Variant report

Variant	rs548366724
Chromosome Location	chr3:139653375-139653376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr3:139653000-139654183	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
2	RAD21	chr3:139653237-139653780	MCF-7	breast:	n/a	n/a
3	CTCF	chr3:139653360-139653510	GM12867	blood:	n/a	n/a
4	RAD21	chr3:139653176-139653942	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:139653266-139653772	HCT-116	colon:	n/a	n/a
6	USF2	chr3:139653346-139653675	H1-hESC	embryonic stem cell:	n/a	n/a
7	NR2F2	chr3:139653250-139654333	MCF-7	breast:	n/a	n/a
8	CTBP2	chr3:139653274-139655142	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:139653220-139654254	A549	lung:	n/a	n/a
10	RAD21	chr3:139653337-139653655	HepG2	liver:	n/a	n/a
11	CTCF	chr3:139653370-139653718	T-47D	breast:	n/a	n/a
12	POLR2A	chr3:139653329-139653796	H1-neurons	neurons:	n/a	n/a
13	CTCF	chr3:139653192-139654642	SK-N-SH	brain:	n/a	n/a
14	SMC3	chr3:139653152-139655240	SK-N-SH	brain:	n/a	n/a
15	TAF1	chr3:139653151-139653521	H1-neurons	neurons:	n/a	n/a
16	CTCF	chr3:139653316-139653757	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr3:139653148-139654466	H1-hESC	embryonic stem cell:	n/a	n/a
18	RFX5	chr3:139652845-139654280	SK-N-SH	brain:	n/a	n/a
19	RAD21	chr3:139653263-139654447	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr3:139653340-139653490	GM12873	blood:	n/a	n/a
21	CTCF	chr3:139653360-139653510	GM12864	blood:	n/a	n/a
22	MAX	chr3:139653344-139654370	MCF-7	breast:	n/a	chr3:139653355-139653365
23	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
24	CTCF	chr3:139653360-139653510	HAc	cerebellar:	n/a	n/a
25	RFX5	chr3:139653311-139653749	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr3:139653362-139653782	H1-hESC	embryonic stem cell:	n/a	n/a
27	CREB1	chr3:139653164-139654436	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
28	RAD21	chr3:139653358-139653692	HepG2	liver:	n/a	n/a
29	YY1	chr3:139653350-139653824	H1-hESC	embryonic stem cell:	n/a	chr3:139653431-139653442 chr3:139653351-139653360 chr3:139653354-139653363
30	RAD21	chr3:139652400-139655036	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr3:139653312-139653837	MCF-7	breast:	n/a	n/a
32	RAD21	chr3:139653266-139653779	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr3:139653289-139653852	H1-hESC	embryonic stem cell:	n/a	chr3:139653431-139653442 chr3:139653351-139653360 chr3:139653354-139653363
34	SIN3A	chr3:139653358-139655518	H1-hESC	embryonic stem cell:	n/a	chr3:139653432-139653445 chr3:139653991-139654004
35	NANOG	chr3:139653325-139653700	H1-hESC	embryonic stem cell:	n/a	chr3:139653371-139653380
36	ZNF143	chr3:139653364-139653704	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr3:139653342-139653683	T-47D	breast:	n/a	n/a
38	RAD21	chr3:139653275-139653780	SK-N-SH_RA	brain:	n/a	n/a
39	RAD21	chr3:139653255-139653785	HCT-116	colon:	n/a	n/a
40	JUND	chr3:139653359-139654300	H1-hESC	embryonic stem cell:	n/a	chr3:139653973-139653982

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:139653328-139653378	HPAEpiC	pulmonary alveolar:	n/a
2	chr3:139653328-139653378	AG10803	skin:	n/a
3	chr3:139653328-139653378	PFSK-1	brain:	n/a
4	chr3:139653328-139653378	MCF-7	breast:	n/a
5	chr3:139653328-139653378	NT2-D1	testis:	n/a
6	chr3:139653328-139653378	HMEC	breast:	n/a
7	chr3:139653328-139653378	HAEpiC	amniotic membrane:	n/a
8	chr3:139653328-139653378	BJ	skin:	n/a
9	chr3:139653328-139653378	BE2_C	brain:	n/a
10	chr3:139653328-139653378	SK-N-MC	brain:	n/a
11	chr3:139653328-139653378	LNCaP	prostate:	n/a
12	chr3:139653328-139653378	H1-hESC	embryonic stem cell:	embryo
13	chr3:139653328-139653378	ECC-1	luminal epithelium:	n/a
14	chr3:139653328-139653378	A549	lung:	n/a
15	chr3:139653328-139653378	AG04449	skin:	fetal
16	chr3:139653328-139653378	SKMC	muscle:	n/a
17	chr3:139653328-139653378	SK-N-SH	brain:	n/a
18	chr3:139653328-139653378	Hepatocyte	liver:	n/a
19	chr3:139653328-139653378	GM12892	blood:	n/a
20	chr3:139653328-139653378	RPTEC	kidney:	n/a
21	chr3:139653328-139653378	NB4	blood:	n/a
22	chr3:139653328-139653378	Jurkat	blood:	n/a
23	chr3:139653328-139653378	HRPEpiC	eye:	n/a
24	chr3:139653328-139653378	HepG2	liver:	n/a
25	chr3:139653328-139653378	NHBE	bronchial:	n/a
26	chr3:139653328-139653378	HEEpiC	esophagus:	n/a
27	chr3:139653328-139653378	MCF10A-Er-Src	breast:	n/a
28	chr3:139653328-139653378	HRE	kidney:	n/a
29	chr3:139653328-139653378	HCT-116	colon:	n/a
30	chr3:139653328-139653378	IMR90	lung:	fetal
31	chr3:139653328-139653378	AG04450	lung:	fetal
32	chr3:139653328-139653378	HRCEpiC	kidney:	n/a
33	chr3:139653328-139653378	U87	brain:	n/a
34	chr3:139653328-139653378	HCF	heart:	n/a
35	chr3:139653328-139653378	SAEC	small airway:	n/a
36	chr3:139653328-139653378	HNPCEpiC	eye:	n/a
37	chr3:139653328-139653378	HCM	heart:	n/a
38	chr3:139653328-139653378	K562	blood:	n/a
39	chr3:139653328-139653378	HUVEC	blood vessel:	n/a
40	chr3:139653328-139653378	HL-60	blood:	n/a
41	chr3:139653328-139653378	HCPEpiC	choroid plexus:	n/a
42	chr3:139653328-139653378	AoSMC	blood vessel:	n/a
43	chr3:139653328-139653378	GM06990	blood:	n/a
44	chr3:139653328-139653378	GM12878	blood:	n/a
45	chr3:139653328-139653378	AG09309	skin:	n/a
46	chr3:139653328-139653378	NHDF-neo	bronchial:	n/a
47	chr3:139653328-139653378	ovcar-3	ovarian:	n/a
48	chr3:139653328-139653378	ProgFib	skin:	n/a
49	chr3:139653328-139653378	HIPEpiC	eye:	n/a
50	chr3:139653328-139653378	Caco-2	colon:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:139307203..139308238-chr3:139653078..139653999,6	MCF-7	breast:
2	chr3:139438799..139439673-chr3:139652877..139653733,2	MCF-7	breast:
3	chr3:139437070..139437910-chr3:139653098..139654016,8	MCF-7	breast:
4	chr3:139270922..139271855-chr3:139653137..139653973,3	MCF-7	breast:
5	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:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139649600-139653400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:139653200-139653400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:139653200-139653400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:139653200-139653400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
5	chr3:139653200-139653400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:139653200-139653400	Bivalent Enhancer	Adipose Nuclei	Adipose
7	chr3:139653200-139653400	Enhancers	Brain Angular Gyrus	brain
8	chr3:139653200-139653400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr3:139653200-139653400	Enhancers	Ovary	ovary
10	chr3:139653200-139653400	Enhancers	Pancreas	Pancrea
11	chr3:139653200-139653400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:139653200-139653400	Flanking Bivalent TSS/Enh	HSMMtube	muscle
13	chr3:139653200-139653600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:139653200-139653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:139653200-139653600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:139653200-139653600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:139653200-139653600	Bivalent Enhancer	Fetal Intestine Small	intestine
18	chr3:139653200-139653600	Bivalent Enhancer	Placenta	Placenta
19	chr3:139653200-139654000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:139653200-139654200	Enhancers	Fetal Brain Male	brain
21	chr3:139653200-139654800	Active TSS	Brain Anterior Caudate	brain
22	chr3:139653200-139655000	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:139653200-139655400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:139653200-139655600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr3:139653200-139655600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr3:139653200-139656000	Active TSS	Brain Inferior Temporal Lobe	brain

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