Variant report

Variant	rs5743834
Chromosome Location	chr3:52262323-52262324
allele	A/G
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	POLR2A	chr3:52262193-52262567	K562	blood:	n/a	n/a
2	POLR2A	chr3:52261323-52262605	K562	blood:	n/a	n/a
3	POLR2A	chr3:52261654-52262503	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:52261035-52264306	HL-60	blood:	n/a	n/a
5	POLR2A	chr3:52262215-52264058	K562	blood:	n/a	n/a
6	EGR1	chr3:52262289-52262610	K562	blood:	n/a	chr3:52262459-52262474 chr3:52262460-52262473 chr3:52262461-52262471 chr3:52262460-52262473 chr3:52262461-52262472 chr3:52262459-52262473 chr3:52262460-52262473

No.	Distal block	Cell Line	Cell type
1	chr3:52255294..52257505-chr3:52260666..52263088,3	K562	blood:
2	chr3:52251268..52253019-chr3:52261280..52262997,2	MCF-7	breast:
3	chr3:52259472..52263342-chr3:52269626..52274061,4	MCF-7	breast:
4	chr3:52261632..52263332-chr3:52263715..52265724,2	MCF-7	breast:

Variant related genes	Relation type
TLR9	TF binding region
ENSG00000173366	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000239732	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10212380	1.00[EUR][1000 genomes]
rs10212560	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10440116	1.00[EUR][1000 genomes]
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]
rs9813448	1.00[EUR][1000 genomes]
rs9813468	1.00[EUR][1000 genomes]
rs9813489	1.00[EUR][1000 genomes]
rs9813653	1.00[EUR][1000 genomes]
rs9815559	1.00[EUR][1000 genomes]
rs9821916	1.00[EUR][1000 genomes]
rs9824342	1.00[EUR][1000 genomes]
rs9828432	1.00[EUR][1000 genomes]
rs9828488	0.81[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	1.00[EUR][1000 genomes]
rs9843055	1.00[EUR][1000 genomes]
rs9844178	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9868332	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	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
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247200-52263000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:52249600-52263400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:52249800-52262400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52249800-52262400	Weak transcription	Aorta	Aorta
6	chr3:52250000-52262600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:52250200-52262800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:52251000-52266600	Weak transcription	Fetal Brain Male	brain
9	chr3:52251400-52263200	Weak transcription	A549	lung
10	chr3:52251600-52262400	Weak transcription	NHLF	lung
11	chr3:52251600-52262400	Weak transcription	Osteobl	bone
12	chr3:52251600-52262800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:52251600-52262800	Weak transcription	NHDF-Ad	bronchial
14	chr3:52251600-52263600	Weak transcription	HSMM	muscle
15	chr3:52251600-52264200	Weak transcription	HSMMtube	muscle
16	chr3:52251600-52266600	Weak transcription	Psoas Muscle	Psoas
17	chr3:52253000-52262800	Weak transcription	Small Intestine	intestine
18	chr3:52253200-52263000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:52253200-52269600	Weak transcription	Fetal Kidney	kidney
20	chr3:52253400-52262400	Weak transcription	NH-A	brain
21	chr3:52253400-52263400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:52253400-52264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:52253800-52263200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:52254000-52263000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:52255000-52262400	Weak transcription	Pancreas	Pancrea
26	chr3:52255000-52262600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:52255000-52262800	Weak transcription	Brain Angular Gyrus	brain
28	chr3:52255000-52263000	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:52255000-52263200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:52255000-52263800	Weak transcription	HUVEC	blood vessel
31	chr3:52255000-52263800	Weak transcription	K562	blood
32	chr3:52255000-52268600	Weak transcription	Right Atrium	heart
33	chr3:52255200-52262400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:52255200-52263200	Weak transcription	HMEC	breast
35	chr3:52255200-52263600	Weak transcription	Stomach Mucosa	stomach
36	chr3:52255200-52270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:52255400-52262800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:52255400-52264200	Weak transcription	Hela-S3	cervix
39	chr3:52256400-52263200	Weak transcription	Fetal Lung	lung
40	chr3:52256800-52262800	Weak transcription	Ovary	ovary
41	chr3:52259600-52268200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:52259800-52263200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:52260000-52263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:52260200-52262400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:52260200-52262800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:52260400-52263400	Genic enhancers	Fetal Thymus	thymus
47	chr3:52260600-52262600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:52260600-52265600	Strong transcription	Esophagus	oesophagus
49	chr3:52260800-52262400	Weak transcription	Fetal Intestine Large	intestine
50	chr3:52260800-52263000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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