Variant report

Variant	rs536402258
Chromosome Location	chr3:52279318-52279319
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	RCOR1	chr3:52278092-52279638	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:52278923-52280296	GM19193	blood:	n/a	n/a
3	POU2F2	chr3:52278729-52279638	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:52278063-52279526	GM12878	blood:	n/a	n/a
5	TBP	chr3:52278909-52279494	GM12878	blood:	n/a	n/a
6	MTA3	chr3:52277652-52279590	GM12878	blood:	n/a	n/a
7	ELK1	chr3:52278940-52279376	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr3:52278076-52279621	GM12878	blood:	n/a	n/a
9	RUNX3	chr3:52277852-52279708	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:52277921-52279621	GM12892	blood:	n/a	n/a
11	WRNIP1	chr3:52278889-52279379	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:52278806-52280260	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:52279203-52280263	GM18951	blood:	n/a	n/a
14	POLR2A	chr3:52277954-52280665	GM12878	blood:	n/a	n/a
15	CHD1	chr3:52279015-52279626	GM12878	blood:	n/a	n/a
16	MAZ	chr3:52278887-52280307	GM12878	blood:	n/a	chr3:52279824-52279834
17	MAX	chr3:52279261-52280339	ECC-1	luminal epithelium:	n/a	chr3:52279824-52279834
18	FOXM1	chr3:52278021-52279327	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:52277713-52280381	GM18505	blood:	n/a	n/a
20	POLR2A	chr3:52278939-52280285	MCF-7	breast:	n/a	n/a
21	POLR2A	chr3:52278818-52280201	GM12878	blood:	n/a	n/a
22	EBF1	chr3:52277812-52280262	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:52278021-52280334	GM12892	blood:	n/a	n/a
24	STAT5A	chr3:52278797-52279593	GM12878	blood:	n/a	n/a
25	PML	chr3:52277831-52279574	GM12878	blood:	n/a	chr3:52278233-52278242
26	IRF4	chr3:52278805-52279322	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:52278960-52280260	GM15510	blood:	n/a	n/a
28	CEBPB	chr3:52277837-52279367	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:52277951-52280233	GM19099	blood:	n/a	n/a
30	EP300	chr3:52278044-52279531	GM12878	blood:	n/a	chr3:52278473-52278487 chr3:52278231-52278240 chr3:52278901-52278914 chr3:52278242-52278255
31	SPI1	chr3:52277753-52279584	GM12878	blood:	n/a	chr3:52278471-52278484 chr3:52279034-52279043
32	MTA3	chr3:52277397-52279759	GM12878	blood:	n/a	n/a
33	YY1	chr3:52278992-52279370	GM12892	blood:	n/a	n/a
34	POLR2A	chr3:52279055-52280266	GM18526	blood:	n/a	n/a
35	POLR2A	chr3:52278927-52280465	GM12891	blood:	n/a	n/a
36	POLR2A	chr3:52277466-52280409	GM12892	blood:	n/a	n/a
37	YY1	chr3:52278794-52280163	GM12892	blood:	n/a	chr3:52279823-52279834 chr3:52279685-52279696 chr3:52279860-52279874
38	PAX5	chr3:52277914-52279342	GM12878	blood:	n/a	chr3:52279034-52279043
39	STAT5A	chr3:52277957-52279805	GM12878	blood:	n/a	chr3:52278528-52278535
40	POLR2A	chr3:52277692-52280195	GM12878	blood:	n/a	n/a
41	NFIC	chr3:52277858-52279690	GM12878	blood:	n/a	n/a
42	YY1	chr3:52278793-52280249	GM12878	blood:	n/a	chr3:52279823-52279834 chr3:52279685-52279696 chr3:52279860-52279874
43	YY1	chr3:52278778-52280056	GM12878	blood:	n/a	chr3:52279823-52279834 chr3:52279685-52279696 chr3:52279860-52279874
44	TCF3	chr3:52278774-52279595	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:52277908-52280223	GM12892	blood:	n/a	n/a
46	BHLHE40	chr3:52278137-52280324	GM12878	blood:	n/a	chr3:52279883-52279899
47	POLR2A	chr3:52277873-52280423	GM12892	blood:	n/a	n/a
48	MAX	chr3:52279318-52280420	HepG2	liver:	n/a	chr3:52279824-52279834
49	RUNX3	chr3:52277865-52279743	GM12878	blood:	n/a	n/a
50	RELA	chr3:52277557-52279708	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62608645..62609618-chr3:52279287..52279787,2	Hela-S3	cervix:
2	chr3:52278055..52281861-chr3:52310588..52314481,6	K562	blood:
3	chr3:52278277..52281486-chr3:52282865..52288389,9	K562	blood:
4	chr3:52278055..52281861-chr3:52310505..52315451,9	K562	blood:
5	chr3:52278407..52281355-chr3:52281666..52283628,3	MCF-7	breast:
6	chr3:52277680..52279387-chr3:52372909..52375320,2	K562	blood:
7	chr3:52277093..52279461-chr3:52290667..52292256,2	MCF-7	breast:
8	chr3:52278070..52281652-chr3:52320199..52323338,4	MCF-7	breast:
9	chr3:52278312..52281288-chr3:52312020..52314246,3	MCF-7	breast:

Variant related genes	Relation type
PPM1M	TF binding region
ENSG00000164088	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv876791	chr3:52269491-52286825	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	esv3369308	chr3:52279062-52280960	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52274400-52279400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:52275200-52279400	Weak transcription	Brain Angular Gyrus	brain
3	chr3:52277600-52279400	Enhancers	Lung	lung
4	chr3:52277600-52279600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:52277600-52279600	Enhancers	HMEC	breast
6	chr3:52277600-52282000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:52278000-52279400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:52278000-52279600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr3:52278000-52279600	Flanking Active TSS	Hela-S3	cervix
10	chr3:52278200-52279600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:52278400-52279400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:52278400-52280600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:52278600-52279600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr3:52278800-52279600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:52278800-52279600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr3:52278800-52279600	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr3:52278800-52279600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:52278800-52279600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr3:52278800-52279600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:52278800-52279600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr3:52278800-52279600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr3:52278800-52279600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:52278800-52279600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr3:52278800-52279600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:52278800-52279600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
26	chr3:52278800-52279600	Flanking Active TSS	GM12878-XiMat	blood
27	chr3:52278800-52280800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:52278800-52281400	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr3:52279000-52279400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52279000-52279400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:52279000-52279400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr3:52279000-52279400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr3:52279000-52279400	Enhancers	Brain Substantia Nigra	brain
34	chr3:52279000-52279400	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr3:52279000-52279400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr3:52279000-52279400	Bivalent Enhancer	Fetal Brain Male	brain
37	chr3:52279000-52279400	Flanking Active TSS	Fetal Thymus	thymus
38	chr3:52279000-52279400	Flanking Active TSS	Rectal Smooth Muscle	rectum
39	chr3:52279000-52279400	Flanking Active TSS	Thymus	Thymus
40	chr3:52279000-52279400	Flanking Active TSS	NHDF-Ad	bronchial
41	chr3:52279000-52279600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:52279000-52279600	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr3:52279000-52279600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr3:52279000-52279600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr3:52279000-52279600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:52279000-52279600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:52279000-52279600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr3:52279000-52279600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:52279000-52279600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:52279000-52279600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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