Variant report

Variant	rs375958257
Chromosome Location	chr3:48698761-48698762
allele	C/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	REST	chr3:48698726-48700055	PFSK-1	brain:	n/a	n/a
2	SREBP1	chr3:48698687-48699855	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:48698203-48699000	MCF-7	breast:	n/a	n/a
4	REST	chr3:48698585-48700084	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:48698737-48698930	MCF10A-Er-Src	breast:	n/a	n/a
6	REST	chr3:48697968-48700052	U87	brain:	n/a	n/a
7	REST	chr3:48698714-48699936	GM12878	blood:	n/a	n/a
8	MAX	chr3:48698761-48699591	ECC-1	luminal epithelium:	n/a	n/a
9	REST	chr3:48698724-48700110	PFSK-1	brain:	n/a	n/a
10	REST	chr3:48698516-48700039	A549	lung:	n/a	n/a
11	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
12	POLR2A	chr3:48698670-48702902	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr3:48698049-48699791	U87	brain:	n/a	n/a
14	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
15	MXI1	chr3:48698269-48699941	IMR90	lung:	n/a	n/a
16	MAX	chr3:48698608-48699577	ECC-1	luminal epithelium:	n/a	n/a
17	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
18	REST	chr3:48698540-48700148	ECC-1	luminal epithelium:	n/a	n/a
19	REST	chr3:48698723-48700033	HepG2	liver:	n/a	n/a
20	MAZ	chr3:48698507-48699594	IMR90	lung:	n/a	n/a
21	REST	chr3:48698400-48700694	HL-60	blood:	n/a	chr3:48700550-48700563 chr3:48700448-48700466 chr3:48700547-48700560 chr3:48700447-48700467 chr3:48700453-48700467 chr3:48700547-48700556
22	REST	chr3:48698577-48698792	GM12878	blood:	n/a	n/a
23	REST	chr3:48698756-48699762	HepG2	liver:	n/a	n/a
24	REST	chr3:48697968-48700054	U87	brain:	n/a	n/a
25	REST	chr3:48698557-48700097	HepG2	liver:	n/a	n/a
26	REST	chr3:48698415-48700056	K562	blood:	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
ENSG00000178252	Chromatin interaction
ENSG00000263898	Chromatin interaction
ENSG00000271973	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000183396	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000213672	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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48694000-48698800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:48694200-48699000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:48694400-48698800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:48694400-48698800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:48694400-48698800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:48694400-48698800	Weak transcription	HUVEC	blood vessel
7	chr3:48694600-48698800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:48694600-48698800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:48694800-48698800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:48694800-48698800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:48694800-48698800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:48695000-48698800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:48696200-48698800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr3:48696800-48699000	Enhancers	Spleen	Spleen
15	chr3:48697200-48699000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:48697600-48699000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:48697800-48698800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:48697800-48698800	Enhancers	Fetal Brain Male	brain
19	chr3:48697800-48699800	Weak transcription	A549	lung
20	chr3:48698000-48698800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:48698000-48698800	Weak transcription	Brain Anterior Caudate	brain
22	chr3:48698000-48698800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
23	chr3:48698000-48698800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr3:48698000-48698800	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr3:48698200-48698800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:48698200-48698800	Enhancers	Right Ventricle	heart
27	chr3:48698400-48698800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:48698400-48698800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:48698400-48698800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:48698400-48698800	Bivalent Enhancer	Primary B cells from cord blood	blood
31	chr3:48698400-48698800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:48698400-48698800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr3:48698400-48698800	Bivalent Enhancer	Fetal Lung	lung
34	chr3:48698400-48698800	Bivalent Enhancer	Placenta	Placenta
35	chr3:48698400-48698800	Bivalent Enhancer	Fetal Thymus	thymus
36	chr3:48698400-48699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:48698400-48699000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr3:48698400-48699000	Enhancers	Colonic Mucosa	Colon
39	chr3:48698400-48699000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
40	chr3:48698400-48699400	Enhancers	Ovary	ovary
41	chr3:48698400-48700000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:48698400-48700400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:48698400-48700400	Enhancers	Fetal Heart	heart
44	chr3:48698400-48700600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
45	chr3:48698400-48700800	Enhancers	Lung	lung
46	chr3:48698400-48701800	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr3:48698600-48698800	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:48698600-48698800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:48698600-48698800	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr3:48698600-48698800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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