Variant report

Variant	rs528330062
Chromosome Location	chr3:139653817-139653818
allele	A/G
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	CREB1	chr3:139653000-139654183	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
2	RAD21	chr3:139653176-139653942	MCF-7	breast:	n/a	n/a
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	NR2F2	chr3:139653250-139654333	MCF-7	breast:	n/a	n/a
6	CTBP2	chr3:139653274-139655142	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr3:139653220-139654254	A549	lung:	n/a	n/a
8	CTCF	chr3:139653192-139654642	SK-N-SH	brain:	n/a	n/a
9	SMC3	chr3:139653152-139655240	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:139653798-139654452	MCF-7	breast:	n/a	n/a
11	RAD21	chr3:139653148-139654466	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr3:139653794-139654707	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:139653518-139653848	H1-hESC	embryonic stem cell:	n/a	n/a
14	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
15	RFX5	chr3:139652845-139654280	SK-N-SH	brain:	n/a	n/a
16	RAD21	chr3:139653263-139654447	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr3:139653344-139654370	MCF-7	breast:	n/a	chr3:139653355-139653365
18	CREB1	chr3:139653808-139654178	A549	lung:	n/a	chr3:139653971-139653984
19	CREB1	chr3:139653164-139654436	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
20	YY1	chr3:139653350-139653824	H1-hESC	embryonic stem cell:	n/a	chr3:139653431-139653442 chr3:139653351-139653360 chr3:139653354-139653363
21	RAD21	chr3:139652400-139655036	SK-N-SH	brain:	n/a	n/a
22	CTCF	chr3:139653312-139653837	MCF-7	breast:	n/a	n/a
23	RAD21	chr3:139653424-139653835	HCT-116	colon:	n/a	n/a
24	YY1	chr3:139653289-139653852	H1-hESC	embryonic stem cell:	n/a	chr3:139653431-139653442 chr3:139653351-139653360 chr3:139653354-139653363
25	POLR2A	chr3:139653812-139655134	H1-neurons	neurons:	n/a	n/a
26	SIN3A	chr3:139653358-139655518	H1-hESC	embryonic stem cell:	n/a	chr3:139653432-139653445 chr3:139653991-139654004
27	TAF1	chr3:139653784-139654268	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr3:139653770-139654489	H1-neurons	neurons:	n/a	n/a
29	REST	chr3:139653581-139655533	H1-neurons	neurons:	n/a	chr3:139654636-139654649 chr3:139653848-139653857
30	CTCF	chr3:139653397-139653844	MCF-7	breast:	n/a	n/a
31	JUND	chr3:139653359-139654300	H1-hESC	embryonic stem cell:	n/a	chr3:139653973-139653982

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	chr3:139437070..139437910-chr3:139653098..139654016,8	MCF-7	breast:
4	chr3:139270922..139271855-chr3:139653137..139653973,3	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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139653200-139654000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:139653200-139654200	Enhancers	Fetal Brain Male	brain
3	chr3:139653200-139654800	Active TSS	Brain Anterior Caudate	brain
4	chr3:139653200-139655000	Active TSS	Brain Cingulate Gyrus	brain
5	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:139653200-139655400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:139653200-139655600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:139653200-139655600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:139653200-139656000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr3:139653400-139654000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr3:139653400-139654000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
14	chr3:139653400-139654000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
15	chr3:139653400-139654000	Enhancers	Gastric	stomach
16	chr3:139653400-139654000	Bivalent Enhancer	Spleen	Spleen
17	chr3:139653400-139654200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:139653400-139654200	Active TSS	Brain Hippocampus Middle	brain
19	chr3:139653400-139654200	Active TSS	Rectal Smooth Muscle	rectum
20	chr3:139653400-139654200	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr3:139653400-139654400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr3:139653400-139654400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr3:139653400-139654400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:139653400-139654400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:139653400-139654400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:139653400-139654400	Bivalent/Poised TSS	HSMM	muscle
27	chr3:139653400-139654400	Active TSS	NH-A	brain
28	chr3:139653400-139654600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:139653400-139654600	Active TSS	Fetal Brain Female	brain
30	chr3:139653400-139654600	Active TSS	Fetal Kidney	kidney
31	chr3:139653400-139654800	Active TSS	Brain Substantia Nigra	brain
32	chr3:139653400-139655000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
33	chr3:139653400-139655000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:139653400-139655000	Flanking Active TSS	Pancreas	Pancrea
35	chr3:139653400-139655000	Bivalent/Poised TSS	A549	lung
36	chr3:139653400-139655200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:139653400-139655200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:139653400-139655200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:139653400-139655400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr3:139653400-139655400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:139653400-139655600	Bivalent Enhancer	Liver	Liver
42	chr3:139653400-139656200	Active TSS	Brain Angular Gyrus	brain
43	chr3:139653400-139657000	Active TSS	HSMMtube	muscle
44	chr3:139653600-139654000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr3:139653600-139654000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
46	chr3:139653600-139654000	Bivalent/Poised TSS	Colonic Mucosa	Colon
47	chr3:139653600-139654000	Bivalent/Poised TSS	Esophagus	oesophagus
48	chr3:139653600-139654000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr3:139653600-139654000	Flanking Bivalent TSS/Enh	Placenta	Placenta
50	chr3:139653600-139654000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion

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