Variant report

Variant	rs45536040
Chromosome Location	chr5:40678808-40678809
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	GTF2F1	chr5:40678805-40680138	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr5:40678612-40679131	MCF-7	breast:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
3	POLR2A	chr5:40678244-40680457	NB4	blood:	n/a	n/a
4	TCF12	chr5:40678786-40679832	A549	lung:	n/a	chr5:40679806-40679813
5	MAX	chr5:40678144-40680687	NB4	blood:	n/a	n/a
6	RAD21	chr5:40678153-40679736	Hela-S3	cervix:	n/a	chr5:40679296-40679306 chr5:40679294-40679306
7	CEBPB	chr5:40678184-40680090	Hela-S3	cervix:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
8	TBP	chr5:40678152-40680190	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr5:40678671-40678992	K562	blood:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
10	POLR2A	chr5:40678512-40680410	U87	brain:	n/a	n/a
11	MXI1	chr5:40678177-40680144	Hela-S3	cervix:	n/a	n/a
12	FOS	chr5:40678151-40678905	MCF10A-Er-Src	breast:	n/a	chr5:40678453-40678462
13	CHD2	chr5:40678769-40680438	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr5:40678555-40679069	A549	lung:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
15	CEBPB	chr5:40678667-40679358	A549	lung:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
16	POLR2A	chr5:40678546-40680369	PANC-1	pancreas:	n/a	n/a
17	RFX5	chr5:40678219-40680202	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr5:40678688-40679020	HepG2	liver:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
19	E2F4	chr5:40678789-40680148	MCF10A-Er-Src	breast:	n/a	chr5:40679536-40679545
20	POLR2A	chr5:40678798-40680512	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF2	chr5:40678625-40679641	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr5:40678596-40680801	HL-60	blood:	n/a	n/a
23	CEBPB	chr5:40678652-40679420	IMR90	lung:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
24	SMARCC1	chr5:40678796-40680595	Hela-S3	cervix:	n/a	n/a
25	FOS	chr5:40678761-40678990	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr5:40678674-40680297	Hela-S3	cervix:	n/a	n/a
27	FOXA1	chr5:40678631-40678871	T-47D	breast:	n/a	chr5:40678756-40678771
28	STAT3	chr5:40678190-40679418	Hela-S3	cervix:	n/a	chr5:40678336-40678347 chr5:40678826-40678840 chr5:40678828-40678837 chr5:40678827-40678838 chr5:40679028-40679042 chr5:40678829-40678838 chr5:40678832-40678840 chr5:40678844-40678852
29	POLR2A	chr5:40678746-40680275	U87	brain:	n/a	n/a
30	POLR2A	chr5:40677912-40680908	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr5:40678223-40680323	HUVEC	blood vessel:	n/a	n/a
32	CEBPB	chr5:40678709-40679279	H1-hESC	embryonic stem cell:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
33	POLR2A	chr5:40678513-40682518	HUVEC	blood vessel:	n/a	n/a
34	CEBPB	chr5:40678702-40679035	MCF-7	breast:	n/a	chr5:40678841-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678843-40678852 chr5:40678841-40678854 chr5:40678843-40678852 chr5:40678841-40678852 chr5:40678842-40678853 chr5:40678841-40678854
35	STAT1	chr5:40678305-40680617	Hela-S3	cervix:	n/a	chr5:40678336-40678347 chr5:40678826-40678840 chr5:40678828-40678837 chr5:40679028-40679042 chr5:40678829-40678838 chr5:40678832-40678840 chr5:40678844-40678852
36	POLR2A	chr5:40678573-40680352	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr5:40678769-40680678	Raji	blood:	n/a	n/a
38	POLR2A	chr5:40678805-40680443	HUVEC	blood vessel:	n/a	n/a
39	RCOR1	chr5:40678649-40680348	Hela-S3	cervix:	n/a	n/a
40	MYC	chr5:40677879-40679478	MCF10A-Er-Src	breast:	n/a	n/a
41	STAT3	chr5:40678064-40679404	MCF10A-Er-Src	breast:	n/a	chr5:40678336-40678347 chr5:40678826-40678840 chr5:40678828-40678837 chr5:40678827-40678838 chr5:40679028-40679042 chr5:40678829-40678838 chr5:40678832-40678840 chr5:40678844-40678852
42	MYC	chr5:40678668-40680140	MCF10A-Er-Src	breast:	n/a	n/a
43	MYC	chr5:40678136-40680339	NB4	blood:	n/a	n/a
44	ZNF263	chr5:40678777-40680788	HEK293-T-REx	kidney:	n/a	chr5:40679211-40679232
45	POLR2A	chr5:40678630-40678855	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr5:40678296-40680410	U87	brain:	n/a	n/a
47	BRCA1	chr5:40678232-40680046	Hela-S3	cervix:	n/a	chr5:40678413-40678420
48	MYC	chr5:40678769-40678937	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAFK	chr5:40678642-40680121	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr5:40677884-40680287	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:40678741..40679756-chr6:26123548..26124204,3	Hela-S3	cervix:
2	chr14:94547017..94547649-chr5:40678640..40679465,2	Hela-S3	cervix:
3	chr15:65321890..65322402-chr5:40678654..40679608,2	NB4	blood:
4	chr5:40678654..40679643-chr5:89705625..89706304,2	NB4	blood:
5	chr5:40673402..40675876-chr5:40676322..40679263,4	K562	blood:
6	chr5:40505949..40508818-chr5:40677222..40679235,2	MCF-7	breast:
7	chr5:40677072..40679518-chr5:40680792..40683406,4	MCF-7	breast:
8	chr14:75745262..75745853-chr5:40678732..40679322,2	Hela-S3	cervix:
9	chr2:204103696..204104264-chr5:40678600..40679556,2	Hela-S3	cervix:

Variant related genes	Relation type
PTGER4	TF binding region
ENSG00000103707	Chromatin interaction
ENSG00000119004	Chromatin interaction
ENSG00000171522	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000089737	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000165948	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880993	chr5:40521648-40682550	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
2	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3397684	chr5:40678645-40681143	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40675800-40679000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:40676000-40679000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:40676000-40679000	Weak transcription	Esophagus	oesophagus
4	chr5:40676800-40679200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:40676800-40679200	Flanking Active TSS	HUVEC	blood vessel
6	chr5:40677000-40679000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:40677000-40679000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr5:40677400-40679000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:40677400-40679000	Weak transcription	Gastric	stomach
10	chr5:40677400-40679000	Weak transcription	Pancreas	Pancrea
11	chr5:40677400-40679000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:40677400-40679000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:40677400-40680800	Active TSS	Duodenum Mucosa	Duodenum
14	chr5:40677400-40681000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr5:40677600-40679000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:40677600-40679000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:40677600-40679200	Weak transcription	Small Intestine	intestine
18	chr5:40677600-40679400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr5:40677800-40679400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr5:40677800-40680200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr5:40677800-40681000	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr5:40678000-40679400	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr5:40678200-40679200	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr5:40678200-40679400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:40678200-40679400	Bivalent/Poised TSS	Fetal Kidney	kidney
26	chr5:40678200-40680400	Active TSS	Stomach Smooth Muscle	stomach
27	chr5:40678200-40680800	Active TSS	Dnd41	blood
28	chr5:40678400-40679000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr5:40678400-40679000	Active TSS	Fetal Muscle Leg	muscle
30	chr5:40678400-40679000	Active TSS	Fetal Thymus	thymus
31	chr5:40678400-40679200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr5:40678400-40679400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr5:40678400-40679400	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr5:40678400-40680800	Active TSS	A549	lung
35	chr5:40678400-40681000	Active TSS	Fetal Intestine Small	intestine
36	chr5:40678400-40681000	Active TSS	Thymus	Thymus
37	chr5:40678400-40681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:40678400-40682000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:40678400-40683800	Active TSS	HSMM	muscle
40	chr5:40678400-40684600	Active TSS	HSMMtube	muscle
41	chr5:40678600-40679000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
42	chr5:40678600-40679000	Enhancers	Primary B cells from peripheral blood	blood
43	chr5:40678600-40679000	Active TSS	Primary T cells fromperipheralblood	blood
44	chr5:40678600-40679000	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr5:40678600-40679000	Bivalent/Poised TSS	Fetal Stomach	stomach
46	chr5:40678600-40679200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
47	chr5:40678600-40679200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:40678600-40679200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr5:40678600-40679200	Flanking Active TSS	NH-A	brain
50	chr5:40678600-40679200	Flanking Active TSS	Osteobl	bone

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