Variant report

Variant	rs530549463
Chromosome Location	chr3:52324415-52324416
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	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	CTCF	chr3:52324400-52324550	GM12869	blood:	n/a	n/a
8	BRCA1	chr3:52324038-52324475	HepG2	liver:	n/a	n/a
9	CTCF	chr3:52324380-52324530	HRPEpiC	eye:	n/a	n/a
10	MAX	chr3:52323890-52324612	HepG2	liver:	n/a	n/a
11	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
12	TAF1	chr3:52323752-52324749	HepG2	liver:	n/a	n/a
13	MYBL2	chr3:52323420-52324709	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	POLR2A	chr3:52323413-52325803	HepG2	liver:	n/a	n/a
17	TAF1	chr3:52323815-52324699	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:52323636-52325349	HepG2	liver:	n/a	n/a
19	RCOR1	chr3:52323512-52324493	HepG2	liver:	n/a	n/a
20	TBP	chr3:52323812-52324677	HepG2	liver:	n/a	n/a
21	MYBL2	chr3:52323298-52324681	HepG2	liver:	n/a	n/a
22	CTCF	chr3:52324380-52324590	HRE	kidney:	n/a	n/a
23	CHD2	chr3:52323810-52324488	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:52323848-52324617	HepG2	liver:	n/a	n/a
25	CTCF	chr3:52324400-52324550	GM12868	blood:	n/a	n/a
26	HEY1	chr3:52323266-52324685	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:52320120-52326729	HepG2	liver:	n/a	n/a
28	EP300	chr3:52323925-52324577	HepG2	liver:	n/a	n/a
29	CTCF	chr3:52324300-52324450	A549	lung:	n/a	n/a
30	YY1	chr3:52323704-52324647	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:52323904-52324589	HepG2	liver:	n/a	n/a
32	CTCF	chr3:52324360-52324510	NHEK	skin:	n/a	n/a
33	CTCF	chr3:52324360-52324510	Caco-2	colon:	n/a	n/a
34	RAD21	chr3:52323988-52324728	HepG2	liver:	n/a	n/a
35	CTCF	chr3:52324360-52324510	SAEC	small airway:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52318594..52322784-chr3:52322985..52327026,4	MCF-7	breast:
2	chr3:52271022..52275105-chr3:52320320..52325575,6	K562	blood:
3	chr3:52321086..52323733-chr3:52324166..52327461,5	MCF-7	breast:
4	chr3:52310660..52314319-chr3:52321399..52324807,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR82-1	chr3:52324335-52324901	NONHSAT089912

Variant related genes	Relation type
WDR82	TF binding region
GLYCTK	TF binding region
ENSG00000247596	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000239732	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	chr3:52322400-52324600	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr3:52322400-52325200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
3	chr3:52322600-52324600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:52322600-52324600	Enhancers	Pancreas	Pancrea
5	chr3:52322600-52324800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:52322600-52325200	Weak transcription	Ovary	ovary
7	chr3:52322600-52325400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:52322600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:52322600-52332000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
11	chr3:52322800-52324600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr3:52322800-52324600	Weak transcription	Esophagus	oesophagus
13	chr3:52322800-52324800	Enhancers	A549	lung
14	chr3:52322800-52325000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:52322800-52325800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:52322800-52326400	Weak transcription	Fetal Brain Female	brain
17	chr3:52322800-52330800	Weak transcription	Brain Germinal Matrix	brain
18	chr3:52322800-52331400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:52322800-52331400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:52322800-52331600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:52322800-52331800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:52323000-52324600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:52323000-52324600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:52323000-52324600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr3:52323000-52324800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:52323000-52324800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:52323000-52324800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr3:52323000-52324800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:52323000-52324800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:52323000-52324800	Weak transcription	Left Ventricle	heart
31	chr3:52323000-52325000	Weak transcription	Fetal Lung	lung
32	chr3:52323000-52325800	Weak transcription	NHEK	skin
33	chr3:52323000-52326000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:52323000-52326000	Weak transcription	Aorta	Aorta
35	chr3:52323000-52328200	Weak transcription	Psoas Muscle	Psoas
36	chr3:52323000-52332600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:52323200-52324800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:52323200-52325000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:52323200-52325000	Weak transcription	Brain Substantia Nigra	brain
40	chr3:52323200-52325000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:52323200-52325000	Weak transcription	Osteobl	bone
42	chr3:52323200-52325200	Weak transcription	Fetal Thymus	thymus
43	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
44	chr3:52323400-52324600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:52323400-52324600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:52323400-52324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:52323400-52324800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr3:52323400-52324800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:52323400-52324800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:52323400-52325000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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