Variant report

Variant	rs187439730
Chromosome Location	chr3:43327773-43327774
allele	A/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	CTCF	chr3:43327673-43327823	GM19238	blood:	n/a	chr3:43327712-43327725
2	CTCF	chr3:43327558-43328348	GM12878	blood:	n/a	chr3:43327712-43327725
3	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
4	SIN3AK20	chr3:43327662-43328193	HepG2	liver:	n/a	n/a
5	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
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	CTCF	chr3:43327696-43327807	Gliobla	brain:	n/a	chr3:43327712-43327725
13	TBP	chr3:43327737-43328279	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr3:43327660-43327810	HUVEC	blood vessel:	n/a	chr3:43327712-43327725
15	TCF3	chr3:43327667-43328141	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:43327749-43328257	A549	lung:	n/a	n/a
17	EBF1	chr3:43327721-43327982	GM12878	blood:	n/a	n/a
18	YY1	chr3:43327625-43328018	ECC-1	luminal epithelium:	n/a	chr3:43327714-43327725 chr3:43327871-43327882
19	SIN3AK20	chr3:43327611-43328031	K562	blood:	n/a	n/a
20	SIN3AK20	chr3:43327592-43328009	SK-N-SH	brain:	n/a	n/a
21	MYC	chr3:43327469-43327972	H1-hESC	embryonic stem cell:	n/a	chr3:43327715-43327725 chr3:43327830-43327840
22	CTCF	chr3:43327700-43327850	HL-60	blood:	n/a	chr3:43327712-43327725
23	POLR2A	chr3:43327685-43328272	H1-hESC	embryonic stem cell:	n/a	n/a
24	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
25	RAD21	chr3:43327609-43328306	IMR90	lung:	n/a	chr3:43327712-43327722 chr3:43327711-43327724 chr3:43327710-43327722
26	CTCF	chr3:43327694-43327828	NHEK	skin:	n/a	chr3:43327712-43327725
27	CTCF	chr3:43327640-43327790	A549	lung:	n/a	chr3:43327712-43327725
28	POLR2A	chr3:43327712-43328618	GM12892	blood:	n/a	n/a
29	NFIC	chr3:43327607-43328059	ECC-1	luminal epithelium:	n/a	n/a
30	CTCF	chr3:43327640-43327790	HEEpiC	esophagus:	n/a	chr3:43327712-43327725
31	EP300	chr3:43327604-43327820	K562	blood:	n/a	n/a
32	CTCF	chr3:43327680-43327830	Caco-2	colon:	n/a	chr3:43327712-43327725
33	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
34	POLR2A	chr3:43327694-43328200	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:43327659-43328338	Raji	blood:	n/a	n/a
36	TBL1XR1	chr3:43327658-43328283	K562	blood:	n/a	n/a
37	HEY1	chr3:43327701-43328333	K562	blood:	n/a	chr3:43327998-43328007 chr3:43327996-43328005 chr3:43328126-43328141
38	POLR2A	chr3:43327536-43328360	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr3:43327653-43328285	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr3:43327660-43327810	HMEC	breast:	n/a	chr3:43327712-43327725
41	MYC	chr3:43327697-43328037	MCF-7	breast:	n/a	chr3:43327715-43327725 chr3:43327830-43327840
42	CTCF	chr3:43327640-43327790	SAEC	small airway:	n/a	chr3:43327712-43327725
43	POLR2A	chr3:43327650-43328322	HL-60	blood:	n/a	n/a
44	CTCF	chr3:43327640-43327790	AG04450	lung:	n/a	chr3:43327712-43327725
45	CTCF	chr3:43327581-43327904	IMR90	lung:	n/a	chr3:43327712-43327725
46	POLR2A	chr3:43327719-43328473	ProgFib	skin:	n/a	n/a
47	CTCF	chr3:43327652-43327808	GM19240	blood:	n/a	chr3:43327712-43327725
48	POLR2A	chr3:43327748-43328179	U87	brain:	n/a	n/a
49	TAF7	chr3:43327720-43328229	H1-hESC	embryonic stem cell:	n/a	n/a
50	ARID3A	chr3:43327734-43328196	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:43305979..43308043-chr3:43325669..43327950,2	MCF-7	breast:
2	chr3:43314193..43316141-chr3:43325214..43327876,2	K562	blood:
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	chr19:1249504..1250049-chr3:43327521..43328330,2	Hela-S3	cervix:

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

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43318800-43327800	Weak transcription	Small Intestine	intestine
2	chr3:43327200-43327800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr3:43327200-43327800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:43327200-43327800	Flanking Active TSS	Dnd41	blood
5	chr3:43327200-43328800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr3:43327200-43328800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:43327200-43328800	Active TSS	Brain Germinal Matrix	brain
8	chr3:43327200-43328800	Active TSS	Brain Hippocampus Middle	brain
9	chr3:43327200-43329000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:43327200-43329000	Active TSS	Fetal Brain Female	brain
11	chr3:43327200-43329200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:43327200-43329200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:43327400-43327800	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr3:43327400-43327800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr3:43327400-43327800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr3:43327400-43327800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:43327400-43327800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr3:43327400-43327800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:43327400-43327800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:43327400-43327800	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr3:43327400-43327800	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr3:43327400-43327800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr3:43327400-43327800	Flanking Active TSS	NHEK	skin
24	chr3:43327400-43328000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr3:43327400-43328000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr3:43327400-43328600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:43327400-43328600	Active TSS	HepG2	liver
28	chr3:43327400-43328800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:43327400-43328800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:43327400-43328800	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr3:43327400-43328800	Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:43327400-43328800	Active TSS	Fetal Lung	lung
33	chr3:43327400-43329000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:43327400-43329000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:43327400-43329200	Active TSS	Lung	lung
36	chr3:43327400-43329400	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr3:43327400-43329800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:43327400-43330200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr3:43327400-43330600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:43327400-43332000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:43327600-43327800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:43327600-43327800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:43327600-43327800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr3:43327600-43327800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr3:43327600-43327800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:43327600-43327800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:43327600-43327800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:43327600-43327800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:43327600-43327800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:43327600-43327800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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