Variant report

Variant	rs539141585
Chromosome Location	chr3:48699207-48699208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:252)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:252 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr3:48699111-48699446	GM12891	blood:	n/a	n/a
2	YY1	chr3:48699061-48699405	K562	blood:	n/a	n/a
3	ELF1	chr3:48699094-48699370	K562	blood:	n/a	n/a
4	REST	chr3:48698992-48699711	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr3:48699199-48699472	MCF10A-Er-Src	breast:	n/a	n/a
6	SIN3AK20	chr3:48698909-48699720	MCF-7	breast:	n/a	n/a
7	CHD1	chr3:48698915-48699304	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr3:48699044-48699520	MCF-7	breast:	n/a	n/a
9	SIN3A	chr3:48698800-48699957	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr3:48699127-48699502	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3AK20	chr3:48699068-48699500	HepG2	liver:	n/a	n/a
12	RFX5	chr3:48699140-48699384	K562	blood:	n/a	n/a
13	HDAC2	chr3:48699083-48699475	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:48699003-48699419	HUVEC	blood vessel:	n/a	n/a
15	NFIC	chr3:48699110-48699434	HepG2	liver:	n/a	n/a
16	SIN3AK20	chr3:48699102-48699488	A549	lung:	n/a	n/a
17	POLR2A	chr3:48698961-48699783	H1-hESC	embryonic stem cell:	n/a	n/a
18	REST	chr3:48698829-48700050	MCF-7	breast:	n/a	n/a
19	CTCF	chr3:48699179-48699355	Spleen_OC	spleen:	n/a	n/a
20	SPI1	chr3:48699094-48699372	GM12878	blood:	n/a	n/a
21	ZBTB7A	chr3:48698860-48699499	ECC-1	luminal epithelium:	n/a	n/a
22	RUNX3	chr3:48699076-48699436	GM12878	blood:	n/a	n/a
23	ELF1	chr3:48698877-48699851	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:48698903-48702611	H1-hESC	embryonic stem cell:	n/a	n/a
25	REST	chr3:48698726-48700055	PFSK-1	brain:	n/a	n/a
26	MAZ	chr3:48699183-48699482	HepG2	liver:	n/a	n/a
27	SREBP1	chr3:48698687-48699855	GM12878	blood:	n/a	n/a
28	ATF2	chr3:48699005-48699484	H1-hESC	embryonic stem cell:	n/a	n/a
29	STAT1	chr3:48699131-48699376	GM12878	blood:	n/a	n/a
30	ETS1	chr3:48699021-48699500	K562	blood:	n/a	n/a
31	REST	chr3:48698585-48700084	GM12878	blood:	n/a	n/a
32	SIN3AK20	chr3:48698971-48699691	MCF-7	breast:	n/a	n/a
33	NRF1	chr3:48699127-48699374	HepG2	liver:	n/a	chr3:48699249-48699260
34	ATF2	chr3:48699029-48699495	GM12878	blood:	n/a	n/a
35	TAF7	chr3:48699015-48699538	H1-hESC	embryonic stem cell:	n/a	n/a
36	MYBL2	chr3:48698930-48699549	HepG2	liver:	n/a	n/a
37	RCOR1	chr3:48699089-48699629	GM12878	blood:	n/a	n/a
38	MAX	chr3:48699099-48699396	K562	blood:	n/a	n/a
39	SIN3AK20	chr3:48699062-48699437	PANC-1	pancreas:	n/a	n/a
40	ZMIZ1	chr3:48699154-48699375	K562	blood:	n/a	n/a
41	HDAC2	chr3:48699059-48699424	MCF-7	breast:	n/a	n/a
42	PAX5	chr3:48698846-48699413	GM12878	blood:	n/a	n/a
43	SIN3AK20	chr3:48699068-48699464	H1-hESC	embryonic stem cell:	n/a	n/a
44	CHD2	chr3:48699103-48699431	K562	blood:	n/a	n/a
45	REST	chr3:48698881-48699818	PANC-1	pancreas:	n/a	n/a
46	REST	chr3:48698779-48699894	H1-hESC	embryonic stem cell:	n/a	n/a
47	ARID3A	chr3:48699155-48699487	HepG2	liver:	n/a	n/a
48	NR2F2	chr3:48698995-48699502	K562	blood:	n/a	n/a
49	SIN3AK20	chr3:48698880-48699604	H1-hESC	embryonic stem cell:	n/a	n/a
50	POU2F2	chr3:48699139-48699509	GM12878	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48697809..48699544-chr3:49049957..49052349,2	MCF-7	breast:
2	chr3:48670997..48674874-chr3:48698947..48702118,7	MCF-7	breast:
3	chr3:48698129..48704726-chr3:48706101..48715056,13	MCF-7	breast:
4	chr3:48695950..48699824-chr3:48710158..48713070,3	K562	blood:
5	chr3:48698351..48700757-chr3:49057854..49060697,2	K562	blood:
6	chr3:48670764..48674544-chr3:48699167..48702803,6	K562	blood:
7	chr3:48698197..48700148-chr3:48700175..48701734,2	MCF-7	breast:
8	chr3:48675163..48677992-chr3:48697938..48699928,2	K562	blood:
9	chr3:48670764..48674544-chr3:48698929..48702803,9	K562	blood:
10	chr3:48647141..48648853-chr3:48697785..48700969,3	MCF-7	breast:
11	chr3:48698738..48703197-chr3:48713751..48717809,8	K562	blood:
12	chr3:48667529..48675453-chr3:48697968..48703139,10	MCF-7	breast:
13	chr3:48659070..48661619-chr3:48697247..48699239,2	K562	blood:
14	chr3:48678686..48683466-chr3:48696483..48700259,5	K562	blood:
15	chr3:48686566..48688475-chr3:48697453..48700260,2	MCF-7	breast:
16	chr3:48593030..48597118-chr3:48698507..48702121,6	MCF-7	breast:
17	chr3:48602276..48604378-chr3:48697664..48699278,2	K562	blood:
18	chr3:48678987..48680520-chr3:48698680..48701564,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228350	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000271973	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000263898	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000183396	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000178252	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	esv3359935	chr3:48696498-48699296	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
10	esv3409347	chr3:48697698-48701896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv822075	chr3:48698492-48699585	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48697800-48699800	Weak transcription	A549	lung
2	chr3:48698400-48699400	Enhancers	Ovary	ovary
3	chr3:48698400-48700000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:48698400-48700400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:48698400-48700400	Enhancers	Fetal Heart	heart
6	chr3:48698400-48700600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr3:48698400-48700800	Enhancers	Lung	lung
8	chr3:48698400-48701800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:48698600-48699400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:48698600-48699400	Flanking Active TSS	Pancreas	Pancrea
11	chr3:48698600-48699400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
12	chr3:48698600-48699600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
13	chr3:48698600-48699600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr3:48698600-48699600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:48698600-48699600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
16	chr3:48698600-48699800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:48698600-48700000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
18	chr3:48698600-48700000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr3:48698600-48700000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:48698600-48700200	Enhancers	Gastric	stomach
21	chr3:48698600-48700200	Enhancers	HMEC	breast
22	chr3:48698600-48700400	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:48698600-48701800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:48698600-48702400	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr3:48698800-48699400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr3:48698800-48699400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
27	chr3:48698800-48699400	Bivalent Enhancer	Liver	Liver
28	chr3:48698800-48699400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
29	chr3:48698800-48699400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
30	chr3:48698800-48699400	Flanking Active TSS	Right Ventricle	heart
31	chr3:48698800-48699400	Flanking Bivalent TSS/Enh	Thymus	Thymus
32	chr3:48698800-48699400	Active TSS	HSMMtube	muscle
33	chr3:48698800-48699600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:48698800-48699600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
35	chr3:48698800-48699600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr3:48698800-48699600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:48698800-48699800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
38	chr3:48698800-48699800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:48698800-48700000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:48698800-48700000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr3:48698800-48700400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr3:48698800-48700400	Enhancers	Right Atrium	heart
43	chr3:48698800-48701600	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:48698800-48701800	Active TSS	H1 Cell Line	embryonic stem cell
45	chr3:48698800-48701800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:48698800-48701800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:48698800-48701800	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr3:48698800-48702000	Active TSS	H9 Cell Line	embryonic stem cell
49	chr3:48699000-48699400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:48699000-48699400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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