Variant report

Variant	rs145270816
Chromosome Location	chr3:48698904-48698905
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	SIN3A	chr3:48698800-48699957	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr3:48698829-48700050	MCF-7	breast:	n/a	n/a
3	ZBTB7A	chr3:48698860-48699499	ECC-1	luminal epithelium:	n/a	n/a
4	ELF1	chr3:48698877-48699851	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:48698903-48702611	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr3:48698726-48700055	PFSK-1	brain:	n/a	n/a
7	SREBP1	chr3:48698687-48699855	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:48698203-48699000	MCF-7	breast:	n/a	n/a
9	REST	chr3:48698585-48700084	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:48698737-48698930	MCF10A-Er-Src	breast:	n/a	n/a
11	PAX5	chr3:48698846-48699413	GM12878	blood:	n/a	n/a
12	REST	chr3:48698881-48699818	PANC-1	pancreas:	n/a	n/a
13	REST	chr3:48698779-48699894	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3AK20	chr3:48698880-48699604	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr3:48697968-48700052	U87	brain:	n/a	n/a
16	PML	chr3:48698894-48699562	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:48698811-48699170	H1-hESC	embryonic stem cell:	n/a	n/a
18	REST	chr3:48698714-48699936	GM12878	blood:	n/a	n/a
19	REST	chr3:48698816-48702243	H1-neurons	neurons:	n/a	chr3:48700747-48700767 chr3:48700550-48700563 chr3:48700448-48700466 chr3:48700747-48700761 chr3:48700547-48700560 chr3:48700447-48700467 chr3:48700453-48700467 chr3:48700547-48700556
20	REST	chr3:48698818-48699992	MCF-7	breast:	n/a	n/a
21	REST	chr3:48698786-48700095	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr3:48698806-48700068	PFSK-1	brain:	n/a	n/a
23	MAX	chr3:48698761-48699591	ECC-1	luminal epithelium:	n/a	n/a
24	REST	chr3:48698724-48700110	PFSK-1	brain:	n/a	n/a
25	MAX	chr3:48698849-48699508	H1-hESC	embryonic stem cell:	n/a	n/a
26	REST	chr3:48698516-48700039	A549	lung:	n/a	n/a
27	POLR2A	chr3:48698839-48700010	HepG2	liver:	n/a	n/a
28	REST	chr3:48698808-48699747	GM12878	blood:	n/a	n/a
29	TCF12	chr3:48698892-48699556	ECC-1	luminal epithelium:	n/a	n/a
30	ZBTB7A	chr3:48698836-48699644	ECC-1	luminal epithelium:	n/a	n/a
31	PAX5	chr3:48698791-48699545	GM12892	blood:	n/a	n/a
32	GABPA	chr3:48698806-48699423	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr3:48697975-48701977	HL-60	blood:	n/a	chr3:48700747-48700767 chr3:48700550-48700563 chr3:48700448-48700466 chr3:48700747-48700761 chr3:48700547-48700560 chr3:48700447-48700467 chr3:48700453-48700467 chr3:48700547-48700556
34	HMGN3	chr3:48698900-48699477	K562	blood:	n/a	n/a
35	RCOR1	chr3:48698861-48699548	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:48698670-48702902	H1-hESC	embryonic stem cell:	n/a	n/a
37	E2F6	chr3:48698883-48699034	K562	blood:	n/a	n/a
38	REST	chr3:48698049-48699791	U87	brain:	n/a	n/a
39	REST	chr3:48698396-48701302	ECC-1	luminal epithelium:	n/a	chr3:48700747-48700767 chr3:48700550-48700563 chr3:48700448-48700466 chr3:48700747-48700761 chr3:48700547-48700560 chr3:48700447-48700467 chr3:48700453-48700467 chr3:48700547-48700556
40	MXI1	chr3:48698269-48699941	IMR90	lung:	n/a	n/a
41	REST	chr3:48698812-48699867	HepG2	liver:	n/a	n/a
42	MAX	chr3:48698608-48699577	ECC-1	luminal epithelium:	n/a	n/a
43	REST	chr3:48698174-48701803	A549	lung:	n/a	chr3:48700747-48700767 chr3:48700550-48700563 chr3:48700448-48700466 chr3:48700747-48700761 chr3:48700547-48700560 chr3:48700447-48700467 chr3:48700453-48700467 chr3:48700547-48700556
44	MAX	chr3:48698869-48699453	H1-hESC	embryonic stem cell:	n/a	n/a
45	CBX3	chr3:48698904-48699488	K562	blood:	n/a	n/a
46	REST	chr3:48698540-48700148	ECC-1	luminal epithelium:	n/a	n/a
47	REST	chr3:48698850-48700044	HCT-116	colon:	n/a	n/a
48	REST	chr3:48698723-48700033	HepG2	liver:	n/a	n/a
49	MAZ	chr3:48698507-48699594	IMR90	lung:	n/a	n/a
50	REST	chr3:48698797-48700043	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48697809..48699544-chr3:49049957..49052349,2	MCF-7	breast:
2	chr3:48698129..48704726-chr3:48706101..48715056,13	MCF-7	breast:
3	chr3:48686766..48690063-chr3:48696074..48699163,3	MCF-7	breast:
4	chr3:48695950..48699824-chr3:48710158..48713070,3	K562	blood:
5	chr3:48698351..48700757-chr3:49057854..49060697,2	K562	blood:
6	chr3:48698197..48700148-chr3:48700175..48701734,2	MCF-7	breast:
7	chr3:48675163..48677992-chr3:48697938..48699928,2	K562	blood:
8	chr3:48647141..48648853-chr3:48697785..48700969,3	MCF-7	breast:
9	chr3:48698738..48703197-chr3:48713751..48717809,8	K562	blood:
10	chr3:48667529..48675453-chr3:48697968..48703139,10	MCF-7	breast:
11	chr3:48659070..48661619-chr3:48697247..48699239,2	K562	blood:
12	chr3:48678686..48683466-chr3:48696483..48700259,5	K562	blood:
13	chr3:48686566..48688475-chr3:48697453..48700260,2	MCF-7	breast:
14	chr3:48593030..48597118-chr3:48698507..48702121,6	MCF-7	breast:
15	chr3:48602276..48604378-chr3:48697664..48699278,2	K562	blood:
16	chr3:48678987..48680520-chr3:48698680..48701564,2	K562	blood:

Variant related genes	Relation type
ENSG00000228350	TF binding region
ENSG00000178149	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000183396	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000263898	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000271973	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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48694200-48699000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:48696800-48699000	Enhancers	Spleen	Spleen
3	chr3:48697200-48699000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:48697600-48699000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:48697800-48699800	Weak transcription	A549	lung
6	chr3:48698400-48699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:48698400-48699000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr3:48698400-48699000	Enhancers	Colonic Mucosa	Colon
9	chr3:48698400-48699000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
10	chr3:48698400-48699400	Enhancers	Ovary	ovary
11	chr3:48698400-48700000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:48698400-48700400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:48698400-48700400	Enhancers	Fetal Heart	heart
14	chr3:48698400-48700600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr3:48698400-48700800	Enhancers	Lung	lung
16	chr3:48698400-48701800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:48698600-48699000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:48698600-48699000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:48698600-48699000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr3:48698600-48699000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
21	chr3:48698600-48699000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:48698600-48699000	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr3:48698600-48699000	Enhancers	Esophagus	oesophagus
24	chr3:48698600-48699000	Enhancers	Left Ventricle	heart
25	chr3:48698600-48699000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
26	chr3:48698600-48699000	Flanking Active TSS	HepG2	liver
27	chr3:48698600-48699000	Active TSS	HSMM	muscle
28	chr3:48698600-48699200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr3:48698600-48699200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:48698600-48699200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:48698600-48699400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:48698600-48699400	Flanking Active TSS	Pancreas	Pancrea
33	chr3:48698600-48699400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
34	chr3:48698600-48699600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
35	chr3:48698600-48699600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr3:48698600-48699600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:48698600-48699600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
38	chr3:48698600-48699800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:48698600-48700000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
40	chr3:48698600-48700000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr3:48698600-48700000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:48698600-48700200	Enhancers	Gastric	stomach
43	chr3:48698600-48700200	Enhancers	HMEC	breast
44	chr3:48698600-48700400	Active TSS	Brain Cingulate Gyrus	brain
45	chr3:48698600-48701800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr3:48698600-48702400	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr3:48698800-48699000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:48698800-48699000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:48698800-48699000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:48698800-48699000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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