Variant report

Variant	rs527533008
Chromosome Location	chr3:49591777-49591778
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	POLR2A	chr3:49591524-49592002	HUVEC	blood vessel:	n/a	n/a
2	E2F6	chr3:49591619-49592041	K562	blood:	n/a	chr3:49591894-49591903 chr3:49591940-49591950
3	REST	chr3:49591685-49591949	PFSK-1	brain:	n/a	n/a
4	REST	chr3:49591575-49592555	U87	brain:	n/a	n/a
5	MAX	chr3:49591226-49592017	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:49591487-49592088	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:49591566-49591993	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:49591186-49592081	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOXA1	chr3:49591681-49591924	T-47D	breast:	n/a	n/a
10	REST	chr3:49591641-49592496	Hela-S3	cervix:	n/a	n/a
11	TCF12	chr3:49591355-49591974	ECC-1	luminal epithelium:	n/a	chr3:49591403-49591413 chr3:49591404-49591411
12	POLR2A	chr3:49591535-49591841	U87	brain:	n/a	n/a
13	MAX	chr3:49591293-49592008	A549	lung:	n/a	n/a
14	MAZ	chr3:49591551-49591954	HepG2	liver:	n/a	n/a
15	ELF1	chr3:49591695-49591961	K562	blood:	n/a	chr3:49591942-49591951 chr3:49591911-49591920
16	POLR2A	chr3:49591470-49591948	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:49591410-49592072	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr3:49591564-49592106	HepG2	liver:	n/a	n/a
19	EP300	chr3:49591556-49592413	SK-N-SH	brain:	n/a	chr3:49592274-49592290 chr3:49591802-49591818 chr3:49591902-49591918 chr3:49591802-49591811 chr3:49591951-49591960 chr3:49591950-49591959
20	REST	chr3:49591668-49592709	HepG2	liver:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
21	E2F6	chr3:49591515-49592003	A549	lung:	n/a	chr3:49591894-49591903 chr3:49591940-49591950
22	POLR2A	chr3:49591506-49592083	HEK293	kidney:	n/a	n/a
23	POLR2A	chr3:49591485-49592045	K562	blood:	n/a	n/a
24	POLR2A	chr3:49591552-49591917	HUVEC	blood vessel:	n/a	n/a
25	REST	chr3:49591593-49592485	MCF-7	breast:	n/a	n/a
26	REST	chr3:49590593-49593431	HL-60	blood:	n/a	chr3:49591201-49591211 chr3:49590761-49590779 chr3:49592639-49592653 chr3:49590764-49590777 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
27	POLR2A	chr3:49591632-49591987	A549	lung:	n/a	n/a
28	REST	chr3:49591469-49592776	U87	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
29	POLR2A	chr3:49591587-49591826	MCF-7	breast:	n/a	n/a
30	PAX5	chr3:49591524-49591870	GM12878	blood:	n/a	chr3:49591800-49591809
31	CREB1	chr3:49591316-49592050	H1-hESC	embryonic stem cell:	n/a	n/a
32	REST	chr3:49591481-49592787	GM12878	blood:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
33	HEY1	chr3:49591612-49591827	K562	blood:	n/a	n/a
34	EGR1	chr3:49591628-49591973	K562	blood:	n/a	chr3:49591800-49591809 chr3:49591894-49591903 chr3:49591876-49591889
35	TBP	chr3:49591432-49591920	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:49591505-49592058	MCF-7	breast:	n/a	n/a
37	RCOR1	chr3:49591526-49592427	HepG2	liver:	n/a	n/a
38	MAZ	chr3:49591231-49592453	IMR90	lung:	n/a	n/a
39	HMGN3	chr3:49591560-49592397	K562	blood:	n/a	n/a
40	REST	chr3:49591558-49592740	SK-N-SH	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
41	MYC	chr3:49591632-49591940	K562	blood:	n/a	n/a
42	TAF1	chr3:49591734-49592068	H1-neurons	neurons:	n/a	n/a
43	REST	chr3:49591648-49592672	H1-hESC	embryonic stem cell:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
44	POLR2A	chr3:49591613-49591807	A549	lung:	n/a	n/a
45	POLR2A	chr3:49591578-49591959	Gliobla	brain:	n/a	n/a
46	MYBL2	chr3:49591366-49591782	HepG2	liver:	n/a	n/a
47	NRF1	chr3:49591400-49592220	SK-N-SH	brain:	n/a	chr3:49591802-49591811 chr3:49591893-49591902 chr3:49591893-49591907 chr3:49591893-49591904 chr3:49591890-49591904 chr3:49591911-49591922 chr3:49591895-49591904 chr3:49591893-49591904
48	YY1	chr3:49591678-49592071	K562	blood:	n/a	chr3:49591911-49591925 chr3:49591905-49591916 chr3:49591802-49591816 chr3:49591908-49591922 chr3:49591943-49591954 chr3:49591939-49591953 chr3:49591951-49591960 chr3:49591945-49591959 chr3:49591935-49591943 chr3:49591911-49591920 chr3:49591922-49591944 chr3:49591905-49591919
49	E2F4	chr3:49591662-49591955	MCF10A-Er-Src	breast:	n/a	chr3:49591838-49591849 chr3:49591894-49591903 chr3:49591940-49591950
50	POLR2A	chr3:49591541-49591911	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49591748-49591798	HCM	heart:	n/a
2	chr3:49591741-49591791	HRCEpiC	kidney:	n/a
3	chr3:49591748-49591798	HCT-116	colon:	n/a
4	chr3:49591748-49591798	HAEpiC	amniotic membrane:	n/a
5	chr3:49591752-49591802	AG09319	gingival:	n/a
6	chr3:49591748-49591798	HMEC	breast:	n/a
7	chr3:49591741-49591791	IMR90	lung:	fetal
8	chr3:49591741-49591791	A549	lung:	n/a
9	chr3:49591741-49591791	NT2-D1	testis:	n/a
10	chr3:49591752-49591802	T-47D	breast:	n/a
11	chr3:49591752-49591802	ovcar-3	ovarian:	n/a
12	chr3:49591748-49591798	HRCEpiC	kidney:	n/a
13	chr3:49591752-49591802	AoSMC	blood vessel:	n/a
14	chr3:49591741-49591791	HCF	heart:	n/a
15	chr3:49591748-49591798	SK-N-SH	brain:	n/a
16	chr3:49591752-49591802	Caco-2	colon:	n/a
17	chr3:49591741-49591791	PANC-1	pancreas:	n/a
18	chr3:49591752-49591802	AG04449	skin:	fetal
19	chr3:49591752-49591802	HMEC	breast:	n/a
20	chr3:49591752-49591802	HCT-116	colon:	n/a
21	chr3:49591752-49591802	HRCEpiC	kidney:	n/a
22	chr3:49591748-49591798	HEK293	kidney:	embryo
23	chr3:49591741-49591791	LNCaP	prostate:	n/a
24	chr3:49591741-49591791	RPTEC	kidney:	n/a
25	chr3:49591752-49591802	AG10803	skin:	n/a
26	chr3:49591741-49591791	GM12891	blood:	n/a
27	chr3:49591748-49591798	Hepatocyte	liver:	n/a
28	chr3:49591741-49591791	Jurkat	blood:	n/a
29	chr3:49591752-49591802	NB4	blood:	n/a
30	chr3:49591748-49591798	SK-N-SH_RA	brain:	n/a
31	chr3:49591752-49591802	HEK293	kidney:	embryo
32	chr3:49591741-49591791	K562	blood:	n/a
33	chr3:49591748-49591798	NT2-D1	testis:	n/a
34	chr3:49591748-49591798	HIPEpiC	eye:	n/a
35	chr3:49591752-49591802	SAEC	small airway:	n/a
36	chr3:49591741-49591791	GM19239	blood:	n/a
37	chr3:49591748-49591798	U87	brain:	n/a
38	chr3:49591741-49591791	GM12892	blood:	n/a
39	chr3:49591752-49591802	HAEpiC	amniotic membrane:	n/a
40	chr3:49591741-49591791	CMK	blood:	n/a
41	chr3:49591741-49591791	SK-N-SH	brain:	n/a
42	chr3:49591748-49591798	GM12892	blood:	n/a
43	chr3:49591752-49591802	LNCaP	prostate:	n/a
44	chr3:49591748-49591798	SK-N-MC	brain:	n/a
45	chr3:49591752-49591802	Hela-S3	cervix:	n/a
46	chr3:49591752-49591802	PrEC	prostate:	n/a
47	chr3:49591741-49591791	Hela-S3	cervix:	n/a
48	chr3:49591748-49591798	BJ	skin:	n/a
49	chr3:49591748-49591798	PrEC	prostate:	n/a
50	chr3:49591752-49591802	A549	lung:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49590547..49592695-chr3:49709214..49711684,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NICN1-1	chr3:49591474-49591799	ENSG00000226913

Variant related genes	Relation type
BSN	TF binding region
BSN-AS2	TF binding region
BSN	CpG island
BSN-AS2	CpG island
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers 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 target site	56 gene(s)	inside rSNPs	diseases
2	esv3325224	chr3:49590473-49593321	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49590600-49591800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:49590600-49591800	Flanking Active TSS	Dnd41	blood
3	chr3:49590800-49591800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
4	chr3:49590800-49592400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:49591000-49591800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr3:49591000-49591800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:49591000-49591800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr3:49591000-49591800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:49591000-49591800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr3:49591000-49591800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
11	chr3:49591000-49591800	Flanking Active TSS	HUVEC	blood vessel
12	chr3:49591000-49591800	Flanking Active TSS	NHEK	skin
13	chr3:49591000-49592200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:49591000-49592400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr3:49591000-49592400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:49591000-49592800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:49591200-49591800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr3:49591200-49591800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
19	chr3:49591200-49591800	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr3:49591200-49591800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr3:49591200-49591800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
22	chr3:49591200-49591800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
23	chr3:49591200-49591800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
24	chr3:49591200-49591800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:49591200-49591800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:49591200-49591800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:49591200-49591800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
28	chr3:49591200-49591800	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr3:49591200-49591800	Flanking Active TSS	Placenta	Placenta
30	chr3:49591200-49592000	Flanking Active TSS	Esophagus	oesophagus
31	chr3:49591200-49592400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:49591200-49592400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:49591200-49592400	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr3:49591200-49592400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr3:49591200-49592400	Bivalent/Poised TSS	HepG2	liver
36	chr3:49591200-49592400	Active TSS	NHLF	lung
37	chr3:49591200-49592600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:49591200-49592600	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr3:49591200-49592600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:49591200-49592600	Active TSS	Fetal Brain Female	brain
41	chr3:49591200-49592800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
42	chr3:49591400-49591800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
43	chr3:49591400-49591800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr3:49591400-49591800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr3:49591400-49591800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:49591400-49591800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:49591400-49591800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:49591400-49591800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:49591400-49591800	Flanking Active TSS	HMEC	breast
50	chr3:49591400-49592000	Flanking Active TSS	Spleen	Spleen

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