Variant report

Variant	rs58285779
Chromosome Location	chr4:148541468-148541469
allele	A/C
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	SPI1	chr4:148541457-148541795	GM12891	blood:	n/a	n/a
2	SPI1	chr4:148541384-148541900	HL-60	blood:	n/a	n/a
3	POLR2A	chr4:148540812-148542114	K562	blood:	n/a	n/a
4	POLR2A	chr4:148541465-148541474	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:148538481..148540071-chr4:148540760..148542427,2	MCF-7	breast:
2	chr4:148541060..148543503-chr4:148546785..148549015,2	MCF-7	breast:
3	chr4:148536735..148540067-chr4:148540690..148544003,4	MCF-7	breast:
4	chr4:148541017..148543001-chr4:148604004..148606704,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251298	TF binding region
ENSG00000164169	Chromatin interaction
ENSG00000164168	Chromatin interaction
ENSG00000251298	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10011891	0.83[AMR][1000 genomes]
rs10023419	0.83[AMR][1000 genomes]
rs10029636	0.83[AMR][1000 genomes]
rs10034181	0.83[AMR][1000 genomes]
rs11931510	0.83[AMR][1000 genomes]
rs11932755	1.00[AMR][1000 genomes]
rs11932883	1.00[AMR][1000 genomes]
rs17023581	0.85[AMR][1000 genomes]
rs28416885	0.83[AMR][1000 genomes]
rs28579791	0.83[AMR][1000 genomes]
rs28676674	0.85[AMR][1000 genomes]
rs34001293	1.00[AMR][1000 genomes]
rs57632432	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58012022	1.00[AMR][1000 genomes]
rs58965352	0.83[AMR][1000 genomes]
rs59938265	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61312957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61355480	1.00[AMR][1000 genomes]
rs61363583	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945871	1.00[AMR][1000 genomes]
rs72945873	1.00[AMR][1000 genomes]
rs72945877	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945879	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947824	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947833	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947849	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947870	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947876	1.00[AMR][1000 genomes]
rs72947892	1.00[AMR][1000 genomes]
rs72949789	1.00[AMR][1000 genomes]
rs72949795	1.00[AMR][1000 genomes]
rs72949796	1.00[AMR][1000 genomes]
rs72949798	0.83[AMR][1000 genomes]
rs72951406	0.83[AMR][1000 genomes]
rs72951412	0.83[AMR][1000 genomes]
rs72951422	0.83[AMR][1000 genomes]
rs72951423	0.83[AMR][1000 genomes]
rs72953473	0.83[AMR][1000 genomes]
rs72953477	0.83[AMR][1000 genomes]
rs72953481	0.83[AMR][1000 genomes]
rs72953502	0.83[AMR][1000 genomes]
rs72955506	0.83[AMR][1000 genomes]
rs9993312	0.85[AMR][1000 genomes]
rs9996365	0.83[AMR][1000 genomes]
rs9997304	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830110	chr4:148432125-148595119	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv428776	chr4:148432125-148595119	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1019205	chr4:148524852-148576265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr4:148539400-148543200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr4:148539400-148543600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:148539400-148543800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:148539400-148547000	Weak transcription	Lung	lung
5	chr4:148539400-148547200	Weak transcription	Esophagus	oesophagus
6	chr4:148539400-148548200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:148539400-148576800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:148539600-148541600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:148539600-148542000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:148539600-148542400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr4:148539600-148542800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr4:148539600-148543000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:148539600-148544000	Weak transcription	Fetal Stomach	stomach
14	chr4:148539600-148546800	Weak transcription	Colonic Mucosa	Colon
15	chr4:148539600-148547000	Weak transcription	Aorta	Aorta
16	chr4:148539600-148547800	Weak transcription	HSMMtube	muscle
17	chr4:148539600-148554200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:148539800-148541600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr4:148539800-148541600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:148539800-148541600	Enhancers	Hela-S3	cervix
21	chr4:148539800-148542000	Weak transcription	Osteobl	bone
22	chr4:148539800-148542200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:148539800-148542400	Enhancers	Brain Angular Gyrus	brain
24	chr4:148539800-148542600	Enhancers	Liver	Liver
25	chr4:148539800-148543200	Weak transcription	Right Atrium	heart
26	chr4:148539800-148544600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:148539800-148545000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:148539800-148546600	Weak transcription	NHLF	lung
29	chr4:148539800-148547600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:148539800-148550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr4:148539800-148557200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:148540000-148541600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:148540000-148541600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr4:148540000-148543400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr4:148540000-148543800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:148540000-148543800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:148540000-148543800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:148540200-148541600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr4:148540200-148542000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr4:148540200-148542200	Weak transcription	NH-A	brain
41	chr4:148540200-148543800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:148540200-148547000	Weak transcription	Pancreas	Pancrea
43	chr4:148540400-148541600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:148540400-148541800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr4:148540600-148541600	Strong transcription	Placenta	Placenta
46	chr4:148540600-148541800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:148540600-148542000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:148540600-148544000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:148540800-148541600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:148540800-148541600	Strong transcription	HSMM	muscle

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