896600	Weak transcription	Brain Angular Gyrus	brain
32	chr4:56840000-56865800	Weak transcription	Esophagus	oesophagus
33	chr4:56840200-56865800	Weak transcription	Fetal Brain Female	brain
34	chr4:56840200-56878000	Weak transcription	NHEK	skin
35	chr4:56840200-56884600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr4:56840600-56866600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:56842800-56890800	Weak transcription	Osteobl	bone
38	chr4:56844200-56891000	Weak transcription	Colonic Mucosa	Colon
39	chr4:56847000-56873800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr4:56847200-56891000	Weak transcription	Right Ventricle	heart
41	chr4:56847400-56864400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:56847600-56866400	Weak transcription	Placenta	Placenta
43	chr4:56848400-56859400	Weak transcription	HUVEC	blood vessel
44	chr4:56848400-56865400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:56848400-56865600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr4:56848400-56865600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:56848400-56865600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr4:56848600-56865600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:56848800-56864200	Weak transcription	NH-A	brain
50	chr4:56848800-56878000	Weak transcription	HSMM	muscle

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