Variant report

Variant	rs534129713
Chromosome Location	chr3:52279666-52279667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:92)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:92 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52278923-52280296	GM19193	blood:	n/a	n/a
2	POLR2A	chr3:52279597-52280387	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3AK20	chr3:52279571-52280158	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr3:52279565-52280316	HUVEC	blood vessel:	n/a	n/a
5	MAX	chr3:52279453-52280393	H1-hESC	embryonic stem cell:	n/a	chr3:52279824-52279834
6	HDAC2	chr3:52279520-52280062	HepG2	liver:	n/a	n/a
7	TBP	chr3:52279614-52279757	K562	blood:	n/a	n/a
8	CCNT2	chr3:52279514-52280141	K562	blood:	n/a	chr3:52279685-52279694 chr3:52280077-52280086
9	POLR2A	chr3:52279582-52280073	GM12878	blood:	n/a	n/a
10	RCOR1	chr3:52279471-52279671	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:52279434-52280252	GM12891	blood:	n/a	n/a
12	HA-E2F1	chr3:52279535-52280287	MCF-7	breast:	n/a	chr3:52279827-52279837
13	RUNX3	chr3:52277852-52279708	GM12878	blood:	n/a	n/a
14	TAF1	chr3:52279467-52280223	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr3:52279555-52280480	HUVEC	blood vessel:	n/a	n/a
16	UBTF	chr3:52279503-52280197	K562	blood:	n/a	n/a
17	E2F6	chr3:52279451-52280361	H1-hESC	embryonic stem cell:	n/a	chr3:52279827-52279837
18	MAZ	chr3:52279475-52280319	K562	blood:	n/a	chr3:52279824-52279834
19	E2F6	chr3:52279499-52280261	K562	blood:	n/a	chr3:52279827-52279837
20	POLR2A	chr3:52278806-52280260	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:52279203-52280263	GM18951	blood:	n/a	n/a
22	POLR2A	chr3:52277954-52280665	GM12878	blood:	n/a	n/a
23	MAX	chr3:52279337-52280574	H1-hESC	embryonic stem cell:	n/a	chr3:52279824-52279834
24	POLR2A	chr3:52279413-52279749	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:52279495-52280259	HUVEC	blood vessel:	n/a	n/a
26	MAZ	chr3:52278887-52280307	GM12878	blood:	n/a	chr3:52279824-52279834
27	MAX	chr3:52279261-52280339	ECC-1	luminal epithelium:	n/a	chr3:52279824-52279834
28	MXI1	chr3:52279418-52280105	GM12878	blood:	n/a	n/a
29	MAX	chr3:52279391-52280369	SK-N-SH	brain:	n/a	chr3:52279824-52279834
30	POLR2A	chr3:52277713-52280381	GM18505	blood:	n/a	n/a
31	E2F6	chr3:52279428-52280317	K562	blood:	n/a	chr3:52279449-52279459 chr3:52279827-52279837
32	POLR2A	chr3:52279510-52280175	GM10847	blood:	n/a	n/a
33	POLR2A	chr3:52278939-52280285	MCF-7	breast:	n/a	n/a
34	POLR2A	chr3:52278818-52280201	GM12878	blood:	n/a	n/a
35	EBF1	chr3:52277812-52280262	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:52278021-52280334	GM12892	blood:	n/a	n/a
37	GABPA	chr3:52279634-52280073	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZNF143	chr3:52279526-52280244	H1-hESC	embryonic stem cell:	n/a	chr3:52280120-52280130 chr3:52279672-52279682
39	POLR2A	chr3:52278960-52280260	GM15510	blood:	n/a	n/a
40	POLR2A	chr3:52277951-52280233	GM19099	blood:	n/a	n/a
41	MAX	chr3:52279457-52280385	A549	lung:	n/a	chr3:52279824-52279834
42	MTA3	chr3:52277397-52279759	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:52279055-52280266	GM18526	blood:	n/a	n/a
44	POLR2A	chr3:52278927-52280465	GM12891	blood:	n/a	n/a
45	POLR2A	chr3:52277466-52280409	GM12892	blood:	n/a	n/a
46	YY1	chr3:52278794-52280163	GM12892	blood:	n/a	chr3:52279823-52279834 chr3:52279685-52279696 chr3:52279860-52279874
47	POLR2A	chr3:52279577-52280230	A549	lung:	n/a	n/a
48	STAT5A	chr3:52277957-52279805	GM12878	blood:	n/a	chr3:52278528-52278535
49	ELF1	chr3:52279541-52280313	GM12878	blood:	n/a	chr3:52279864-52279877
50	HA-E2F1	chr3:52279580-52280237	Hela-S3	cervix:	n/a	chr3:52279827-52279837

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52279625-52279675	HNPCEpiC	eye:	n/a
2	chr3:52279625-52279675	NT2-D1	testis:	n/a
3	chr3:52279625-52279675	T-47D	breast:	n/a
4	chr3:52279625-52279675	PFSK-1	brain:	n/a
5	chr3:52279625-52279675	HRE	kidney:	n/a
6	chr3:52279625-52279675	AG09309	skin:	n/a
7	chr3:52279625-52279675	ProgFib	skin:	n/a
8	chr3:52279625-52279675	ECC-1	luminal epithelium:	n/a
9	chr3:52279625-52279675	AG04449	skin:	fetal
10	chr3:52279625-52279675	AG09319	gingival:	n/a
11	chr3:52279625-52279675	NB4	blood:	n/a
12	chr3:52279625-52279675	HEEpiC	esophagus:	n/a
13	chr3:52279625-52279675	LNCaP	prostate:	n/a
14	chr3:52279625-52279675	GM12892	blood:	n/a
15	chr3:52279625-52279675	HAEpiC	amniotic membrane:	n/a
16	chr3:52279625-52279675	HEK293	kidney:	embryo
17	chr3:52279625-52279675	HRCEpiC	kidney:	n/a
18	chr3:52279625-52279675	IMR90	lung:	fetal
19	chr3:52279625-52279675	HIPEpiC	eye:	n/a
20	chr3:52279625-52279675	HCM	heart:	n/a
21	chr3:52279625-52279675	AG10803	skin:	n/a
22	chr3:52279625-52279675	Hepatocyte	liver:	n/a
23	chr3:52279625-52279675	SK-N-MC	brain:	n/a
24	chr3:52279625-52279675	H1-hESC	embryonic stem cell:	embryo
25	chr3:52279625-52279675	SK-N-SH_RA	brain:	n/a
26	chr3:52279625-52279675	HCT-116	colon:	n/a
27	chr3:52279625-52279675	HCPEpiC	choroid plexus:	n/a
28	chr3:52279625-52279675	SKMC	muscle:	n/a
29	chr3:52279625-52279675	HPAEpiC	pulmonary alveolar:	n/a
30	chr3:52279625-52279675	ovcar-3	ovarian:	n/a
31	chr3:52279625-52279675	SAEC	small airway:	n/a
32	chr3:52279625-52279675	AG04450	lung:	fetal
33	chr3:52279625-52279675	GM12878	blood:	n/a
34	chr3:52279625-52279675	HCF	heart:	n/a
35	chr3:52279625-52279675	BJ	skin:	n/a
36	chr3:52279625-52279675	NHDF-neo	bronchial:	n/a
37	chr3:52279625-52279675	GM06990	blood:	n/a
38	chr3:52279625-52279675	Caco-2	colon:	n/a
39	chr3:52279625-52279675	NHBE	bronchial:	n/a
40	chr3:52279625-52279675	GM12891	blood:	n/a
41	chr3:52279625-52279675	BE2_C	brain:	n/a
42	chr3:52279625-52279675	CMK	blood:	n/a
43	chr3:52279625-52279675	MCF-7	breast:	n/a
44	chr3:52279625-52279675	K562	blood:	n/a
45	chr3:52279625-52279675	GM19239	blood:	n/a
46	chr3:52279625-52279675	Hela-S3	cervix:	n/a
47	chr3:52279625-52279675	HL-60	blood:	n/a
48	chr3:52279625-52279675	PrEC	prostate:	n/a
49	chr3:52279625-52279675	RPTEC	kidney:	n/a
50	chr3:52279625-52279675	Jurkat	blood:	n/a

(count:7 , 50 per page) page: 1

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	chr3:52278070..52281652-chr3:52320199..52323338,4	MCF-7	breast:
7	chr3:52278312..52281288-chr3:52312020..52314246,3	MCF-7	breast:

No data

Variant related genes	Relation type
PPM1M	TF binding region
PPM1M	CpG island
ENSG00000133316	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000168237	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52277600-52282000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr3:52278400-52280600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:52278800-52280800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:52278800-52281400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr3:52279000-52279800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr3:52279000-52280400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:52279000-52280400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr3:52279000-52280600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:52279000-52280600	Enhancers	Fetal Heart	heart
10	chr3:52279000-52281400	Flanking Active TSS	Dnd41	blood
11	chr3:52279000-52281400	Active TSS	Osteobl	bone
12	chr3:52279000-52281800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:52279200-52280000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
14	chr3:52279200-52280200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr3:52279200-52280200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:52279200-52280400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:52279200-52280400	Active TSS	Aorta	Aorta
18	chr3:52279200-52280400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:52279200-52280400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:52279200-52280600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:52279200-52280600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
22	chr3:52279200-52280600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:52279200-52280600	Active TSS	Fetal Kidney	kidney
24	chr3:52279200-52280800	Active TSS	Right Atrium	heart
25	chr3:52279400-52280000	Active TSS	Left Ventricle	heart
26	chr3:52279400-52280000	Active TSS	Psoas Muscle	Psoas
27	chr3:52279400-52280000	Active TSS	Thymus	Thymus
28	chr3:52279400-52280200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr3:52279400-52280200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:52279400-52280200	Active TSS	Colon Smooth Muscle	Colon
31	chr3:52279400-52280200	Active TSS	Ovary	ovary
32	chr3:52279400-52280200	Active TSS	Placenta Amnion	Placenta Amnion
33	chr3:52279400-52280200	Active TSS	Rectal Smooth Muscle	rectum
34	chr3:52279400-52280200	Active TSS	Small Intestine	intestine
35	chr3:52279400-52280400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:52279400-52280400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr3:52279400-52280400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:52279400-52280400	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr3:52279400-52280400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr3:52279400-52280400	Active TSS	Lung	lung
41	chr3:52279400-52280400	Active TSS	NHDF-Ad	bronchial
42	chr3:52279400-52280600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:52279400-52281000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:52279600-52279800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:52279600-52279800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:52279600-52279800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:52279600-52279800	Active TSS	Colonic Mucosa	Colon
48	chr3:52279600-52280000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:52279600-52280000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:52279600-52280000	Active TSS	Primary monocytes fromperipheralblood	blood

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