Variant report

Variant	rs62289280
Chromosome Location	chr4:7812818-7812819
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	chr4:7808655..7810334-chr4:7810904..7813896,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11721583	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11721609	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11724632	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11728778	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11729332	0.88[EUR][1000 genomes]
rs11729602	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11730169	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11731942	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11733311	0.84[EUR][1000 genomes]
rs11734524	0.87[EUR][1000 genomes]
rs11734860	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11737447	0.85[EUR][1000 genomes]
rs13113113	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13117918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13121514	0.81[AFR][1000 genomes]
rs13125295	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13132939	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17382379	0.86[EUR][1000 genomes]
rs17382393	0.86[EUR][1000 genomes]
rs17466895	0.86[EUR][1000 genomes]
rs34250310	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34352176	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34949259	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35041036	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35161247	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35281689	0.84[AFR][1000 genomes]
rs35509185	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35515779	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35592594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35617438	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35672467	0.91[AFR][1000 genomes]
rs35870249	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35889107	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3934645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41264705	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4443284	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4594724	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55698135	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55740648	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56270003	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56352084	0.84[EUR][1000 genomes]
rs58457272	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61036795	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62289276	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62291980	0.86[EUR][1000 genomes]
rs62291982	0.84[AFR][1000 genomes]
rs62291983	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62291984	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs885260	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs885261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
3	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr4:7800600-7828800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:7802200-7819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:7804000-7829200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:7805200-7822600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:7805600-7816400	Genic enhancers	Fetal Stomach	stomach
10	chr4:7806000-7814000	Enhancers	Adipose Nuclei	Adipose
11	chr4:7806200-7819200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:7806400-7824600	Weak transcription	Fetal Thymus	thymus
13	chr4:7807800-7817800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:7808000-7823000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:7808600-7814000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr4:7808600-7830000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:7808800-7818400	Weak transcription	Psoas Muscle	Psoas
18	chr4:7809200-7813400	Genic enhancers	Fetal Muscle Leg	muscle
19	chr4:7809200-7816600	Weak transcription	Fetal Brain Male	brain
20	chr4:7809400-7813200	Strong transcription	Fetal Brain Female	brain
21	chr4:7809400-7814800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:7809400-7814800	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr4:7809400-7815200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:7809600-7813200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:7809600-7814000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:7809600-7815600	Weak transcription	Brain Anterior Caudate	brain
27	chr4:7809600-7819000	Genic enhancers	A549	lung
28	chr4:7809600-7822400	Weak transcription	Brain Substantia Nigra	brain
29	chr4:7809600-7823000	Weak transcription	Brain Angular Gyrus	brain
30	chr4:7809600-7828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:7809800-7813000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:7809800-7813200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:7809800-7813400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:7809800-7814200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:7809800-7820000	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:7809800-7823400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:7809800-7823400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:7810000-7813000	Strong transcription	Brain Germinal Matrix	brain
39	chr4:7810000-7815400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:7810000-7816200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:7810000-7816200	Weak transcription	Aorta	Aorta
42	chr4:7810000-7823400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:7810200-7821000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:7810400-7813600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:7810600-7813800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:7810600-7814600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:7810600-7814800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:7810600-7814800	Strong transcription	Osteobl	bone
49	chr4:7810600-7816200	Weak transcription	Left Ventricle	heart
50	chr4:7810800-7813200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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