Variant report

Variant	rs539386647
Chromosome Location	chr3:52323829-52323830
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	MYC	chr3:52323795-52324589	HepG2	liver:	n/a	n/a
2	MBD4	chr3:52323569-52324735	HepG2	liver:	n/a	n/a
3	MXI1	chr3:52323397-52324700	HepG2	liver:	n/a	n/a
4	MAX	chr3:52322696-52324934	HepG2	liver:	n/a	chr3:52323578-52323587
5	BHLHE40	chr3:52323814-52324618	HepG2	liver:	n/a	n/a
6	HEY1	chr3:52323718-52324781	HepG2	liver:	n/a	n/a
7	MAFK	chr3:52323742-52324201	HepG2	liver:	n/a	n/a
8	RXRA	chr3:52323629-52324211	HepG2	liver:	n/a	chr3:52323662-52323678
9	HNF4A	chr3:52323467-52324681	HepG2	liver:	n/a	chr3:52324051-52324069 chr3:52324054-52324067 chr3:52324052-52324067 chr3:52324052-52324067 chr3:52324058-52324066 chr3:52324054-52324066 chr3:52323629-52323644 chr3:52324052-52324067 chr3:52323630-52323644 chr3:52324054-52324066 chr3:52323629-52323644 chr3:52323629-52323644 chr3:52324054-52324067 chr3:52324053-52324067
10	TAF1	chr3:52323752-52324749	HepG2	liver:	n/a	n/a
11	MYBL2	chr3:52323420-52324709	HepG2	liver:	n/a	n/a
12	HNF4G	chr3:52323754-52324389	HepG2	liver:	n/a	chr3:52324051-52324069 chr3:52324054-52324067 chr3:52324052-52324067 chr3:52324058-52324066 chr3:52324054-52324066 chr3:52324052-52324067 chr3:52324054-52324066 chr3:52324054-52324067 chr3:52324053-52324067
13	ARID3A	chr3:52323580-52324259	HepG2	liver:	n/a	n/a
14	HNF4A	chr3:52323693-52324527	HepG2	liver:	n/a	chr3:52324051-52324069 chr3:52324054-52324067 chr3:52324052-52324067 chr3:52324052-52324067 chr3:52324058-52324066 chr3:52324054-52324066 chr3:52324052-52324067 chr3:52324054-52324066 chr3:52324054-52324067 chr3:52324053-52324067
15	POLR2A	chr3:52323434-52324729	HepG2	liver:	n/a	n/a
16	SP1	chr3:52323469-52324304	HepG2	liver:	n/a	chr3:52323909-52323916
17	POLR2A	chr3:52323413-52325803	HepG2	liver:	n/a	n/a
18	TAF1	chr3:52323815-52324699	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:52323636-52325349	HepG2	liver:	n/a	n/a
20	ELF1	chr3:52323708-52324268	HepG2	liver:	n/a	n/a
21	REST	chr3:52323746-52324253	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:52323779-52323831	MCF10A-Er-Src	breast:	n/a	n/a
23	EP300	chr3:52323555-52324325	HepG2	liver:	n/a	n/a
24	RCOR1	chr3:52323512-52324493	HepG2	liver:	n/a	n/a
25	TBP	chr3:52323812-52324677	HepG2	liver:	n/a	n/a
26	MYBL2	chr3:52323298-52324681	HepG2	liver:	n/a	n/a
27	HNF4G	chr3:52323480-52324313	HepG2	liver:	n/a	chr3:52324051-52324069 chr3:52324054-52324067 chr3:52324052-52324067 chr3:52324058-52324066 chr3:52324054-52324066 chr3:52323629-52323644 chr3:52324052-52324067 chr3:52323630-52323644 chr3:52324054-52324066 chr3:52323629-52323644 chr3:52323629-52323644 chr3:52324054-52324067 chr3:52324053-52324067
28	HDAC2	chr3:52323608-52324279	HepG2	liver:	n/a	n/a
29	RFX5	chr3:52323720-52324261	HepG2	liver:	n/a	n/a
30	CHD2	chr3:52323810-52324488	HepG2	liver:	n/a	n/a
31	USF1	chr3:52323813-52324186	HepG2	liver:	n/a	n/a
32	SIN3AK20	chr3:52323713-52324262	HepG2	liver:	n/a	n/a
33	ELF1	chr3:52323691-52324245	HepG2	liver:	n/a	n/a
34	NFIC	chr3:52323523-52324376	HepG2	liver:	n/a	n/a
35	FOXA1	chr3:52323642-52324148	HepG2	liver:	n/a	n/a
36	JUND	chr3:52323814-52324172	HepG2	liver:	n/a	n/a
37	HNF4A	chr3:52323546-52324310	HepG2	liver:	n/a	chr3:52324051-52324069 chr3:52324054-52324067 chr3:52324052-52324067 chr3:52324052-52324067 chr3:52324058-52324066 chr3:52324054-52324066 chr3:52323629-52323644 chr3:52324052-52324067 chr3:52323630-52323644 chr3:52324054-52324066 chr3:52323629-52323644 chr3:52323629-52323644 chr3:52324054-52324067 chr3:52324053-52324067
38	HDAC2	chr3:52323614-52324262	HepG2	liver:	n/a	n/a
39	CEBPD	chr3:52323690-52324317	HepG2	liver:	n/a	n/a
40	HEY1	chr3:52323266-52324685	HepG2	liver:	n/a	n/a
41	FOXA1	chr3:52323560-52324349	HepG2	liver:	n/a	n/a
42	EP300	chr3:52323586-52324321	HepG2	liver:	n/a	n/a
43	JUND	chr3:52323749-52324235	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:52320120-52326729	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr3:52323719-52324241	HepG2	liver:	n/a	n/a
46	FOXA2	chr3:52323707-52324224	HepG2	liver:	n/a	n/a
47	YY1	chr3:52323704-52324647	HepG2	liver:	n/a	n/a
48	TEAD4	chr3:52323549-52324366	HepG2	liver:	n/a	n/a
49	MAZ	chr3:52323602-52324250	HepG2	liver:	n/a	n/a
50	NFIC	chr3:52323651-52324294	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52318594..52322784-chr3:52322985..52327026,4	MCF-7	breast:
2	chr3:52272181..52276088-chr3:52318615..52323958,11	MCF-7	breast:
3	chr3:52271022..52275105-chr3:52320320..52325575,6	K562	blood:
4	chr3:52310660..52314319-chr3:52321399..52324807,9	K562	blood:
5	chr3:52321744..52323842-chr3:52332822..52334732,2	MCF-7	breast:
6	chr3:52321768..52324071-chr3:52488633..52490328,2	K562	blood:
7	chr3:52271015..52274727-chr3:52321912..52324165,4	K562	blood:

Variant related genes	Relation type
GLYCTK	TF binding region
WDR82	TF binding region
ENSG00000242797	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000247596	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
10	esv3402579	chr3:52323712-52330410	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 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	chr3:52322400-52324400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:52322400-52324600	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr3:52322400-52325200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr3:52322600-52324000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:52322600-52324000	Enhancers	Fetal Intestine Large	intestine
6	chr3:52322600-52324000	Enhancers	Fetal Intestine Small	intestine
7	chr3:52322600-52324000	Flanking Active TSS	HepG2	liver
8	chr3:52322600-52324200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:52322600-52324200	Enhancers	Gastric	stomach
10	chr3:52322600-52324600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:52322600-52324600	Enhancers	Pancreas	Pancrea
12	chr3:52322600-52324800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:52322600-52325200	Weak transcription	Ovary	ovary
14	chr3:52322600-52325400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:52322600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:52322600-52332000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
18	chr3:52322800-52324000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:52322800-52324400	Enhancers	Placenta	Placenta
20	chr3:52322800-52324600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr3:52322800-52324600	Weak transcription	Esophagus	oesophagus
22	chr3:52322800-52324800	Enhancers	A549	lung
23	chr3:52322800-52325000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:52322800-52325800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:52322800-52326400	Weak transcription	Fetal Brain Female	brain
26	chr3:52322800-52330800	Weak transcription	Brain Germinal Matrix	brain
27	chr3:52322800-52331400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:52322800-52331400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:52322800-52331600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:52322800-52331800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:52323000-52324000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:52323000-52324000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:52323000-52324000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr3:52323000-52324000	Enhancers	K562	blood
35	chr3:52323000-52324200	Weak transcription	Fetal Stomach	stomach
36	chr3:52323000-52324400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:52323000-52324600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr3:52323000-52324600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:52323000-52324600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:52323000-52324800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:52323000-52324800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:52323000-52324800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr3:52323000-52324800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr3:52323000-52324800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:52323000-52324800	Weak transcription	Left Ventricle	heart
46	chr3:52323000-52325000	Weak transcription	Fetal Lung	lung
47	chr3:52323000-52325800	Weak transcription	NHEK	skin
48	chr3:52323000-52326000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:52323000-52326000	Weak transcription	Aorta	Aorta
50	chr3:52323000-52328200	Weak transcription	Psoas Muscle	Psoas

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