Variant report

Variant	rs6863202
Chromosome Location	chr5:178306719-178306720
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	chr5:178306684..178308564-chr5:178323715..178325258,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10039708	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11249599	0.82[EUR][1000 genomes]
rs11948175	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11948664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11948690	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949180	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949181	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949892	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949941	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11950641	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11950746	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11952790	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11954382	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11955047	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11958804	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11958887	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11958941	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11960942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12186577	0.82[EUR][1000 genomes]
rs12186584	0.83[EUR][1000 genomes]
rs12187167	0.83[EUR][1000 genomes]
rs12553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1566106	0.93[EUR][1000 genomes]
rs28539861	0.80[EUR][1000 genomes]
rs35609799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35957383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56814168	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56872885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56932649	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56951084	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57153194	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57426447	0.93[EUR][1000 genomes]
rs58354049	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58554591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58672680	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58679434	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58941917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59242428	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59736551	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59829327	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59849584	0.83[EUR][1000 genomes]
rs59994898	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60178472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60277514	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60417551	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60601817	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60813042	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61295075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61310482	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61492890	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61744382	0.83[EUR][1000 genomes]
rs62395084	0.81[EUR][1000 genomes]
rs6600991	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6859174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6861717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6863160	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6863603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6865216	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6866591	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6870926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6877663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6878353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6882396	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6883566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6887256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6890083	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6894878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6895371	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7706558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7724141	0.82[EUR][1000 genomes]
rs7727497	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7729560	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7729717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7731067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
5	chr5:178296000-178319200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr5:178296200-178315600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr5:178296200-178319200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:178296400-178311200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
9	chr5:178296400-178317600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr5:178297200-178315800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
11	chr5:178297400-178315600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr5:178297400-178317400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:178297400-178317400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
14	chr5:178297400-178317400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:178297600-178317400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:178298800-178317800	ZNF genes & repeats	Primary T cells from cord blood	blood
17	chr5:178299000-178310600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
18	chr5:178299000-178317600	ZNF genes & repeats	Fetal Brain Female	brain
19	chr5:178299200-178314000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr5:178299400-178310200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:178299400-178317400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:178299600-178309000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
23	chr5:178299600-178317400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
24	chr5:178299800-178317400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:178299800-178317600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:178300200-178311400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
27	chr5:178300200-178315600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
28	chr5:178301000-178307400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:178301000-178308600	ZNF genes & repeats	Lung	lung
30	chr5:178301000-178308800	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr5:178301000-178308800	ZNF genes & repeats	Fetal Stomach	stomach
32	chr5:178301000-178308800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
33	chr5:178301000-178314800	ZNF genes & repeats	Fetal Muscle Leg	muscle
34	chr5:178301000-178317400	ZNF genes & repeats	Adipose Nuclei	Adipose
35	chr5:178301200-178308800	ZNF genes & repeats	Fetal Thymus	thymus
36	chr5:178301200-178309600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:178301400-178311400	ZNF genes & repeats	Fetal Intestine Large	intestine
38	chr5:178301400-178317200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:178301600-178317600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:178302200-178306800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:178302800-178317600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:178303400-178307600	Weak transcription	K562	blood
43	chr5:178303400-178310200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:178303600-178306800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr5:178304200-178307600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:178304400-178308200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:178304800-178307600	Weak transcription	HSMMtube	muscle
48	chr5:178305000-178307400	Weak transcription	Osteobl	bone
49	chr5:178305000-178307600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:178305000-178307600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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