Variant report

Variant	rs369254623
Chromosome Location	chr5:40679458-40679459
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	GTF2F1	chr5:40678805-40680138	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:40678901-40680830	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr5:40678961-40679833	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr5:40678244-40680457	NB4	blood:	n/a	n/a
5	TCF12	chr5:40678786-40679832	A549	lung:	n/a	chr5:40679806-40679813
6	MAX	chr5:40678144-40680687	NB4	blood:	n/a	n/a
7	POLR2A	chr5:40679110-40679845	A549	lung:	n/a	n/a
8	RAD21	chr5:40678153-40679736	Hela-S3	cervix:	n/a	chr5:40679296-40679306 chr5:40679294-40679306
9	POLR2A	chr5:40679045-40680651	MCF-7	breast:	n/a	n/a
10	RELA	chr5:40679068-40679938	GM18951	blood:	n/a	n/a
11	ZNF143	chr5:40679187-40679850	Hela-S3	cervix:	n/a	chr5:40679775-40679794 chr5:40679302-40679312
12	TAF1	chr5:40678937-40680275	A549	lung:	n/a	n/a
13	EBF1	chr5:40678996-40679760	GM12878	blood:	n/a	n/a
14	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
15	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
16	TBP	chr5:40678152-40680190	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:40678512-40680410	U87	brain:	n/a	n/a
18	POLR2A	chr5:40679015-40680302	A549	lung:	n/a	n/a
19	REST	chr5:40679016-40680444	HL-60	blood:	n/a	chr5:40679637-40679650 chr5:40679808-40679821
20	POLR2A	chr5:40678947-40680277	ECC-1	luminal epithelium:	n/a	n/a
21	MXI1	chr5:40678177-40680144	Hela-S3	cervix:	n/a	n/a
22	GTF2F1	chr5:40679227-40679488	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIN3A	chr5:40679009-40679787	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr5:40679061-40680761	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr5:40679066-40680298	Gliobla	brain:	n/a	n/a
26	TAF7	chr5:40679008-40679475	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr5:40679053-40680240	HCT-116	colon:	n/a	n/a
28	CHD2	chr5:40678769-40680438	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr5:40679137-40679473	MCF-7	breast:	n/a	n/a
30	TFAP2C	chr5:40679017-40680425	Hela-S3	cervix:	n/a	n/a
31	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
32	POLR2A	chr5:40678949-40680237	Hela-S3	cervix:	n/a	n/a
33	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
34	POLR2A	chr5:40678546-40680369	PANC-1	pancreas:	n/a	n/a
35	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
36	RFX5	chr5:40678219-40680202	Hela-S3	cervix:	n/a	n/a
37	ETS1	chr5:40679084-40679465	A549	lung:	n/a	n/a
38	E2F4	chr5:40678789-40680148	MCF10A-Er-Src	breast:	n/a	chr5:40679536-40679545
39	ZKSCAN1	chr5:40678910-40680342	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr5:40678997-40680264	IMR90	lung:	n/a	n/a
41	POLR2A	chr5:40679004-40680208	HCT-116	colon:	n/a	n/a
42	MAX	chr5:40678934-40680545	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr5:40678798-40680512	H1-hESC	embryonic stem cell:	n/a	n/a
44	RELA	chr5:40679088-40680240	GM19099	blood:	n/a	n/a
45	POLR2A	chr5:40679110-40680347	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr5:40679158-40680275	GM19099	blood:	n/a	n/a
47	MAX	chr5:40678843-40680600	A549	lung:	n/a	n/a
48	USF2	chr5:40678625-40679641	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:40678596-40680801	HL-60	blood:	n/a	n/a
50	POLR2A	chr5:40679281-40680482	PFSK-1	brain:	n/a	n/a

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	chr5:40679443..40679992-chrX:135180311..135180826,2	NB4	blood:
7	chr20:44563060..44564177-chr5:40679045..40679695,3	Hela-S3	cervix:
8	chr17:43224484..43225221-chr5:40678825..40679523,2	NB4	blood:
9	chr2:43453677..43454419-chr5:40679281..40680059,2	NB4	blood:
10	chr15:65321890..65322402-chr5:40678654..40679608,2	NB4	blood:
11	chr16:103497..104162-chr5:40679412..40680348,2	Hela-S3	cervix:
12	chr1:36235070..36236025-chr5:40679016..40679937,2	Hela-S3	cervix:
13	chr11:62358977..62359711-chr5:40679405..40680068,2	NB4	blood:
14	chr5:40679274..40679984-chr7:27778984..27779514,2	Hela-S3	cervix:
15	chr19:17448276..17448931-chr5:40679198..40679839,2	Hela-S3	cervix:
16	chr19:55896877..55897816-chr5:40679285..40679925,2	Hela-S3	cervix:
17	chr17:39844981..39845752-chr5:40679190..40679932,2	Hela-S3	cervix:
18	chr5:40678654..40679643-chr5:89705625..89706304,2	NB4	blood:
19	chr15:31619156..31619701-chr5:40678819..40679598,2	Hela-S3	cervix:
20	chr11:68039254..68040142-chr5:40679338..40680207,2	Hela-S3	cervix:
21	chr15:59225159..59225758-chr5:40679380..40680198,2	Hela-S3	cervix:
22	chr5:40679393..40679913-chr7:112090483..112090996,2	Hela-S3	cervix:
23	chr20:62259613..62260132-chr5:40679006..40679597,2	Hela-S3	cervix:
24	chr2:209119316..209119842-chr5:40679091..40679725,2	Hela-S3	cervix:
25	chr1:174968214..174968853-chr5:40679191..40679960,2	Hela-S3	cervix:
26	chr11:62608481..62609314-chr5:40678890..40679963,4	Hela-S3	cervix:
27	chr5:40677072..40679518-chr5:40680792..40683406,4	MCF-7	breast:
28	chr1:242011208..242011713-chr5:40678933..40679886,2	Hela-S3	cervix:
29	chr2:85822216..85823096-chr5:40679131..40679668,2	Hela-S3	cervix:
30	chr2:204103696..204104264-chr5:40678600..40679556,2	Hela-S3	cervix:

Variant related genes	Relation type
PTGER4	TF binding region
ENSG00000180596	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000089737	Chromatin interaction
ENSG00000171522	Chromatin interaction
ENSG00000171067	Chromatin interaction
ENSG00000106052	Chromatin interaction
ENSG00000092853	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000161981	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000186834	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000165948	Chromatin interaction
ENSG00000100982	Chromatin interaction
ENSG00000174371	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000103707	Chromatin interaction
ENSG00000130299	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000152518	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000138413	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000119004	Chromatin interaction
ENSG00000161980	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000231513	Chromatin interaction
ENSG00000006652	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:126 , 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	chr5:40677800-40680200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr5:40677800-40681000	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr5:40678200-40680400	Active TSS	Stomach Smooth Muscle	stomach
6	chr5:40678200-40680800	Active TSS	Dnd41	blood
7	chr5:40678400-40680800	Active TSS	A549	lung
8	chr5:40678400-40681000	Active TSS	Fetal Intestine Small	intestine
9	chr5:40678400-40681000	Active TSS	Thymus	Thymus
10	chr5:40678400-40681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:40678400-40682000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:40678400-40683800	Active TSS	HSMM	muscle
13	chr5:40678400-40684600	Active TSS	HSMMtube	muscle
14	chr5:40678600-40680000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr5:40678600-40680400	Active TSS	Colonic Mucosa	Colon
16	chr5:40678600-40680400	Active TSS	Right Ventricle	heart
17	chr5:40678600-40680600	Active TSS	Stomach Mucosa	stomach
18	chr5:40678600-40680800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr5:40678600-40681000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:40678600-40681200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:40678600-40681200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:40678600-40681200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:40678600-40682200	Active TSS	NHEK	skin
24	chr5:40678600-40684400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr5:40678600-40685800	Active TSS	Right Atrium	heart
26	chr5:40678800-40680200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:40678800-40680200	Active TSS	Fetal Lung	lung
28	chr5:40678800-40680200	Active TSS	Hela-S3	cervix
29	chr5:40678800-40680400	Bivalent/Poised TSS	Psoas Muscle	Psoas
30	chr5:40678800-40680600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr5:40678800-40680800	Active TSS	HMEC	breast
32	chr5:40678800-40681000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:40678800-40681000	Active TSS	NHDF-Ad	bronchial
34	chr5:40678800-40681200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:40678800-40681200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:40678800-40683000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:40679000-40679800	Bivalent/Poised TSS	Fetal Brain Male	brain
38	chr5:40679000-40680000	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr5:40679000-40680000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:40679000-40680000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:40679000-40680000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr5:40679000-40680200	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr5:40679000-40680200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:40679000-40680200	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr5:40679000-40680200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:40679000-40680200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
47	chr5:40679000-40680200	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr5:40679000-40680400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr5:40679000-40680400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:40679000-40680400	Active TSS	H9 Cell Line	embryonic stem cell

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