Variant report

Variant	rs4687543
Chromosome Location	chr3:52510982-52510983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52510130..52511955-chr3:52570408..52572081,2	MCF-7	breast:
2	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
3	chr3:52508946..52511340-chr3:52565152..52566782,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168268	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000168273	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1011062	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1011063	0.83[ASN][1000 genomes]
rs1011064	0.85[EUR][1000 genomes]
rs1035002	0.83[EUR][1000 genomes]
rs1035003	0.85[EUR][1000 genomes]
rs10865972	0.89[EUR][1000 genomes]
rs11721286	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13074649	0.85[EUR][1000 genomes]
rs1541495	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2109558	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2109559	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2215466	0.83[EUR][1000 genomes]
rs2335928	0.83[EUR][1000 genomes]
rs2335929	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34261027	0.83[ASN][1000 genomes]
rs3755810	0.83[EUR][1000 genomes]
rs3774409	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs409803	0.81[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs4312651	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4687541	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4687544	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687614	0.83[EUR][1000 genomes]
rs4687617	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687618	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4687619	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4687621	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs613519	0.81[EUR][1000 genomes]
rs6414568	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6445484	0.85[EUR][1000 genomes]
rs6445485	0.85[EUR][1000 genomes]
rs6445486	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6445506	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs676034	0.83[EUR][1000 genomes]
rs6771558	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6782162	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6784615	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6787493	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6800707	0.83[ASN][1000 genomes]
rs6810027	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs728408	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs758800	0.85[EUR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7620015	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs887514	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs887515	0.83[ASN][1000 genomes]
rs929528	0.85[EUR][1000 genomes]
rs929529	0.83[EUR][1000 genomes]
rs9846089	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9847332	0.85[EUR][1000 genomes]
rs9850471	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9855470	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9863753	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9867823	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
2	chr3:52491800-52517200	Strong transcription	Fetal Stomach	stomach
3	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:52492000-52516800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:52492000-52517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:52499200-52517200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
14	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:52500200-52517000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:52501000-52515200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
18	chr3:52502800-52517200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:52503400-52517200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:52504200-52517200	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr3:52504200-52526600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr3:52504200-52526800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:52504200-52527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:52504200-52527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:52504200-52527600	Strong transcription	Dnd41	blood
26	chr3:52504200-52527800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:52504200-52528000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:52504200-52528000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
30	chr3:52504400-52517000	Strong transcription	GM12878-XiMat	blood
31	chr3:52504400-52517400	Strong transcription	NHEK	skin
32	chr3:52504400-52517600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:52504400-52523600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:52504400-52523800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:52504400-52527400	Strong transcription	Osteobl	bone
36	chr3:52504400-52527600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:52504400-52527600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:52504400-52528000	Strong transcription	Fetal Brain Female	brain
39	chr3:52504600-52515800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:52504600-52517000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:52504600-52517000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:52504600-52517000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:52504600-52517000	Strong transcription	HSMMtube	muscle
44	chr3:52504600-52517200	Strong transcription	NH-A	brain
45	chr3:52504600-52517400	Strong transcription	Fetal Lung	lung
46	chr3:52504600-52518000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:52504800-52516200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:52504800-52517000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:52504800-52517200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:52504800-52517200	Strong transcription	Colon Smooth Muscle	Colon

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