Variant report

Variant	rs6790314
Chromosome Location	chr3:52871107-52871108
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	chr3:52865265..52868196-chr3:52870244..52872785,3	K562	blood:
2	chr3:52866935..52869268-chr3:52870360..52872444,2	K562	blood:

Variant related genes	Relation type
ENSG00000272573	Chromatin interaction
ENSG00000243696	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13072536	0.89[YRI][hapmap]
rs13083728	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs13325325	1.00[MEX][hapmap]
rs1573815	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs2239547	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs2276815	0.88[YRI][hapmap]
rs2276817	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs2276825	0.89[YRI][hapmap]
rs3733047	0.81[ASW][hapmap];0.82[YRI][hapmap]
rs4687554	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs4687657	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs4687658	0.89[YRI][hapmap]
rs4687663	0.89[YRI][hapmap]
rs6445538	0.89[ASW][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs6445539	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6803519	0.89[YRI][hapmap]
rs9682464	0.88[YRI][hapmap]
rs9836894	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:52865600-52875200	Weak transcription	Dnd41	blood
9	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
10	chr3:52866000-52884800	Weak transcription	HMEC	breast
11	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
13	chr3:52866200-52885200	Weak transcription	NHEK	skin
14	chr3:52866400-52871800	Strong transcription	Primary T cells from cord blood	blood
15	chr3:52866400-52872400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:52866600-52873600	Weak transcription	Hela-S3	cervix
17	chr3:52866600-52879200	Weak transcription	Osteobl	bone
18	chr3:52866800-52872000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
21	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
22	chr3:52867000-52871200	Weak transcription	Pancreas	Pancrea
23	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:52867200-52871400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:52867600-52871800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:52867800-52871200	Enhancers	Right Ventricle	heart
30	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:52868400-52871400	Enhancers	Fetal Heart	heart
33	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
34	chr3:52868600-52872000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:52868600-52875200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:52868800-52873000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:52868800-52876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:52869000-52873400	Strong transcription	Brain Anterior Caudate	brain
39	chr3:52869000-52878800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:52869000-52879400	Strong transcription	Fetal Intestine Small	intestine
41	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
42	chr3:52869200-52871200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:52869200-52871600	Enhancers	Right Atrium	heart
44	chr3:52869200-52871800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:52869200-52871800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr3:52869200-52873000	Strong transcription	Primary B cells from cord blood	blood
47	chr3:52869400-52871200	Enhancers	Left Ventricle	heart
48	chr3:52869400-52872800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:52869400-52874200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:52869400-52875200	Weak transcription	Muscle Satellite Cultured Cells	--

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