Variant report

Variant	rs530647525
Chromosome Location	chr3:139654015-139654016
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	CCNT2	chr3:139654009-139654199	K562	blood:	n/a	n/a
2	CREB1	chr3:139653000-139654183	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
3	POLR2A	chr3:139653685-139655172	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr3:139653589-139654518	MCF-7	breast:	n/a	n/a
5	TBP	chr3:139653902-139654178	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:139653863-139654336	MCF-7	breast:	n/a	n/a
7	NR2F2	chr3:139653250-139654333	MCF-7	breast:	n/a	n/a
8	ZNF143	chr3:139653927-139654335	H1-hESC	embryonic stem cell:	n/a	n/a
9	GABPA	chr3:139653849-139654351	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTBP2	chr3:139653274-139655142	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:139653220-139654254	A549	lung:	n/a	n/a
12	TAF1	chr3:139653907-139654189	H1-hESC	embryonic stem cell:	n/a	n/a
13	KAP1	chr3:139654000-139654323	HEK293	kidney:	n/a	n/a
14	CTCF	chr3:139653192-139654642	SK-N-SH	brain:	n/a	n/a
15	SMC3	chr3:139653152-139655240	SK-N-SH	brain:	n/a	n/a
16	CTCF	chr3:139653980-139654130	GM12871	blood:	n/a	n/a
17	POLR2A	chr3:139653798-139654452	MCF-7	breast:	n/a	n/a
18	RAD21	chr3:139653954-139654338	SK-N-SH_RA	brain:	n/a	n/a
19	RAD21	chr3:139653148-139654466	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr3:139653794-139654707	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr3:139653888-139654376	H1-hESC	embryonic stem cell:	n/a	n/a
22	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
23	RFX5	chr3:139652845-139654280	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr3:139654006-139654395	MCF-7	breast:	n/a	n/a
25	RAD21	chr3:139653263-139654447	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr3:139653917-139654434	MCF-7	breast:	n/a	n/a
27	POU2F2	chr3:139653825-139654095	GM12891	blood:	n/a	chr3:139653939-139653952 chr3:139653939-139653953 chr3:139653941-139653954 chr3:139653942-139653956 chr3:139653941-139653954 chr3:139653941-139653954
28	MAX	chr3:139653344-139654370	MCF-7	breast:	n/a	chr3:139653355-139653365
29	CREB1	chr3:139653808-139654178	A549	lung:	n/a	chr3:139653971-139653984
30	ZNF263	chr3:139653965-139654850	HEK293-T-REx	kidney:	n/a	n/a
31	CREB1	chr3:139653164-139654436	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
32	RAD21	chr3:139652400-139655036	SK-N-SH	brain:	n/a	n/a
33	TAF1	chr3:139653888-139654177	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr3:139653812-139655134	H1-neurons	neurons:	n/a	n/a
35	SIN3A	chr3:139653358-139655518	H1-hESC	embryonic stem cell:	n/a	chr3:139653432-139653445 chr3:139653991-139654004
36	MYC	chr3:139653910-139654442	MCF-7	breast:	n/a	n/a
37	MYC	chr3:139653924-139654061	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:139653978-139654452	MCF-7	breast:	n/a	n/a
39	GABPA	chr3:139653899-139654325	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF1	chr3:139653784-139654268	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr3:139654012-139654084	ProgFib	skin:	n/a	n/a
42	POLR2A	chr3:139653770-139654489	H1-neurons	neurons:	n/a	n/a
43	REST	chr3:139653581-139655533	H1-neurons	neurons:	n/a	chr3:139654636-139654649 chr3:139653848-139653857
44	JUND	chr3:139653359-139654300	H1-hESC	embryonic stem cell:	n/a	chr3:139653973-139653982
45	POLR2A	chr3:139653961-139654180	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139437070..139437910-chr3:139653098..139654016,8	MCF-7	breast:

Variant related genes	Relation type
CLSTN2	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:19 , 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
18	esv17722	chr3:139653748-139654307	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv591858	chr3:139653776-139654239	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139653200-139654200	Enhancers	Fetal Brain Male	brain
2	chr3:139653200-139654800	Active TSS	Brain Anterior Caudate	brain
3	chr3:139653200-139655000	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:139653200-139655400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr3:139653200-139655600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr3:139653200-139655600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:139653200-139656000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr3:139653400-139654200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:139653400-139654200	Active TSS	Brain Hippocampus Middle	brain
13	chr3:139653400-139654200	Active TSS	Rectal Smooth Muscle	rectum
14	chr3:139653400-139654200	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr3:139653400-139654400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr3:139653400-139654400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:139653400-139654400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:139653400-139654400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:139653400-139654400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:139653400-139654400	Bivalent/Poised TSS	HSMM	muscle
21	chr3:139653400-139654400	Active TSS	NH-A	brain
22	chr3:139653400-139654600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:139653400-139654600	Active TSS	Fetal Brain Female	brain
24	chr3:139653400-139654600	Active TSS	Fetal Kidney	kidney
25	chr3:139653400-139654800	Active TSS	Brain Substantia Nigra	brain
26	chr3:139653400-139655000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr3:139653400-139655000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:139653400-139655000	Flanking Active TSS	Pancreas	Pancrea
29	chr3:139653400-139655000	Bivalent/Poised TSS	A549	lung
30	chr3:139653400-139655200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:139653400-139655200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:139653400-139655200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:139653400-139655400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr3:139653400-139655400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:139653400-139655600	Bivalent Enhancer	Liver	Liver
36	chr3:139653400-139656200	Active TSS	Brain Angular Gyrus	brain
37	chr3:139653400-139657000	Active TSS	HSMMtube	muscle
38	chr3:139653600-139654200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:139653600-139654200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:139653600-139654200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:139653600-139654400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:139653600-139654400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:139653600-139654400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:139653600-139654400	Active TSS	Aorta	Aorta
45	chr3:139653600-139654400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr3:139653600-139654400	Bivalent/Poised TSS	HepG2	liver
47	chr3:139653600-139654400	Bivalent/Poised TSS	NHEK	skin
48	chr3:139653600-139654600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:139653600-139654600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
50	chr3:139653600-139654600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum

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