Variant report

Variant	rs9813489
Chromosome Location	chr3:52326751-52326752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52326721-52333108	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52318594..52322784-chr3:52322985..52327026,4	MCF-7	breast:
2	chr3:52309930..52312660-chr3:52325068..52328067,2	K562	blood:
3	chr3:52321086..52323733-chr3:52324166..52327461,5	MCF-7	breast:
4	chr3:52326037..52327688-chr3:52417410..52420365,2	K562	blood:
5	chr3:52324588..52327004-chr3:52442941..52444727,2	MCF-7	breast:
6	chr11:64544225..64546734-chr3:52326528..52328188,2	MCF-7	breast:

No data

Variant related genes	Relation type
WDR82	TF binding region
ENSG00000163930	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10212380	1.00[EUR][1000 genomes]
rs10212560	1.00[EUR][1000 genomes]
rs10440116	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865972	0.90[LWK][hapmap]
rs1541495	0.90[LWK][hapmap]
rs17052143	1.00[EUR][1000 genomes]
rs28413740	1.00[EUR][1000 genomes]
rs28434358	1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	1.00[EUR][1000 genomes]
rs4687614	0.90[LWK][hapmap]
rs5743834	1.00[EUR][1000 genomes]
rs5743846	1.00[CHB][hapmap]
rs9813448	1.00[EUR][1000 genomes]
rs9813468	1.00[EUR][1000 genomes]
rs9813653	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9815559	1.00[EUR][1000 genomes]
rs9821916	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9824342	1.00[EUR][1000 genomes]
rs9828432	1.00[EUR][1000 genomes]
rs9828488	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9831689	1.00[EUR][1000 genomes]
rs9834363	1.00[EUR][1000 genomes]
rs9836166	1.00[EUR][1000 genomes]
rs9842960	0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[EUR][1000 genomes]
rs9843055	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[EUR][1000 genomes]
rs9844178	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	1.00[EUR][1000 genomes]
rs9857947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9868332	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers 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	45 gene(s)	inside rSNPs	diseases
10	esv3402579	chr3:52323712-52330410	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52322600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52322600-52332000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
4	chr3:52322800-52330800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:52322800-52331400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:52322800-52331400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52322800-52331600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:52322800-52331800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:52323000-52328200	Weak transcription	Psoas Muscle	Psoas
10	chr3:52323000-52332600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
12	chr3:52323400-52333200	Weak transcription	HUVEC	blood vessel
13	chr3:52323600-52326800	Weak transcription	Hela-S3	cervix
14	chr3:52323600-52328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:52323600-52330400	Weak transcription	HSMM	muscle
16	chr3:52323800-52329800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:52324000-52331800	Weak transcription	K562	blood
18	chr3:52324000-52332800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:52324200-52328200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:52324200-52331400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:52324400-52328800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:52324400-52328800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:52324400-52329600	Strong transcription	Thymus	Thymus
24	chr3:52324400-52330200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:52324400-52331000	Strong transcription	Primary T cells from cord blood	blood
26	chr3:52324400-52332000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:52324600-52326800	Genic enhancers	Gastric	stomach
28	chr3:52324600-52327800	Strong transcription	Esophagus	oesophagus
29	chr3:52324600-52328200	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr3:52324600-52329000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:52324600-52329200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:52324600-52329400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:52324600-52329600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:52324600-52329600	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:52324600-52330200	Strong transcription	Placenta	Placenta
36	chr3:52324600-52330400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:52324600-52330600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:52324800-52326800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:52324800-52327200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:52324800-52327200	Strong transcription	Left Ventricle	heart
41	chr3:52324800-52327200	Strong transcription	Dnd41	blood
42	chr3:52324800-52327200	Strong transcription	GM12878-XiMat	blood
43	chr3:52324800-52327400	Strong transcription	Brain Anterior Caudate	brain
44	chr3:52324800-52327800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:52324800-52328000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52324800-52328000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:52324800-52328200	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:52324800-52328200	Strong transcription	NHLF	lung
49	chr3:52324800-52328400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:52324800-52329000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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