Variant report

Variant	rs12084507
Chromosome Location	chr1:56983704-56983705
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	POLR2A	chr1:56981456-56985428	PFSK-1	brain:	n/a	n/a
2	HMGN3	chr1:56983445-56983832	K562	blood:	n/a	n/a
3	JUN	chr1:56983444-56983833	K562	blood:	n/a	chr1:56983596-56983608 chr1:56983597-56983607 chr1:56983598-56983606 chr1:56983597-56983607
4	POLR2A	chr1:56980412-56984262	HepG2	liver:	n/a	n/a
5	ZNF143	chr1:56982008-56983735	K562	blood:	n/a	chr1:56983633-56983651
6	JUND	chr1:56981492-56983814	K562	blood:	n/a	chr1:56983596-56983608 chr1:56982084-56982093 chr1:56983597-56983607 chr1:56982703-56982712 chr1:56983598-56983606 chr1:56983597-56983607
7	MAFK	chr1:56982048-56983892	K562	blood:	n/a	chr1:56982464-56982478 chr1:56982465-56982476 chr1:56982465-56982481 chr1:56982466-56982477 chr1:56982465-56982476 chr1:56982465-56982480 chr1:56982466-56982477
8	EP300	chr1:56981640-56983854	K562	blood:	n/a	chr1:56982453-56982467 chr1:56982483-56982497 chr1:56982452-56982466 chr1:56982923-56982937 chr1:56982256-56982270 chr1:56982454-56982468
9	GATA3	chr1:56983378-56983706	T-47D	breast:	n/a	chr1:56983596-56983603
10	MAFF	chr1:56983443-56983823	K562	blood:	n/a	n/a
11	RCOR1	chr1:56981263-56983744	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56975331..56977635-chr1:56982955..56985243,2	MCF-7	breast:

Variant related genes	Relation type
PPAP2B	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10157636	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11583161	0.92[ASN][1000 genomes]
rs11590570	0.92[ASN][1000 genomes]
rs12081589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57966457	0.94[ASN][1000 genomes]
rs58289463	0.99[ASN][1000 genomes]
rs60314060	0.94[ASN][1000 genomes]
rs6690245	0.93[ASN][1000 genomes]
rs72664330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512545	0.94[ASN][1000 genomes]
rs7519268	0.90[ASN][1000 genomes]
rs7549894	0.86[ASN][1000 genomes]
rs7554557	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:56971400-56986200	Genic enhancers	Placenta	Placenta
3	chr1:56972400-56990800	Strong transcription	HSMM	muscle
4	chr1:56976400-56991600	Strong transcription	Fetal Stomach	stomach
5	chr1:56976800-56992400	Weak transcription	Brain Germinal Matrix	brain
6	chr1:56977200-56987200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:56977200-56990600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:56977800-56989200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:56977800-56991200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:56977800-56999200	Weak transcription	A549	lung
11	chr1:56978000-56987200	Weak transcription	Thymus	Thymus
12	chr1:56978000-56987600	Weak transcription	Dnd41	blood
13	chr1:56978000-56987800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:56978000-56989200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:56978000-56991400	Weak transcription	Fetal Brain Male	brain
16	chr1:56978000-56992600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:56979200-56984800	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:56979200-56984800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:56979200-56992600	Strong transcription	HepG2	liver
20	chr1:56979800-56986200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:56980000-56984200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:56980000-56984200	Enhancers	Spleen	Spleen
23	chr1:56980200-56983800	Genic enhancers	Fetal Intestine Large	intestine
24	chr1:56980400-56984200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:56980400-56984200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:56980400-56984200	Enhancers	Psoas Muscle	Psoas
27	chr1:56980400-56986200	Genic enhancers	NHDF-Ad	bronchial
28	chr1:56980600-56984000	Enhancers	Brain Hippocampus Middle	brain
29	chr1:56980600-56984200	Enhancers	Pancreas	Pancrea
30	chr1:56980600-56986200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr1:56980600-56991600	Genic enhancers	Left Ventricle	heart
32	chr1:56980800-56983800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr1:56981000-56984000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:56981000-56984200	Enhancers	Duodenum Mucosa	Duodenum
35	chr1:56981000-56987200	Weak transcription	HSMMtube	muscle
36	chr1:56981200-56984200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:56981400-56984200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:56981400-56984200	Genic enhancers	Adipose Nuclei	Adipose
39	chr1:56981400-56984800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:56981400-56985400	Genic enhancers	H1 Cell Line	embryonic stem cell
41	chr1:56981400-56986200	Strong transcription	Ovary	ovary
42	chr1:56981600-56983800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr1:56981600-56984200	Enhancers	Right Ventricle	heart
44	chr1:56981800-56983800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:56981800-56984000	Enhancers	HMEC	breast
46	chr1:56981800-56985800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:56982000-56984200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:56982000-56984200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
49	chr1:56982000-56984200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
50	chr1:56982000-56986400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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