Variant report

Variant	rs724801
Chromosome Location	chr3:52488517-52488518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr3:52487839-52488695	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr3:52488419-52489898	K562	blood:	n/a	n/a
3	HCFC1	chr3:52488514-52490426	Hela-S3	cervix:	n/a	n/a
4	NFIC	chr3:52487889-52488773	ECC-1	luminal epithelium:	n/a	n/a
5	SPI1	chr3:52488394-52488876	HL-60	blood:	n/a	chr3:52488620-52488633 chr3:52488822-52488835
6	MAZ	chr3:52488507-52488546	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:52487592-52491009	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52486786..52490623-chr3:52738506..52740742,3	MCF-7	breast:
2	chr3:52487939..52491238-chr3:52504089..52507877,6	MCF-7	breast:
3	chr3:52312419..52314160-chr3:52485786..52488594,2	MCF-7	breast:
4	chr3:52487901..52490154-chr3:52491189..52493164,2	K562	blood:
5	chr3:52488362..52490407-chr3:52528579..52530282,2	K562	blood:
6	chr3:52487897..52490713-chr3:52565636..52568320,3	K562	blood:
7	chr3:52488315..52491899-chr3:52569459..52572680,4	MCF-7	breast:
8	chr3:52487997..52491865-chr3:52718755..52722667,5	MCF-7	breast:
9	chr3:52485198..52486814-chr3:52487911..52490387,2	K562	blood:
10	chr3:52447983..52449593-chr3:52487471..52490265,2	K562	blood:
11	chr3:52488081..52492441-chr3:52568649..52570860,4	K562	blood:
12	chr3:52481830..52487806-chr3:52487911..52490298,8	K562	blood:

No data

Variant related genes	Relation type
NISCH	TF binding region
TNNC1	TF binding region
ENSG00000016864	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10461028	0.80[EUR][1000 genomes]
rs10865971	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11706515	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11707056	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11708581	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11708811	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11710014	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11713914	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11714358	0.82[EUR][1000 genomes]
rs11715208	0.82[EUR][1000 genomes]
rs11716487	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11717028	0.85[EUR][1000 genomes]
rs11720365	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11721277	0.88[EUR][1000 genomes]
rs1319202	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17052051	1.00[CEU][hapmap]
rs17052052	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17052053	0.91[CEU][hapmap]
rs17052054	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17263770	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1767	0.92[CEU][hapmap]
rs1769	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs35976326	0.82[EUR][1000 genomes]
rs3733063	0.91[CEU][hapmap]
rs3886875	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs55676974	0.82[EUR][1000 genomes]
rs55806905	0.88[EUR][1000 genomes]
rs55813842	0.88[EUR][1000 genomes]
rs56002041	0.88[EUR][1000 genomes]
rs56322342	0.88[EUR][1000 genomes]
rs56899118	0.88[EUR][1000 genomes]
rs57849650	0.88[EUR][1000 genomes]
rs61644644	0.82[EUR][1000 genomes]
rs6445385	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6776759	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6783652	0.82[EUR][1000 genomes]
rs6793317	0.91[CEU][hapmap]
rs729555	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73072990	0.94[EUR][1000 genomes]
rs73088791	0.82[EUR][1000 genomes]
rs73091166	0.88[EUR][1000 genomes]
rs73091168	0.88[EUR][1000 genomes]
rs746239	0.88[EUR][1000 genomes]
rs7615405	0.85[EUR][1000 genomes]
rs7633687	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7643913	0.88[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv876794	chr3:52485876-52496229	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52481200-52490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52483800-52489000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52483800-52489200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:52484600-52488800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:52484600-52489200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:52484800-52489000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:52484800-52489000	Weak transcription	NH-A	brain
8	chr3:52485000-52488600	Weak transcription	Liver	Liver
9	chr3:52485000-52488600	Weak transcription	HMEC	breast
10	chr3:52485200-52489200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:52485400-52489000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:52485600-52489400	Flanking Active TSS	HepG2	liver
13	chr3:52486200-52488600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:52486200-52489200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:52486400-52488800	Weak transcription	Fetal Brain Female	brain
16	chr3:52486600-52488600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr3:52486600-52489000	Enhancers	Fetal Intestine Small	intestine
18	chr3:52486600-52489200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:52486600-52489200	Enhancers	Gastric	stomach
20	chr3:52486800-52488600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:52486800-52488800	Enhancers	Fetal Intestine Large	intestine
22	chr3:52486800-52489000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:52486800-52489000	Enhancers	A549	lung
24	chr3:52487000-52488600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:52487000-52488600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr3:52487200-52488600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:52487200-52488600	Enhancers	Primary T cells fromperipheralblood	blood
28	chr3:52487200-52488600	Enhancers	GM12878-XiMat	blood
29	chr3:52487200-52488800	Enhancers	Esophagus	oesophagus
30	chr3:52487200-52489000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:52487200-52489000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:52487200-52489000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:52487200-52489000	Enhancers	Fetal Lung	lung
34	chr3:52487200-52489400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:52487400-52488600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:52487400-52488600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr3:52487400-52488600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:52487400-52489000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:52487400-52489000	Enhancers	Placenta	Placenta
40	chr3:52487400-52489000	Enhancers	Fetal Thymus	thymus
41	chr3:52487600-52488600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:52487600-52488800	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr3:52487600-52489000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:52487600-52489000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:52487800-52488600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:52487800-52488800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:52487800-52488800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:52487800-52488800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:52487800-52488800	Enhancers	Pancreas	Pancrea
50	chr3:52487800-52489000	Enhancers	HUES64 Cell Line	embryonic stem cell

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