Variant report

Variant	rs564988207
Chromosome Location	chr5:40679958-40679959
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	POLR2A	chr5:40679874-40680266	GM12891	blood:	n/a	n/a
3	RELA	chr5:40679553-40679977	GM19193	blood:	n/a	n/a
4	POLR2A	chr5:40678901-40680830	H1-neurons	neurons:	n/a	n/a
5	E2F6	chr5:40679543-40680075	K562	blood:	n/a	n/a
6	MAZ	chr5:40679588-40680233	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:40678244-40680457	NB4	blood:	n/a	n/a
8	MAX	chr5:40678144-40680687	NB4	blood:	n/a	n/a
9	EGR1	chr5:40679804-40680086	K562	blood:	n/a	chr5:40679976-40679987
10	POLR2A	chr5:40679045-40680651	MCF-7	breast:	n/a	n/a
11	NFYA	chr5:40679587-40680090	Hela-S3	cervix:	n/a	chr5:40679938-40679953 chr5:40679938-40679953 chr5:40679938-40679952
12	TCF12	chr5:40679495-40680455	ECC-1	luminal epithelium:	n/a	chr5:40679806-40679813
13	TAF1	chr5:40678937-40680275	A549	lung:	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	CTCF	chr5:40679880-40680030	HCPEpiC	choroid plexus:	n/a	n/a
16	CTBP2	chr5:40679949-40682335	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr5:40678152-40680190	Hela-S3	cervix:	n/a	n/a
18	HMGN3	chr5:40679648-40680266	K562	blood:	n/a	n/a
19	E2F6	chr5:40679505-40680715	H1-hESC	embryonic stem cell:	n/a	chr5:40679536-40679545
20	MAX	chr5:40679536-40680155	K562	blood:	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	POLR2A	chr5:40678947-40680277	ECC-1	luminal epithelium:	n/a	n/a
25	MXI1	chr5:40678177-40680144	Hela-S3	cervix:	n/a	n/a
26	CREB1	chr5:40679483-40680112	A549	lung:	n/a	n/a
27	MAX	chr5:40679061-40680761	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr5:40679881-40680140	GM12891	blood:	n/a	n/a
29	MAX	chr5:40679479-40680805	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr5:40679066-40680298	Gliobla	brain:	n/a	n/a
31	POLR2A	chr5:40679856-40680227	GM12878	blood:	n/a	n/a
32	NFYB	chr5:40679830-40680135	GM12878	blood:	n/a	chr5:40679938-40679953 chr5:40679938-40679953 chr5:40679935-40679950 chr5:40679938-40679952
33	ZEB1	chr5:40679874-40680359	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:40679053-40680240	HCT-116	colon:	n/a	n/a
35	CHD2	chr5:40678769-40680438	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr5:40679907-40680218	H1-hESC	embryonic stem cell:	n/a	n/a
37	TFAP2C	chr5:40679017-40680425	Hela-S3	cervix:	n/a	n/a
38	FOXA1	chr5:40679861-40680118	T-47D	breast:	n/a	n/a
39	MXI1	chr5:40679633-40680177	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:40679478-40680285	A549	lung:	n/a	n/a
41	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
42	POLR2A	chr5:40678949-40680237	Hela-S3	cervix:	n/a	n/a
43	MAX	chr5:40679489-40680420	MCF-7	breast:	n/a	n/a
44	ELF1	chr5:40679511-40680111	GM12878	blood:	n/a	chr5:40679977-40679986
45	POLR2A	chr5:40678546-40680369	PANC-1	pancreas:	n/a	n/a
46	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
47	RFX5	chr5:40678219-40680202	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr5:40679952-40680107	GM12891	blood:	n/a	n/a
49	E2F4	chr5:40678789-40680148	MCF10A-Er-Src	breast:	n/a	chr5:40679536-40679545
50	ZKSCAN1	chr5:40678910-40680342	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:40679443..40679992-chrX:135180311..135180826,2	NB4	blood:
2	chr2:43453677..43454419-chr5:40679281..40680059,2	NB4	blood:
3	chr16:103497..104162-chr5:40679412..40680348,2	Hela-S3	cervix:
4	chr14:75746315..75746996-chr5:40679492..40680585,3	Hela-S3	cervix:
5	chr11:62358977..62359711-chr5:40679405..40680068,2	NB4	blood:
6	chr5:40679274..40679984-chr7:27778984..27779514,2	Hela-S3	cervix:
7	chr1:149223620..149224423-chr5:40679508..40680359,2	MCF-7	breast:
8	chr11:68039254..68040142-chr5:40679338..40680207,2	Hela-S3	cervix:
9	chr5:40679791..40680505-chr9:140135439..140136378,2	Hela-S3	cervix:
10	chr15:59225159..59225758-chr5:40679380..40680198,2	Hela-S3	cervix:
11	chr1:174968214..174968853-chr5:40679191..40679960,2	Hela-S3	cervix:
12	chr11:62608481..62609314-chr5:40678890..40679963,4	Hela-S3	cervix:

Variant related genes	Relation type
PTGER4	TF binding region
ENSG00000170345	Chromatin interaction
ENSG00000161980	Chromatin interaction
ENSG00000171067	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000152518	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000161981	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000106052	Chromatin interaction
ENSG00000231513	Chromatin interaction
ENSG00000116161	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	chr5:40679000-40680000	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr5:40679000-40680000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr5:40679000-40680000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:40679000-40680000	Active TSS	Placenta Amnion	Placenta Amnion
41	chr5:40679000-40680200	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr5:40679000-40680200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:40679000-40680200	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr5:40679000-40680200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:40679000-40680200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
46	chr5:40679000-40680200	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr5:40679000-40680400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr5:40679000-40680400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:40679000-40680400	Active TSS	H9 Cell Line	embryonic stem cell
50	chr5:40679000-40680400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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