Variant report

Variant	rs55739402
Chromosome Location	chr3:119559163-119559164
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	chr3:119553090..119555920-chr3:119558108..119560664,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs55849075	0.83[AFR][1000 genomes]
rs56181436	0.83[AFR][1000 genomes]
rs57028282	0.92[AFR][1000 genomes]
rs59890455	1.00[AFR][1000 genomes]
rs73854723	0.84[AFR][1000 genomes]
rs73854725	0.92[AFR][1000 genomes]
rs73854727	0.84[AFR][1000 genomes]
rs73854732	1.00[AFR][1000 genomes]
rs73854734	0.92[AFR][1000 genomes]
rs73854742	0.92[AFR][1000 genomes]
rs73854743	0.92[AFR][1000 genomes]
rs73854748	0.92[AFR][1000 genomes]
rs73854754	0.83[AFR][1000 genomes]
rs73854756	0.91[AFR][1000 genomes]
rs73854758	0.91[AFR][1000 genomes]
rs73854759	0.83[AFR][1000 genomes]
rs73854760	0.83[AFR][1000 genomes]
rs73854763	0.87[AFR][1000 genomes]
rs73854768	0.83[AFR][1000 genomes]
rs73854771	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
3	chr3:119536200-119569000	Weak transcription	Esophagus	oesophagus
4	chr3:119536400-119570200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:119536600-119576000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:119536600-119576400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:119539000-119576400	Weak transcription	Ovary	ovary
8	chr3:119540400-119563600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:119540400-119574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:119540400-119576600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:119540800-119577000	Weak transcription	Aorta	Aorta
12	chr3:119541000-119581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:119541200-119561800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:119541200-119587000	Weak transcription	Gastric	stomach
15	chr3:119541800-119559200	Weak transcription	Pancreas	Pancrea
16	chr3:119541800-119560000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:119542400-119581200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:119542600-119560800	Weak transcription	Hela-S3	cervix
19	chr3:119542600-119581600	Weak transcription	HUVEC	blood vessel
20	chr3:119542800-119575000	Weak transcription	Fetal Kidney	kidney
21	chr3:119544000-119561800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:119545000-119559600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:119545000-119576400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:119545200-119559200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:119545200-119559400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:119545200-119561600	Weak transcription	Fetal Stomach	stomach
27	chr3:119545200-119562800	Weak transcription	NHLF	lung
28	chr3:119545200-119575000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:119545200-119575000	Weak transcription	Adipose Nuclei	Adipose
30	chr3:119545200-119575400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:119545200-119583400	Weak transcription	Brain Angular Gyrus	brain
32	chr3:119545800-119560400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:119545800-119576400	Weak transcription	Brain Germinal Matrix	brain
34	chr3:119545800-119581600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:119546000-119561800	Weak transcription	Left Ventricle	heart
36	chr3:119546000-119561800	Weak transcription	Thymus	Thymus
37	chr3:119546000-119569000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:119546000-119571800	Weak transcription	GM12878-XiMat	blood
39	chr3:119546000-119575000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:119546000-119576400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:119546000-119663400	Weak transcription	Lung	lung
42	chr3:119546200-119559400	Weak transcription	Fetal Thymus	thymus
43	chr3:119546200-119561400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:119546200-119569000	Weak transcription	Placenta	Placenta
45	chr3:119546200-119575000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:119546400-119567000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:119546400-119575200	Weak transcription	Liver	Liver
48	chr3:119546400-119580400	Weak transcription	HepG2	liver
49	chr3:119547600-119560400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:119548600-119559600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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