Variant report

Variant	rs566660290
Chromosome Location	chr3:43327909-43327910
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	CTCF	chr3:43327558-43328348	GM12878	blood:	n/a	chr3:43327712-43327725
2	E2F4	chr3:43327418-43328182	MCF10A-Er-Src	breast:	n/a	chr3:43328022-43328031 chr3:43327675-43327687 chr3:43327996-43328005 chr3:43327972-43327983 chr3:43327998-43328007
3	SIN3AK20	chr3:43327662-43328193	HepG2	liver:	n/a	n/a
4	BHLHE40	chr3:43327636-43328158	GM12878	blood:	n/a	chr3:43328124-43328140 chr3:43328135-43328151 chr3:43328051-43328067 chr3:43328127-43328143 chr3:43328126-43328142 chr3:43328052-43328068
5	ZBTB7A	chr3:43327836-43328367	K562	blood:	n/a	n/a
6	RFX5	chr3:43327634-43328173	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr3:43327568-43328205	Hela-S3	cervix:	n/a	n/a
8	MXI1	chr3:43327605-43328306	GM12878	blood:	n/a	n/a
9	MAX	chr3:43327608-43328327	HepG2	liver:	n/a	chr3:43327715-43327725 chr3:43327830-43327840
10	POLR2A	chr3:43327634-43328193	SK-N-MC	brain:	n/a	n/a
11	BHLHE40	chr3:43327568-43328118	K562	blood:	n/a	chr3:43328051-43328067 chr3:43328052-43328068
12	TBP	chr3:43327737-43328279	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF3	chr3:43327667-43328141	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:43327749-43328257	A549	lung:	n/a	n/a
15	EBF1	chr3:43327721-43327982	GM12878	blood:	n/a	n/a
16	YY1	chr3:43327625-43328018	ECC-1	luminal epithelium:	n/a	chr3:43327714-43327725 chr3:43327871-43327882
17	SIN3AK20	chr3:43327611-43328031	K562	blood:	n/a	n/a
18	SIN3AK20	chr3:43327592-43328009	SK-N-SH	brain:	n/a	n/a
19	IRF1	chr3:43327895-43328248	K562	blood:	n/a	n/a
20	MYC	chr3:43327469-43327972	H1-hESC	embryonic stem cell:	n/a	chr3:43327715-43327725 chr3:43327830-43327840
21	POLR2A	chr3:43327685-43328272	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr3:43327599-43328347	K562	blood:	n/a	chr3:43328127-43328138 chr3:43327714-43327725 chr3:43327871-43327882 chr3:43328015-43328029 chr3:43328050-43328059 chr3:43328127-43328136 chr3:43328127-43328141 chr3:43328224-43328238
23	RAD21	chr3:43327609-43328306	IMR90	lung:	n/a	chr3:43327712-43327722 chr3:43327711-43327724 chr3:43327710-43327722
24	POLR2A	chr3:43327712-43328618	GM12892	blood:	n/a	n/a
25	NFIC	chr3:43327607-43328059	ECC-1	luminal epithelium:	n/a	n/a
26	YY1	chr3:43327615-43328158	H1-hESC	embryonic stem cell:	n/a	chr3:43328127-43328138 chr3:43327714-43327725 chr3:43327871-43327882 chr3:43328015-43328029 chr3:43328050-43328059 chr3:43328127-43328136 chr3:43328127-43328141
27	POLR2A	chr3:43327694-43328200	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:43327659-43328338	Raji	blood:	n/a	n/a
29	TBL1XR1	chr3:43327658-43328283	K562	blood:	n/a	n/a
30	HEY1	chr3:43327701-43328333	K562	blood:	n/a	chr3:43327998-43328007 chr3:43327996-43328005 chr3:43328126-43328141
31	POLR2A	chr3:43327536-43328360	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr3:43327653-43328285	Hela-S3	cervix:	n/a	n/a
33	MYC	chr3:43327697-43328037	MCF-7	breast:	n/a	chr3:43327715-43327725 chr3:43327830-43327840
34	POLR2A	chr3:43327650-43328322	HL-60	blood:	n/a	n/a
35	POLR2A	chr3:43327719-43328473	ProgFib	skin:	n/a	n/a
36	JUND	chr3:43327842-43328165	HepG2	liver:	n/a	chr3:43327997-43328006
37	RFX5	chr3:43327857-43328090	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:43327748-43328179	U87	brain:	n/a	n/a
39	TAF7	chr3:43327720-43328229	H1-hESC	embryonic stem cell:	n/a	n/a
40	ARID3A	chr3:43327734-43328196	HepG2	liver:	n/a	n/a
41	ZMIZ1	chr3:43327708-43328106	K562	blood:	n/a	n/a
42	FOXA1	chr3:43327799-43328159	T-47D	breast:	n/a	n/a
43	MYC	chr3:43327535-43328237	NB4	blood:	n/a	chr3:43327715-43327725 chr3:43327830-43327840
44	MAX	chr3:43327199-43328223	HepG2	liver:	n/a	chr3:43327715-43327725 chr3:43327830-43327840
45	POLR2A	chr3:43327584-43328444	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr3:43327697-43328269	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:43327790-43328205	A549	lung:	n/a	n/a
48	TCF7L2	chr3:43327399-43327975	Hela-S3	cervix:	n/a	n/a
49	ELK1	chr3:43327793-43328048	Hela-S3	cervix:	n/a	n/a
50	E2F6	chr3:43327426-43328107	A549	lung:	n/a	chr3:43328022-43328031 chr3:43327675-43327687 chr3:43327996-43328005 chr3:43327998-43328007

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:43327880-43327930	HCT-116	colon:	n/a
2	chr3:43327880-43327930	NT2-D1	testis:	n/a
3	chr3:43327880-43327930	SKMC	muscle:	n/a
4	chr3:43327880-43327930	U87	brain:	n/a
5	chr3:43327880-43327930	Hepatocyte	liver:	n/a
6	chr3:43327880-43327930	GM19239	blood:	n/a
7	chr3:43327880-43327930	HL-60	blood:	n/a
8	chr3:43327880-43327930	MCF10A-Er-Src	breast:	n/a
9	chr3:43327880-43327930	SK-N-MC	brain:	n/a
10	chr3:43327880-43327930	SK-N-SH	brain:	n/a
11	chr3:43327880-43327930	A549	lung:	n/a
12	chr3:43327880-43327930	GM12892	blood:	n/a
13	chr3:43327880-43327930	HEEpiC	esophagus:	n/a
14	chr3:43327880-43327930	CMK	blood:	n/a
15	chr3:43327880-43327930	IMR90	lung:	fetal
16	chr3:43327880-43327930	HCPEpiC	choroid plexus:	n/a
17	chr3:43327880-43327930	PrEC	prostate:	n/a
18	chr3:43327880-43327930	AG04449	skin:	fetal
19	chr3:43327880-43327930	H1-hESC	embryonic stem cell:	embryo
20	chr3:43327880-43327930	RPTEC	kidney:	n/a
21	chr3:43327880-43327930	ProgFib	skin:	n/a
22	chr3:43327880-43327930	GM06990	blood:	n/a
23	chr3:43327880-43327930	NH-A	brain:	n/a
24	chr3:43327880-43327930	ECC-1	luminal epithelium:	n/a
25	chr3:43327880-43327930	AG10803	skin:	n/a
26	chr3:43327880-43327930	NHDF-neo	bronchial:	n/a
27	chr3:43327880-43327930	AG09319	gingival:	n/a
28	chr3:43327880-43327930	AG09309	skin:	n/a
29	chr3:43327880-43327930	HPAEpiC	pulmonary alveolar:	n/a
30	chr3:43327880-43327930	GM12891	blood:	n/a
31	chr3:43327880-43327930	AG04450	lung:	fetal
32	chr3:43327880-43327930	HRCEpiC	kidney:	n/a
33	chr3:43327880-43327930	Jurkat	blood:	n/a
34	chr3:43327880-43327930	HMEC	breast:	n/a
35	chr3:43327880-43327930	HUVEC	blood vessel:	n/a
36	chr3:43327880-43327930	PFSK-1	brain:	n/a
37	chr3:43327880-43327930	SAEC	small airway:	n/a
38	chr3:43327880-43327930	HAEpiC	amniotic membrane:	n/a
39	chr3:43327880-43327930	AoSMC	blood vessel:	n/a
40	chr3:43327880-43327930	HNPCEpiC	eye:	n/a
41	chr3:43327880-43327930	K562	blood:	n/a
42	chr3:43327880-43327930	MCF-7	breast:	n/a
43	chr3:43327880-43327930	LNCaP	prostate:	n/a
44	chr3:43327880-43327930	GM12878	blood:	n/a
45	chr3:43327880-43327930	SK-N-SH_RA	brain:	n/a
46	chr3:43327880-43327930	Hela-S3	cervix:	n/a
47	chr3:43327880-43327930	HEK293	kidney:	embryo
48	chr3:43327880-43327930	NHBE	bronchial:	n/a
49	chr3:43327880-43327930	NB4	blood:	n/a
50	chr3:43327880-43327930	HRE	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:43305979..43308043-chr3:43325669..43327950,2	MCF-7	breast:
2	chr3:43327783..43328333-chr5:32173796..32174464,2	Hela-S3	cervix:
3	chr2:208394589..208395128-chr3:43327696..43328487,2	Hela-S3	cervix:
4	chr10:98346013..98346591-chr3:43327414..43328126,2	Hela-S3	cervix:
5	chr3:43327640..43330625-chr3:43731199..43733951,3	K562	blood:
6	chr20:30192245..30193126-chr3:43327692..43328283,2	Hela-S3	cervix:
7	chr14:103988769..103989622-chr3:43327887..43328473,2	HCT-116	colon:
8	chr19:1249504..1250049-chr3:43327521..43328330,2	Hela-S3	cervix:

Variant related genes	Relation type
SNRK	TF binding region
SNRK	CpG island
ENSG00000166165	Chromatin interaction
ENSG00000118260	Chromatin interaction
ENSG00000077147	Chromatin interaction
ENSG00000011198	Chromatin interaction
ENSG00000167470	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000113384	Chromatin interaction
ENSG00000160746	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3420235	chr3:43326048-43330246	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv876732	chr3:43326887-43360879	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3527908	chr3:43327298-43329521	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	esv3527909	chr3:43327298-43329521	Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv14554	chr3:43327794-43328639	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv590151	chr3:43327821-43328529	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv590152	chr3:43327873-43328529	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv590153	chr3:43327873-43329913	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv590154	chr3:43327873-43334020	Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv590155	chr3:43327873-43334878	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43327200-43328800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:43327200-43328800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:43327200-43328800	Active TSS	Brain Germinal Matrix	brain
4	chr3:43327200-43328800	Active TSS	Brain Hippocampus Middle	brain
5	chr3:43327200-43329000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:43327200-43329000	Active TSS	Fetal Brain Female	brain
7	chr3:43327200-43329200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:43327200-43329200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:43327400-43328000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr3:43327400-43328000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:43327400-43328600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:43327400-43328600	Active TSS	HepG2	liver
13	chr3:43327400-43328800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:43327400-43328800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:43327400-43328800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:43327400-43328800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr3:43327400-43328800	Active TSS	Fetal Lung	lung
18	chr3:43327400-43329000	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:43327400-43329000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:43327400-43329200	Active TSS	Lung	lung
21	chr3:43327400-43329400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:43327400-43329800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:43327400-43330200	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr3:43327400-43330600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:43327400-43332000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr3:43327600-43328000	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr3:43327600-43328600	Active TSS	Brain Substantia Nigra	brain
28	chr3:43327600-43328600	Weak transcription	Stomach Mucosa	stomach
29	chr3:43327600-43328600	Active TSS	K562	blood
30	chr3:43327600-43328800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:43327600-43328800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:43327600-43328800	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr3:43327600-43328800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr3:43327600-43328800	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr3:43327600-43328800	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr3:43327600-43328800	Active TSS	Brain Angular Gyrus	brain
37	chr3:43327600-43328800	Active TSS	Brain Cingulate Gyrus	brain
38	chr3:43327600-43328800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr3:43327600-43328800	Active TSS	Fetal Kidney	kidney
40	chr3:43327600-43328800	Active TSS	HSMMtube	muscle
41	chr3:43327600-43328800	Active TSS	NH-A	brain
42	chr3:43327600-43328800	Active TSS	Osteobl	bone
43	chr3:43327600-43329000	Active TSS	H1 Cell Line	embryonic stem cell
44	chr3:43327600-43329000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:43327600-43329000	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:43327600-43329000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:43327600-43329000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:43327600-43329000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:43327600-43329000	Active TSS	Brain Anterior Caudate	brain
50	chr3:43327600-43329000	Active TSS	Brain Inferior Temporal Lobe	brain

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