Variant report

Variant	rs56961704
Chromosome Location	chr3:52577632-52577633
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52575876..52580851-chr3:52582310..52586446,4	MCF-7	breast:
2	chr3:52574434..52577960-chr3:52578839..52582098,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252768	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs3890123	1.00[AMR][1000 genomes]
rs55971019	1.00[AMR][1000 genomes]
rs56898787	1.00[AMR][1000 genomes]
rs58781613	1.00[AMR][1000 genomes]
rs60499166	1.00[AMR][1000 genomes]
rs60997031	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61734628	1.00[AMR][1000 genomes]
rs6766038	1.00[AMR][1000 genomes]
rs73837049	1.00[AMR][1000 genomes]
rs73837599	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73838354	1.00[AMR][1000 genomes]
rs73839116	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839117	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7638914	1.00[AMR][1000 genomes]
rs7641255	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52571400-52594200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52572200-52581000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:52572200-52584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52572400-52578800	Weak transcription	A549	lung
5	chr3:52572400-52580600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:52572400-52581800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:52572400-52594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52573200-52578600	Weak transcription	Brain Germinal Matrix	brain
10	chr3:52573200-52579000	Weak transcription	Thymus	Thymus
11	chr3:52573200-52582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:52573200-52583400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:52573200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52573200-52586400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:52573200-52589600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:52573200-52590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:52573400-52580600	Weak transcription	Fetal Brain Male	brain
18	chr3:52573400-52585200	Weak transcription	Small Intestine	intestine
19	chr3:52573400-52595000	Weak transcription	Stomach Mucosa	stomach
20	chr3:52573600-52578400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:52573600-52578600	Weak transcription	Aorta	Aorta
22	chr3:52573600-52578800	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:52573600-52578800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:52573600-52578800	Weak transcription	Fetal Brain Female	brain
25	chr3:52573600-52580600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:52573600-52580600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:52573600-52581200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:52573600-52581200	Weak transcription	Esophagus	oesophagus
29	chr3:52573600-52582000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52573600-52582000	Weak transcription	Ovary	ovary
31	chr3:52573600-52583200	Weak transcription	Colonic Mucosa	Colon
32	chr3:52573600-52598400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:52573800-52579000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:52573800-52584600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:52574200-52578800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:52574200-52578800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:52574200-52581800	Weak transcription	Pancreas	Pancrea
38	chr3:52574200-52583200	Weak transcription	Spleen	Spleen
39	chr3:52574200-52588400	Strong transcription	Liver	Liver
40	chr3:52574400-52580600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:52574400-52581200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:52574400-52623800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:52574600-52594200	Weak transcription	K562	blood
44	chr3:52574600-52598800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:52574800-52579600	Strong transcription	Fetal Stomach	stomach
46	chr3:52574800-52605000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:52575000-52579000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:52575200-52580400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:52575200-52580600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:52575400-52580600	Weak transcription	Primary T cells from cord blood	blood

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