Variant report

Variant	rs72789316
Chromosome Location	chr5:108302855-108302856
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	chr5:108300744..108303743-chr5:108308321..108310024,2	MCF-7	breast:

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs11742595	0.82[AFR][1000 genomes]
rs11948881	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11949066	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11949367	0.91[EUR][1000 genomes]
rs11949510	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11949619	0.91[EUR][1000 genomes]
rs11949648	0.93[EUR][1000 genomes]
rs11949706	0.93[EUR][1000 genomes]
rs11951971	0.93[EUR][1000 genomes]
rs11951974	0.93[EUR][1000 genomes]
rs11952227	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11952572	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11953136	0.93[EUR][1000 genomes]
rs11953486	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11954716	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11954988	0.93[EUR][1000 genomes]
rs11955886	0.93[EUR][1000 genomes]
rs11956908	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11957358	0.91[EUR][1000 genomes]
rs11958918	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11959492	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11959577	0.90[EUR][1000 genomes]
rs11959681	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11960713	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17534354	0.89[EUR][1000 genomes]
rs34412145	0.93[EUR][1000 genomes]
rs34679271	0.85[EUR][1000 genomes]
rs3851457	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3851458	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134914	0.80[EUR][1000 genomes]
rs56381733	0.88[EUR][1000 genomes]
rs57404758	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57622369	0.91[EUR][1000 genomes]
rs59055229	0.88[EUR][1000 genomes]
rs59216020	0.93[EUR][1000 genomes]
rs60946864	0.93[EUR][1000 genomes]
rs66485253	0.84[EUR][1000 genomes]
rs66834040	0.83[EUR][1000 genomes]
rs67156774	0.84[EUR][1000 genomes]
rs67338203	0.88[EUR][1000 genomes]
rs72787096	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72787098	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72787099	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72787100	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72787101	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72787102	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789304	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789305	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72789306	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789307	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789308	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789309	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72789312	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72789313	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72789315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72789319	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789320	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72789326	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789332	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789333	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72789335	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789341	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789345	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789347	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789348	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789350	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789352	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72790510	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790512	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790514	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790515	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72790520	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72790521	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72790524	0.93[EUR][1000 genomes]
rs72790525	0.93[EUR][1000 genomes]
rs72790528	0.93[EUR][1000 genomes]
rs72790529	0.93[EUR][1000 genomes]
rs72790530	0.93[EUR][1000 genomes]
rs72790538	0.93[EUR][1000 genomes]
rs72790539	0.93[EUR][1000 genomes]
rs72790542	0.93[EUR][1000 genomes]
rs72790545	0.93[EUR][1000 genomes]
rs72790546	0.93[EUR][1000 genomes]
rs72790548	0.91[EUR][1000 genomes]
rs72790551	0.93[EUR][1000 genomes]
rs72790552	0.93[EUR][1000 genomes]
rs72790559	0.90[EUR][1000 genomes]
rs72790562	0.91[EUR][1000 genomes]
rs72790565	0.91[EUR][1000 genomes]
rs72790567	0.91[EUR][1000 genomes]
rs72790568	0.91[EUR][1000 genomes]
rs72790574	0.91[EUR][1000 genomes]
rs72790577	0.91[EUR][1000 genomes]
rs72790579	0.91[EUR][1000 genomes]
rs72792001	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72793903	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72793905	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72793906	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72793909	0.87[EUR][1000 genomes]
rs72793918	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72793920	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72793922	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72793923	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72793926	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72793927	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72793930	0.83[EUR][1000 genomes]
rs72793933	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73209347	0.84[EUR][1000 genomes]
rs7723264	0.80[EUR][1000 genomes]
rs7723604	0.80[EUR][1000 genomes]
rs7734904	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7735425	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs919771	0.88[EUR][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	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108203800-108323400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:108217600-108323200	Weak transcription	Left Ventricle	heart
3	chr5:108254000-108311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:108277600-108322400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:108278000-108308200	Weak transcription	Fetal Kidney	kidney
6	chr5:108279200-108325600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:108281000-108313400	Weak transcription	Adipose Nuclei	Adipose
8	chr5:108282200-108324600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:108282400-108327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:108283400-108319000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:108287800-108310000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:108289200-108309200	Weak transcription	Hela-S3	cervix
13	chr5:108289200-108318600	Weak transcription	NHDF-Ad	bronchial
14	chr5:108290000-108313600	Weak transcription	Aorta	Aorta
15	chr5:108290000-108322000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:108290000-108328800	Weak transcription	Esophagus	oesophagus
17	chr5:108293400-108303400	Weak transcription	Fetal Lung	lung
18	chr5:108293400-108325600	Weak transcription	NHEK	skin
19	chr5:108294400-108329400	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:108295200-108319400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:108295800-108316600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:108296600-108307800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:108296600-108311800	Weak transcription	HSMMtube	muscle
24	chr5:108297000-108313400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:108298000-108316400	Weak transcription	Brain Substantia Nigra	brain
26	chr5:108298200-108315800	Weak transcription	HepG2	liver
27	chr5:108299600-108328800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:108300400-108314200	Weak transcription	NH-A	brain
29	chr5:108301400-108328600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:108301600-108361200	Weak transcription	Primary T cells from cord blood	blood
31	chr5:108301800-108318600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:108302200-108330200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:108302400-108303000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr5:108302400-108303000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:108302400-108303000	Strong transcription	HSMM	muscle
36	chr5:108302400-108303200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:108302400-108303200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:108302400-108303200	ZNF genes & repeats	Dnd41	blood
39	chr5:108302600-108303000	ZNF genes & repeats	Brain Angular Gyrus	brain
40	chr5:108302600-108303000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
41	chr5:108302600-108303000	ZNF genes & repeats	Pancreas	Pancrea
42	chr5:108302600-108303200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:108302600-108303200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:108302600-108303200	ZNF genes & repeats	Liver	Liver
45	chr5:108302600-108303200	ZNF genes & repeats	Fetal Stomach	stomach
46	chr5:108302600-108303200	ZNF genes & repeats	Ovary	ovary
47	chr5:108302600-108303200	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr5:108302600-108303400	ZNF genes & repeats	Fetal Muscle Leg	muscle
49	chr5:108302600-108303600	Strong transcription	HMEC	breast
50	chr5:108302600-108303800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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