Variant report

Variant	rs73833239
Chromosome Location	chr3:50713088-50713089
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50712677..50713421-chr3:50922505..50923533,3	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1038415	1.00[EUR][1000 genomes]
rs107457	1.00[EUR][1000 genomes]
rs11923336	1.00[EUR][1000 genomes]
rs13092850	1.00[EUR][1000 genomes]
rs1552255	1.00[EUR][1000 genomes]
rs1552256	1.00[EUR][1000 genomes]
rs17051012	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051016	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051017	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051404	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1843073	1.00[EUR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2262848	1.00[EUR][1000 genomes]
rs2355337	1.00[EUR][1000 genomes]
rs2355701	1.00[EUR][1000 genomes]
rs2459450	1.00[EUR][1000 genomes]
rs2609015	1.00[EUR][1000 genomes]
rs2609027	1.00[EUR][1000 genomes]
rs2609030	1.00[EUR][1000 genomes]
rs2675781	1.00[EUR][1000 genomes]
rs2675785	1.00[EUR][1000 genomes]
rs2675823	1.00[EUR][1000 genomes]
rs2675824	1.00[EUR][1000 genomes]
rs2675826	1.00[EUR][1000 genomes]
rs2675833	1.00[EUR][1000 genomes]
rs407164	1.00[EUR][1000 genomes]
rs421689	1.00[EUR][1000 genomes]
rs4234694	1.00[EUR][1000 genomes]
rs4234695	1.00[EUR][1000 genomes]
rs4267639	1.00[EUR][1000 genomes]
rs4340700	1.00[EUR][1000 genomes]
rs4401355	1.00[EUR][1000 genomes]
rs4440121	1.00[EUR][1000 genomes]
rs4560294	1.00[AMR][1000 genomes]
rs4688675	1.00[EUR][1000 genomes]
rs4688704	1.00[EUR][1000 genomes]
rs4688717	1.00[EUR][1000 genomes]
rs55723661	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55852678	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56112107	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56198179	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56341000	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56413944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57077411	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57155820	1.00[AMR][1000 genomes]
rs57756789	1.00[EUR][1000 genomes]
rs57867785	1.00[AMR][1000 genomes]
rs57987466	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58231937	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58854038	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58911362	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59065723	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59337835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59340349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59486246	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59749820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59944295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60132317	1.00[EUR][1000 genomes]
rs60209025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60455882	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs609678	1.00[EUR][1000 genomes]
rs61032466	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61455710	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs621975	1.00[EUR][1000 genomes]
rs628865	1.00[EUR][1000 genomes]
rs6446223	1.00[EUR][1000 genomes]
rs650473	1.00[EUR][1000 genomes]
rs665943	1.00[EUR][1000 genomes]
rs6768539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789552	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7373700	1.00[EUR][1000 genomes]
rs73833231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833242	1.00[AMR][1000 genomes]
rs73833247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833248	1.00[AMR][1000 genomes]
rs73833404	1.00[AMR][1000 genomes]
rs73833406	1.00[AMR][1000 genomes]
rs73833886	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73833935	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833940	1.00[AMR][1000 genomes]
rs73833943	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73833947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835518	1.00[EUR][1000 genomes]
rs73835533	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835535	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835537	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835538	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7433944	1.00[EUR][1000 genomes]
rs7642578	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650772	1.00[EUR][1000 genomes]
rs7653228	1.00[EUR][1000 genomes]
rs936714	1.00[EUR][1000 genomes]
rs9840476	1.00[EUR][1000 genomes]
rs9851304	1.00[EUR][1000 genomes]
rs9857033	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3398465	chr3:50710948-50713996	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50711400-50714000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:50711400-50714400	Active TSS	Brain Angular Gyrus	brain
3	chr3:50711400-50714400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:50711600-50713800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:50711800-50713200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:50711800-50713200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr3:50711800-50713200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:50711800-50713200	Bivalent/Poised TSS	A549	lung
9	chr3:50711800-50713400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:50711800-50714400	Active TSS	HSMMtube	muscle
11	chr3:50712000-50713200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:50712000-50713200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:50712000-50713200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr3:50712000-50713200	Flanking Bivalent TSS/Enh	Thymus	Thymus
15	chr3:50712000-50713400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:50712000-50713400	Active TSS	Fetal Brain Female	brain
17	chr3:50712000-50713600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:50712000-50713600	Active TSS	Brain Substantia Nigra	brain
19	chr3:50712000-50713600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:50712000-50713800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:50712000-50714000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr3:50712000-50714400	Active TSS	Brain Anterior Caudate	brain
23	chr3:50712200-50713200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr3:50712200-50713200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:50712200-50713200	Active TSS	Left Ventricle	heart
26	chr3:50712200-50713200	Active TSS	Right Ventricle	heart
27	chr3:50712200-50713400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:50712200-50713400	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:50712200-50713400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr3:50712200-50713400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:50712200-50713400	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:50712200-50713400	Bivalent Enhancer	Liver	Liver
33	chr3:50712200-50713400	Active TSS	Brain Germinal Matrix	brain
34	chr3:50712200-50713400	Active TSS	Right Atrium	heart
35	chr3:50712200-50713600	Active TSS	Stomach Smooth Muscle	stomach
36	chr3:50712200-50713800	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr3:50712200-50713800	Active TSS	Brain Cingulate Gyrus	brain
38	chr3:50712200-50714000	Active TSS	H1 Cell Line	embryonic stem cell
39	chr3:50712200-50714000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:50712200-50714000	Active TSS	Brain Hippocampus Middle	brain
41	chr3:50712200-50714200	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr3:50712200-50714400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:50712400-50713400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:50712600-50713200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:50712800-50713200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
46	chr3:50712800-50713200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
47	chr3:50712800-50713200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:50712800-50713200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
49	chr3:50712800-50713200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr3:50712800-50713200	Bivalent Enhancer	HUVEC	blood vessel

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