Variant report

Variant	rs539008448
Chromosome Location	chr3:139653444-139653445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr3:139653395-139653699	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr3:139653418-139653735	H1-hESC	embryonic stem cell:	n/a	n/a
3	CREB1	chr3:139653000-139654183	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
4	RAD21	chr3:139653237-139653780	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:139653360-139653510	GM12867	blood:	n/a	n/a
6	RAD21	chr3:139653176-139653942	MCF-7	breast:	n/a	n/a
7	CTCF	chr3:139653400-139653550	AG10803	skin:	n/a	n/a
8	CTCF	chr3:139653440-139653590	BE2_C	brain:	n/a	n/a
9	CTCF	chr3:139653266-139653772	HCT-116	colon:	n/a	n/a
10	USF2	chr3:139653346-139653675	H1-hESC	embryonic stem cell:	n/a	n/a
11	NR2F2	chr3:139653250-139654333	MCF-7	breast:	n/a	n/a
12	CTCF	chr3:139653400-139653550	HVMF	connective:	n/a	n/a
13	CTCF	chr3:139653390-139653742	MCF-7	breast:	n/a	n/a
14	CTCF	chr3:139653440-139653590	GM12869	blood:	n/a	n/a
15	CTCF	chr3:139653377-139653656	HepG2	liver:	n/a	n/a
16	CTCF	chr3:139653440-139653590	HepG2	liver:	n/a	n/a
17	RAD21	chr3:139653420-139653670	A549	lung:	n/a	n/a
18	CTBP2	chr3:139653274-139655142	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr3:139653220-139654254	A549	lung:	n/a	n/a
20	RAD21	chr3:139653337-139653655	HepG2	liver:	n/a	n/a
21	JUN	chr3:139653379-139653650	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr3:139653370-139653718	T-47D	breast:	n/a	n/a
23	POLR2A	chr3:139653329-139653796	H1-neurons	neurons:	n/a	n/a
24	CTCF	chr3:139653408-139653641	SK-N-SH_RA	brain:	n/a	n/a
25	CTCF	chr3:139653192-139654642	SK-N-SH	brain:	n/a	n/a
26	SMC3	chr3:139653152-139655240	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr3:139653420-139653570	MCF-7	breast:	n/a	n/a
28	TAF1	chr3:139653151-139653521	H1-neurons	neurons:	n/a	n/a
29	RAD21	chr3:139653388-139653673	SK-N-SH_RA	brain:	n/a	n/a
30	CTCF	chr3:139653420-139653570	AG09309	skin:	n/a	n/a
31	CTCF	chr3:139653316-139653757	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr3:139653148-139654466	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr3:139653428-139653597	K562	blood:	n/a	n/a
34	HA-E2F1	chr3:139653395-139654922	MCF-7	breast:	n/a	chr3:139653972-139653981 chr3:139654870-139654879 chr3:139653429-139653439 chr3:139653767-139653776 chr3:139653974-139653983
35	CTCF	chr3:139653420-139653570	GM12871	blood:	n/a	n/a
36	CTCF	chr3:139653440-139653590	GM12868	blood:	n/a	n/a
37	RFX5	chr3:139652845-139654280	SK-N-SH	brain:	n/a	n/a
38	RAD21	chr3:139653263-139654447	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr3:139653390-139653648	A549	lung:	n/a	n/a
40	CTCF	chr3:139653440-139653590	HEK293	kidney:	n/a	n/a
41	CTCF	chr3:139653421-139653685	A549	lung:	n/a	n/a
42	CTCF	chr3:139653340-139653490	GM12873	blood:	n/a	n/a
43	CTCF	chr3:139653360-139653510	GM12864	blood:	n/a	n/a
44	MAX	chr3:139653344-139654370	MCF-7	breast:	n/a	chr3:139653355-139653365
45	RAD21	chr3:139653401-139653757	A549	lung:	n/a	n/a
46	CTCF	chr3:139653440-139653590	HAc	cerebellar:	n/a	n/a
47	RXRA	chr3:139653370-139653722	H1-hESC	embryonic stem cell:	n/a	chr3:139653644-139653660 chr3:139653645-139653658 chr3:139653645-139653658 chr3:139653642-139653662 chr3:139653645-139653658
48	CTCF	chr3:139653387-139653658	SK-N-SH_RA	brain:	n/a	n/a
49	RAD21	chr3:139653428-139653663	HepG2	liver:	n/a	n/a
50	CTCF	chr3:139653360-139653510	HAc	cerebellar:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:139653431-139653481	HRE	kidney:	n/a
2	chr3:139653431-139653481	Hela-S3	cervix:	n/a
3	chr3:139653431-139653481	HMEC	breast:	n/a
4	chr3:139653431-139653481	BE2_C	brain:	n/a
5	chr3:139653431-139653481	ovcar-3	ovarian:	n/a
6	chr3:139653431-139653481	A549	lung:	n/a
7	chr3:139653431-139653481	SK-N-SH_RA	brain:	n/a
8	chr3:139653431-139653481	NB4	blood:	n/a
9	chr3:139653431-139653481	HRPEpiC	eye:	n/a
10	chr3:139653431-139653481	T-47D	breast:	n/a
11	chr3:139653431-139653481	HL-60	blood:	n/a
12	chr3:139653431-139653481	HNPCEpiC	eye:	n/a
13	chr3:139653431-139653481	AG09319	gingival:	n/a
14	chr3:139653431-139653481	LNCaP	prostate:	n/a
15	chr3:139653431-139653481	SK-N-MC	brain:	n/a
16	chr3:139653431-139653481	U87	brain:	n/a
17	chr3:139653431-139653481	MCF-7	breast:	n/a
18	chr3:139653431-139653481	AG09309	skin:	n/a
19	chr3:139653431-139653481	SKMC	muscle:	n/a
20	chr3:139653431-139653481	Hepatocyte	liver:	n/a
21	chr3:139653431-139653481	H1-hESC	embryonic stem cell:	embryo
22	chr3:139653431-139653481	HCM	heart:	n/a
23	chr3:139653431-139653481	HRCEpiC	kidney:	n/a
24	chr3:139653431-139653481	ProgFib	skin:	n/a
25	chr3:139653431-139653481	HepG2	liver:	n/a
26	chr3:139653431-139653481	IMR90	lung:	fetal
27	chr3:139653431-139653481	PFSK-1	brain:	n/a
28	chr3:139653431-139653481	Jurkat	blood:	n/a
29	chr3:139653431-139653481	GM12892	blood:	n/a
30	chr3:139653431-139653481	HEK293	kidney:	embryo
31	chr3:139653431-139653481	RPTEC	kidney:	n/a
32	chr3:139653431-139653481	K562	blood:	n/a
33	chr3:139653431-139653481	AG04450	lung:	fetal
34	chr3:139653431-139653481	ECC-1	luminal epithelium:	n/a
35	chr3:139653431-139653481	HCPEpiC	choroid plexus:	n/a
36	chr3:139653431-139653481	AG10803	skin:	n/a
37	chr3:139653431-139653481	SAEC	small airway:	n/a
38	chr3:139653431-139653481	SK-N-SH	brain:	n/a
39	chr3:139653431-139653481	HEEpiC	esophagus:	n/a
40	chr3:139653431-139653481	Caco-2	colon:	n/a
41	chr3:139653431-139653481	AG04449	skin:	fetal
42	chr3:139653431-139653481	HCF	heart:	n/a
43	chr3:139653431-139653481	HPAEpiC	pulmonary alveolar:	n/a
44	chr3:139653431-139653481	GM12891	blood:	n/a
45	chr3:139653431-139653481	CMK	blood:	n/a
46	chr3:139653431-139653481	HUVEC	blood vessel:	n/a
47	chr3:139653431-139653481	GM12878	blood:	n/a
48	chr3:139653431-139653481	GM19239	blood:	n/a
49	chr3:139653431-139653481	NHBE	bronchial:	n/a
50	chr3:139653431-139653481	NT2-D1	testis:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:139307203..139308238-chr3:139653078..139653999,6	MCF-7	breast:
2	chr3:139347937..139348556-chr3:139653424..139653964,2	MCF-7	breast:
3	chr3:139438799..139439673-chr3:139652877..139653733,2	MCF-7	breast:
4	chr3:139437070..139437910-chr3:139653098..139654016,8	MCF-7	breast:
5	chr3:139270922..139271855-chr3:139653137..139653973,3	MCF-7	breast:
6	chr3:139282929..139283874-chr3:139652757..139653752,4	MCF-7	breast:

No data

Variant related genes	Relation type
CLSTN2	TF binding region
CLSTN2	CpG island

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv877544	chr3:139642572-139688415	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv1798342	chr3:139648874-139654211	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1798770	chr3:139648874-139654211	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1806386	chr3:139648874-139654211	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1821044	chr3:139648874-139654211	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1822968	chr3:139648874-139654211	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1832601	chr3:139648874-139654211	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1836664	chr3:139648874-139654211	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1838553	chr3:139648874-139654211	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1844915	chr3:139648874-139654211	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv3486576	chr3:139652862-139656260	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv3486577	chr3:139652862-139656260	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139653200-139653600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:139653200-139653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:139653200-139653600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:139653200-139653600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:139653200-139653600	Bivalent Enhancer	Fetal Intestine Small	intestine
6	chr3:139653200-139653600	Bivalent Enhancer	Placenta	Placenta
7	chr3:139653200-139654000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:139653200-139654200	Enhancers	Fetal Brain Male	brain
9	chr3:139653200-139654800	Active TSS	Brain Anterior Caudate	brain
10	chr3:139653200-139655000	Active TSS	Brain Cingulate Gyrus	brain
11	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:139653200-139655400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:139653200-139655600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:139653200-139655600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr3:139653200-139656000	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:139653400-139653600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:139653400-139653600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:139653400-139653600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:139653400-139653600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
22	chr3:139653400-139653600	Bivalent Enhancer	Fetal Intestine Large	intestine
23	chr3:139653400-139653600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr3:139653400-139653600	Flanking Active TSS	Ovary	ovary
25	chr3:139653400-139653600	Active TSS	Psoas Muscle	Psoas
26	chr3:139653400-139653600	Enhancers	Right Atrium	heart
27	chr3:139653400-139653600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr3:139653400-139653800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr3:139653400-139653800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
33	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
34	chr3:139653400-139653800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
35	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
36	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
37	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Lung	lung
38	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
39	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
40	chr3:139653400-139654000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
41	chr3:139653400-139654000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr3:139653400-139654000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
43	chr3:139653400-139654000	Enhancers	Gastric	stomach
44	chr3:139653400-139654000	Bivalent Enhancer	Spleen	Spleen
45	chr3:139653400-139654200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:139653400-139654200	Active TSS	Brain Hippocampus Middle	brain
47	chr3:139653400-139654200	Active TSS	Rectal Smooth Muscle	rectum
48	chr3:139653400-139654200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr3:139653400-139654400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr3:139653400-139654400	Active TSS	H9 Cell Line	embryonic stem cell

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