Variant report

Variant	rs4687616
Chromosome Location	chr3:52501109-52501110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr3:52500722-52501131	HepG2	liver:	n/a	n/a
2	CEBPB	chr3:52500972-52501162	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52488409..52491834-chr3:52499773..52504333,5	K562	blood:
2	chr3:52498409..52502731-chr3:52503975..52506734,5	MCF-7	breast:

Variant related genes	Relation type
NISCH	TF binding region
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1011062	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1011064	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1035002	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1035003	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10865972	0.82[EUR][1000 genomes]
rs11721286	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13074649	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1541495	0.82[EUR][1000 genomes]
rs2109558	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2109559	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2215466	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2335928	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2335929	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3755810	0.88[EUR][1000 genomes]
rs3774409	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4312651	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687541	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687544	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687614	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4687617	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4687618	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687619	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687621	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6414568	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6445483	0.84[AMR][1000 genomes]
rs6445484	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6445485	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6445486	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6445506	0.84[EUR][1000 genomes]
rs676034	0.88[EUR][1000 genomes]
rs6771558	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6782162	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784615	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6787493	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6810027	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs728408	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs758800	0.90[EUR][1000 genomes]
rs758803	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7620015	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs887514	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs929528	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs929529	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9846089	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9847332	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9850471	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9855470	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9863753	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9867823	0.90[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52491400-52501600	Weak transcription	Right Atrium	heart
2	chr3:52491400-52502200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
4	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
5	chr3:52491800-52502400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:52491800-52502400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:52491800-52502800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:52491800-52506400	Weak transcription	Stomach Mucosa	stomach
9	chr3:52491800-52517200	Strong transcription	Fetal Stomach	stomach
10	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:52492000-52502400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:52492000-52502600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:52492000-52503400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:52492000-52516800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:52492000-52517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:52492200-52506200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:52493000-52502800	Strong transcription	Dnd41	blood
22	chr3:52493000-52506800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:52493200-52507000	Strong transcription	Fetal Thymus	thymus
25	chr3:52493400-52502200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:52493400-52504800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:52493400-52505000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:52493400-52505800	Weak transcription	Psoas Muscle	Psoas
29	chr3:52493400-52506000	Weak transcription	Hela-S3	cervix
30	chr3:52493400-52506000	Weak transcription	K562	blood
31	chr3:52493400-52506400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:52493600-52502400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:52495400-52503200	Weak transcription	Fetal Brain Male	brain
34	chr3:52495400-52504400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:52495400-52504800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:52495400-52505000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:52495400-52507600	Weak transcription	Fetal Kidney	kidney
38	chr3:52495600-52505000	Weak transcription	Aorta	Aorta
39	chr3:52495600-52506200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:52496200-52504800	Weak transcription	Colonic Mucosa	Colon
41	chr3:52496600-52501400	Weak transcription	Ovary	ovary
42	chr3:52497200-52504200	Weak transcription	Brain Germinal Matrix	brain
43	chr3:52497200-52504200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:52497400-52505600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:52497600-52502400	Weak transcription	HMEC	breast
46	chr3:52497600-52502800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:52497800-52503400	Strong transcription	Pancreas	Pancrea
48	chr3:52498000-52502400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:52498000-52506400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:52498400-52502600	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links