Variant report

Variant	rs41292362
Chromosome Location	chr3:52487265-52487266
allele	C/T
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	ZBTB7A	chr3:52486533-52487484	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
ENSG00000114902	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs28997577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35338461	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35342983	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35491443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35654187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41292366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41292370	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55921270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56326215	1.00[EUR][1000 genomes]
rs5743845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59078569	1.00[EUR][1000 genomes]
rs59410274	1.00[EUR][1000 genomes]
rs61418167	1.00[EUR][1000 genomes]
rs61729402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61729450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61734637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61734643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61734653	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61736838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61739897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61749019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][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:74 , 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	chr3:52479400-52488200	Weak transcription	Colonic Mucosa	Colon
3	chr3:52479600-52487400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:52479600-52487600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:52479600-52487600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:52479600-52487800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:52481200-52487600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:52481200-52490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:52481400-52487400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:52481400-52488200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:52483800-52489000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:52483800-52489200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:52484000-52488000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
14	chr3:52484200-52487800	Weak transcription	Spleen	Spleen
15	chr3:52484600-52487400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:52484600-52487600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:52484600-52487800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:52484600-52487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:52484600-52488400	Weak transcription	NHEK	skin
20	chr3:52484600-52488800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:52484600-52489200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:52484800-52487600	Weak transcription	Lung	lung
23	chr3:52484800-52489000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:52484800-52489000	Weak transcription	NH-A	brain
25	chr3:52485000-52488000	Active TSS	Right Atrium	heart
26	chr3:52485000-52488200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:52485000-52488600	Weak transcription	Liver	Liver
28	chr3:52485000-52488600	Weak transcription	HMEC	breast
29	chr3:52485200-52489200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52485400-52489000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:52485600-52487600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:52485600-52489400	Flanking Active TSS	HepG2	liver
33	chr3:52486200-52487400	Weak transcription	Placenta	Placenta
34	chr3:52486200-52487600	Active TSS	Fetal Heart	heart
35	chr3:52486200-52487800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:52486200-52488600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:52486200-52489200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:52486400-52488200	Active TSS	Right Ventricle	heart
39	chr3:52486400-52488400	Active TSS	Left Ventricle	heart
40	chr3:52486400-52488800	Weak transcription	Fetal Brain Female	brain
41	chr3:52486600-52487400	Enhancers	Hela-S3	cervix
42	chr3:52486600-52488000	Flanking Active TSS	HSMM	muscle
43	chr3:52486600-52488600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr3:52486600-52489000	Enhancers	Fetal Intestine Small	intestine
45	chr3:52486600-52489200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr3:52486600-52489200	Enhancers	Gastric	stomach
47	chr3:52486800-52487600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:52486800-52487800	Weak transcription	Pancreas	Pancrea
49	chr3:52486800-52488200	Active TSS	HSMMtube	muscle
50	chr3:52486800-52488600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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