Variant report

Variant	rs541650464
Chromosome Location	chr5:40679349-40679350
allele	-/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	GTF2F1	chr5:40678805-40680138	Hela-S3	cervix:	n/a	n/a
2	ZNF384	chr5:40679066-40679435	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:40678901-40680830	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr5:40678961-40679833	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr5:40678244-40680457	NB4	blood:	n/a	n/a
6	TCF12	chr5:40678786-40679832	A549	lung:	n/a	chr5:40679806-40679813
7	MAX	chr5:40678144-40680687	NB4	blood:	n/a	n/a
8	POLR2A	chr5:40679110-40679845	A549	lung:	n/a	n/a
9	MAX	chr5:40679060-40679427	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr5:40678153-40679736	Hela-S3	cervix:	n/a	chr5:40679296-40679306 chr5:40679294-40679306
11	POLR2A	chr5:40679045-40680651	MCF-7	breast:	n/a	n/a
12	POLR2A	chr5:40679102-40679371	GM12878	blood:	n/a	n/a
13	RELA	chr5:40679068-40679938	GM18951	blood:	n/a	n/a
14	ZNF143	chr5:40679187-40679850	Hela-S3	cervix:	n/a	chr5:40679775-40679794 chr5:40679302-40679312
15	TAF1	chr5:40678937-40680275	A549	lung:	n/a	n/a
16	EBF1	chr5:40678996-40679760	GM12878	blood:	n/a	n/a
17	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
18	SRF	chr5:40679120-40679784	ECC-1	luminal epithelium:	n/a	chr5:40679423-40679441 chr5:40679427-40679438 chr5:40679426-40679441 chr5:40679421-40679438 chr5:40679427-40679441 chr5:40679423-40679437
19	TBP	chr5:40678152-40680190	Hela-S3	cervix:	n/a	n/a
20	TAF1	chr5:40679166-40679373	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr5:40678512-40680410	U87	brain:	n/a	n/a
22	POLR2A	chr5:40679015-40680302	A549	lung:	n/a	n/a
23	REST	chr5:40679016-40680444	HL-60	blood:	n/a	chr5:40679637-40679650 chr5:40679808-40679821
24	TAF1	chr5:40679090-40679443	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr5:40678947-40680277	ECC-1	luminal epithelium:	n/a	n/a
26	MXI1	chr5:40678177-40680144	Hela-S3	cervix:	n/a	n/a
27	GTF2F1	chr5:40679227-40679488	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3A	chr5:40679009-40679787	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr5:40679061-40680761	H1-hESC	embryonic stem cell:	n/a	n/a
30	TBL1XR1	chr5:40679247-40679356	GM12878	blood:	n/a	n/a
31	POLR2A	chr5:40679081-40679456	A549	lung:	n/a	n/a
32	POLR2A	chr5:40679066-40680298	Gliobla	brain:	n/a	n/a
33	ZNF217	chr5:40678929-40679371	MCF-7	breast:	n/a	n/a
34	TAF7	chr5:40679008-40679475	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr5:40679053-40680240	HCT-116	colon:	n/a	n/a
36	POLR2A	chr5:40679111-40679432	SK-N-MC	brain:	n/a	n/a
37	CHD2	chr5:40678769-40680438	Hela-S3	cervix:	n/a	n/a
38	CEBPB	chr5:40679137-40679473	MCF-7	breast:	n/a	n/a
39	TFAP2C	chr5:40679017-40680425	Hela-S3	cervix:	n/a	n/a
40	SP1	chr5:40678898-40680154	A549	lung:	n/a	chr5:40679922-40679931 chr5:40679920-40679932 chr5:40679939-40679960 chr5:40679921-40679935 chr5:40679920-40679932 chr5:40679921-40679930
41	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
42	POLR2A	chr5:40678949-40680237	Hela-S3	cervix:	n/a	n/a
43	SRF	chr5:40679055-40679807	ECC-1	luminal epithelium:	n/a	chr5:40679423-40679441 chr5:40679427-40679438 chr5:40679426-40679441 chr5:40679421-40679438 chr5:40679427-40679441 chr5:40679423-40679437
44	POLR2A	chr5:40678546-40680369	PANC-1	pancreas:	n/a	n/a
45	SRF	chr5:40678953-40680216	MCF-7	breast:	n/a	chr5:40679423-40679441 chr5:40679427-40679438 chr5:40679426-40679441 chr5:40679421-40679438 chr5:40679427-40679441 chr5:40679423-40679437
46	RFX5	chr5:40678219-40680202	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr5:40679126-40679447	A549	lung:	n/a	n/a
48	ETS1	chr5:40679084-40679465	A549	lung:	n/a	n/a
49	SIN3AK20	chr5:40679008-40679450	PANC-1	pancreas:	n/a	n/a
50	E2F4	chr5:40678789-40680148	MCF10A-Er-Src	breast:	n/a	chr5:40679536-40679545

No.	Distal block	Cell Line	Cell type
1	chr12:52444777..52445765-chr5:40679251..40679886,2	Hela-S3	cervix:
2	chr5:40678741..40679756-chr6:26123548..26124204,3	Hela-S3	cervix:
3	chr14:64970114..64971112-chr5:40679140..40679771,2	Hela-S3	cervix:
4	chr14:94547017..94547649-chr5:40678640..40679465,2	Hela-S3	cervix:
5	chr1:155023041..155023664-chr5:40678966..40679570,2	Hela-S3	cervix:
6	chr20:44563060..44564177-chr5:40679045..40679695,3	Hela-S3	cervix:
7	chr17:43224484..43225221-chr5:40678825..40679523,2	NB4	blood:
8	chr2:43453677..43454419-chr5:40679281..40680059,2	NB4	blood:
9	chr15:65321890..65322402-chr5:40678654..40679608,2	NB4	blood:
10	chr1:36235070..36236025-chr5:40679016..40679937,2	Hela-S3	cervix:
11	chr5:40679274..40679984-chr7:27778984..27779514,2	Hela-S3	cervix:
12	chr19:17448276..17448931-chr5:40679198..40679839,2	Hela-S3	cervix:
13	chr19:55896877..55897816-chr5:40679285..40679925,2	Hela-S3	cervix:
14	chr17:39844981..39845752-chr5:40679190..40679932,2	Hela-S3	cervix:
15	chr5:40678654..40679643-chr5:89705625..89706304,2	NB4	blood:
16	chr15:31619156..31619701-chr5:40678819..40679598,2	Hela-S3	cervix:
17	chr11:68039254..68040142-chr5:40679338..40680207,2	Hela-S3	cervix:
18	chr20:62259613..62260132-chr5:40679006..40679597,2	Hela-S3	cervix:
19	chr2:209119316..209119842-chr5:40679091..40679725,2	Hela-S3	cervix:
20	chr1:174968214..174968853-chr5:40679191..40679960,2	Hela-S3	cervix:
21	chr11:62608481..62609314-chr5:40678890..40679963,4	Hela-S3	cervix:
22	chr5:40677072..40679518-chr5:40680792..40683406,4	MCF-7	breast:
23	chr1:242011208..242011713-chr5:40678933..40679886,2	Hela-S3	cervix:
24	chr2:85822216..85823096-chr5:40679131..40679668,2	Hela-S3	cervix:
25	chr2:204103696..204104264-chr5:40678600..40679556,2	Hela-S3	cervix:

Variant related genes	Relation type
PTGER4	TF binding region
ENSG00000173812	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000171067	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000130299	Chromatin interaction
ENSG00000171522	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000119004	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000103707	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000100982	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000186834	Chromatin interaction
ENSG00000165948	Chromatin interaction
ENSG00000138413	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000152518	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000092853	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000089737	Chromatin interaction
ENSG00000106052	Chromatin interaction
ENSG00000174371	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40677400-40680800	Active TSS	Duodenum Mucosa	Duodenum
2	chr5:40677400-40681000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr5:40677600-40679400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr5:40677800-40679400	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr5:40677800-40680200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr5:40677800-40681000	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr5:40678000-40679400	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr5:40678200-40679400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:40678200-40679400	Bivalent/Poised TSS	Fetal Kidney	kidney
10	chr5:40678200-40680400	Active TSS	Stomach Smooth Muscle	stomach
11	chr5:40678200-40680800	Active TSS	Dnd41	blood
12	chr5:40678400-40679400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr5:40678400-40679400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr5:40678400-40680800	Active TSS	A549	lung
15	chr5:40678400-40681000	Active TSS	Fetal Intestine Small	intestine
16	chr5:40678400-40681000	Active TSS	Thymus	Thymus
17	chr5:40678400-40681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:40678400-40682000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:40678400-40683800	Active TSS	HSMM	muscle
20	chr5:40678400-40684600	Active TSS	HSMMtube	muscle
21	chr5:40678600-40679400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr5:40678600-40679400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr5:40678600-40679400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:40678600-40679400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr5:40678600-40679400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:40678600-40680000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr5:40678600-40680400	Active TSS	Colonic Mucosa	Colon
28	chr5:40678600-40680400	Active TSS	Right Ventricle	heart
29	chr5:40678600-40680600	Active TSS	Stomach Mucosa	stomach
30	chr5:40678600-40680800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr5:40678600-40681000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:40678600-40681200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:40678600-40681200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:40678600-40681200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:40678600-40682200	Active TSS	NHEK	skin
36	chr5:40678600-40684400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr5:40678600-40685800	Active TSS	Right Atrium	heart
38	chr5:40678800-40679400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr5:40678800-40679400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr5:40678800-40679400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:40678800-40679400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
42	chr5:40678800-40680200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:40678800-40680200	Active TSS	Fetal Lung	lung
44	chr5:40678800-40680200	Active TSS	Hela-S3	cervix
45	chr5:40678800-40680400	Bivalent/Poised TSS	Psoas Muscle	Psoas
46	chr5:40678800-40680600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr5:40678800-40680800	Active TSS	HMEC	breast
48	chr5:40678800-40681000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:40678800-40681000	Active TSS	NHDF-Ad	bronchial
50	chr5:40678800-40681200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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