Variant report

Variant	rs72965257
Chromosome Location	chr3:52486973-52486974
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	EGR1	chr3:52486718-52487092	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr3:52486592-52487164	ECC-1	luminal epithelium:	n/a	chr3:52486724-52486739 chr3:52486755-52486770
3	ZBTB7A	chr3:52486533-52487484	ECC-1	luminal epithelium:	n/a	n/a
4	ESR1	chr3:52486609-52487045	ECC-1	luminal epithelium:	n/a	chr3:52486724-52486739 chr3:52486755-52486770
5	ESR1	chr3:52486560-52487120	ECC-1	luminal epithelium:	n/a	chr3:52486724-52486739 chr3:52486755-52486770
6	ESR1	chr3:52486490-52487109	ECC-1	luminal epithelium:	n/a	chr3:52486724-52486739 chr3:52486755-52486770
7	NR3C1	chr3:52486816-52487092	ECC-1	luminal epithelium:	n/a	n/a
8	EGR1	chr3:52486644-52487180	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52481830..52487806-chr3:52487911..52490298,8	K562	blood:
2	chr3:52486786..52490623-chr3:52738506..52740742,3	MCF-7	breast:
3	chr3:52312419..52314160-chr3:52485786..52488594,2	MCF-7	breast:

Variant related genes	Relation type
NISCH	TF binding region
TNNC1	TF binding region
ENSG00000114854	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs56898787	1.00[EUR][1000 genomes]
rs58781613	1.00[EUR][1000 genomes]
rs59528332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61734628	1.00[EUR][1000 genomes]
rs61737029	1.00[EUR][1000 genomes]
rs7641255	1.00[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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52478800-52487600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:52479400-52487200	Weak transcription	GM12878-XiMat	blood
3	chr3:52479400-52488200	Weak transcription	Colonic Mucosa	Colon
4	chr3:52479600-52487000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:52479600-52487400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:52479600-52487600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:52479600-52487600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:52479600-52487800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:52481200-52487600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:52481200-52490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:52481400-52487400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:52481400-52488200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:52481600-52487000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:52481600-52487200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:52483800-52489000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:52483800-52489200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:52484000-52488000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
18	chr3:52484200-52487800	Weak transcription	Spleen	Spleen
19	chr3:52484400-52487200	Weak transcription	Esophagus	oesophagus
20	chr3:52484600-52487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:52484600-52487400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:52484600-52487600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:52484600-52487800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:52484600-52487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:52484600-52488400	Weak transcription	NHEK	skin
26	chr3:52484600-52488800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:52484600-52489200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:52484800-52487600	Weak transcription	Lung	lung
29	chr3:52484800-52489000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:52484800-52489000	Weak transcription	NH-A	brain
31	chr3:52485000-52488000	Active TSS	Right Atrium	heart
32	chr3:52485000-52488200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:52485000-52488600	Weak transcription	Liver	Liver
34	chr3:52485000-52488600	Weak transcription	HMEC	breast
35	chr3:52485200-52489200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:52485400-52489000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:52485600-52487600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:52485600-52489400	Flanking Active TSS	HepG2	liver
39	chr3:52486200-52487200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:52486200-52487200	Enhancers	Fetal Muscle Leg	muscle
41	chr3:52486200-52487400	Weak transcription	Placenta	Placenta
42	chr3:52486200-52487600	Active TSS	Fetal Heart	heart
43	chr3:52486200-52487800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:52486200-52488600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:52486200-52489200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:52486400-52487200	Weak transcription	Psoas Muscle	Psoas
47	chr3:52486400-52487200	Enhancers	Stomach Mucosa	stomach
48	chr3:52486400-52488200	Active TSS	Right Ventricle	heart
49	chr3:52486400-52488400	Active TSS	Left Ventricle	heart
50	chr3:52486400-52488800	Weak transcription	Fetal Brain Female	brain

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