Variant report

Variant	rs1035485
Chromosome Location	chr5:57756407-57756408
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	MAX	chr5:57755462-57757152	HCT-116	colon:	n/a	chr5:57756022-57756031
2	TAF1	chr5:57755127-57756430	MCF-7	breast:	n/a	n/a
3	MAX	chr5:57755455-57756969	HepG2	liver:	n/a	chr5:57756022-57756031
4	RAD21	chr5:57754174-57757575	SK-N-SH	brain:	n/a	chr5:57755497-57755509 chr5:57756736-57756755 chr5:57755955-57755967 chr5:57755364-57755374 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
5	POLR2A	chr5:57755502-57756815	GM18526	blood:	n/a	n/a
6	TAF1	chr5:57755612-57756571	HepG2	liver:	n/a	n/a
7	MXI1	chr5:57755749-57757017	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr5:57754101-57757035	IMR90	lung:	n/a	chr5:57755497-57755509 chr5:57756736-57756755 chr5:57755955-57755967 chr5:57755364-57755374 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
9	RAD21	chr5:57755686-57757046	Hela-S3	cervix:	n/a	chr5:57756736-57756755 chr5:57755955-57755967 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
10	RAD21	chr5:57755489-57757166	HCT-116	colon:	n/a	chr5:57755497-57755509 chr5:57756736-57756755 chr5:57755955-57755967 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
11	RAD21	chr5:57754889-57756996	SK-N-SH_RA	brain:	n/a	chr5:57755497-57755509 chr5:57756736-57756755 chr5:57755955-57755967 chr5:57755364-57755374 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
12	POLR2A	chr5:57755230-57756816	A549	lung:	n/a	n/a
13	TAF1	chr5:57755393-57756501	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr5:57745705-57757136	HUVEC	blood vessel:	n/a	n/a
15	CHD2	chr5:57754650-57756867	Hela-S3	cervix:	n/a	n/a
16	MAX	chr5:57755452-57757190	ECC-1	luminal epithelium:	n/a	chr5:57756022-57756031
17	CREB1	chr5:57755653-57756464	ECC-1	luminal epithelium:	n/a	n/a
18	CTCF	chr5:57755720-57757022	IMR90	lung:	n/a	chr5:57756239-57756248 chr5:57756739-57756755 chr5:57756740-57756753 chr5:57756238-57756251 chr5:57756235-57756248 chr5:57756738-57756756 chr5:57756733-57756754
19	EP300	chr5:57754512-57757000	A549	lung:	n/a	chr5:57756094-57756103
20	E2F4	chr5:57755741-57756716	MCF10A-Er-Src	breast:	n/a	chr5:57755947-57755959 chr5:57756117-57756129 chr5:57756045-57756057
21	POLR2A	chr5:57755671-57756895	GM19099	blood:	n/a	n/a
22	PBX3	chr5:57755580-57756983	SK-N-SH	brain:	n/a	chr5:57756617-57756637
23	NFIC	chr5:57755422-57756892	ECC-1	luminal epithelium:	n/a	n/a
24	ZNF143	chr5:57755248-57757041	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr5:57754179-57756864	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:57746016-57757149	HUVEC	blood vessel:	n/a	n/a
27	RAD21	chr5:57755132-57757160	MCF-7	breast:	n/a	chr5:57755497-57755509 chr5:57756736-57756755 chr5:57755955-57755967 chr5:57755364-57755374 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
28	RAD21	chr5:57754545-57757114	HCT-116	colon:	n/a	chr5:57755497-57755509 chr5:57756736-57756755 chr5:57755955-57755967 chr5:57755364-57755374 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
29	SP1	chr5:57755470-57757092	A549	lung:	n/a	chr5:57755998-57756010 chr5:57755999-57756008 chr5:57756227-57756236 chr5:57755957-57755968 chr5:57756000-57756009 chr5:57755954-57755968 chr5:57755958-57755967 chr5:57756622-57756631 chr5:57755999-57756008 chr5:57756226-57756235 chr5:57755998-57756010 chr5:57755999-57756009 chr5:57756620-57756632 chr5:57755957-57755969 chr5:57756621-57756630 chr5:57755946-57755957
30	ETS1	chr5:57755531-57756973	A549	lung:	n/a	n/a
31	SMC3	chr5:57754211-57757082	Hela-S3	cervix:	n/a	chr5:57756242-57756249 chr5:57756237-57756251 chr5:57756235-57756249 chr5:57756740-57756754
32	FOXP2	chr5:57756140-57756856	PFSK-1	brain:	n/a	n/a
33	EP300	chr5:57755428-57757014	SK-N-SH	brain:	n/a	chr5:57756094-57756103
34	POLR2A	chr5:57750892-57756934	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr5:57755270-57756883	MCF-7	breast:	n/a	n/a
36	RAD21	chr5:57755522-57757105	SK-N-SH_RA	brain:	n/a	chr5:57756736-57756755 chr5:57755955-57755967 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
37	CTCF	chr5:57756026-57756936	H1-hESC	embryonic stem cell:	n/a	chr5:57756239-57756248 chr5:57756739-57756755 chr5:57756740-57756753 chr5:57756238-57756251 chr5:57756235-57756248 chr5:57756738-57756756 chr5:57756733-57756754
38	RAD21	chr5:57755129-57757010	H1-hESC	embryonic stem cell:	n/a	chr5:57755497-57755509 chr5:57756736-57756755 chr5:57755955-57755967 chr5:57755364-57755374 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
39	RAD21	chr5:57755777-57757165	A549	lung:	n/a	chr5:57756736-57756755 chr5:57755955-57755967 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
40	TAF1	chr5:57755164-57756911	A549	lung:	n/a	n/a
41	RFX5	chr5:57755678-57757175	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr5:57756132-57756470	GM19239	blood:	n/a	chr5:57756239-57756248 chr5:57756238-57756251 chr5:57756235-57756248
43	HEY1	chr5:57755659-57756809	HepG2	liver:	n/a	chr5:57756226-57756241
44	RCOR1	chr5:57755814-57756876	HepG2	liver:	n/a	n/a
45	POLR2A	chr5:57752745-57756859	MCF10A-Er-Src	breast:	n/a	n/a
46	REST	chr5:57753891-57757088	A549	lung:	n/a	n/a
47	RAD21	chr5:57756080-57757017	MCF-7	breast:	n/a	chr5:57756736-57756755 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
48	ZNF143	chr5:57755657-57756944	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr5:57756104-57756469	Fibrobl	skin:	n/a	chr5:57756239-57756248 chr5:57756238-57756251 chr5:57756235-57756248
50	TCF7L2	chr5:57755578-57756941	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:8937566..8938548-chr5:57755874..57756660,2	Hela-S3	cervix:
2	chr17:56707798..56710603-chr5:57755406..57757452,2	MCF-7	breast:
3	chr17:57923573..57925801-chr5:57753845..57756826,2	MCF-7	breast:
4	chr5:57364074..57376813-chr5:57753679..57758569,26	MCF-7	breast:
5	chr4:122721925..122722763-chr5:57755619..57756423,2	HCT-116	colon:
6	chr5:57168184..57169711-chr5:57754494..57756798,2	MCF-7	breast:
7	chr5:56946261..56947053-chr5:57756221..57757048,2	K562	blood:
8	chr1:11968161..11969978-chr5:57755723..57757847,2	MCF-7	breast:
9	chr5:57754652..57757569-chr8:146051207..146054086,2	MCF-7	breast:

Variant related genes	Relation type
PLK2	TF binding region
ENSG00000074800	Chromatin interaction
ENSG00000238899	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000147789	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000123737	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000236269	Chromatin interaction
ENSG00000266864	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1035484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1042994	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11546180	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12513877	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12513905	0.90[AMR][1000 genomes]
rs12518781	0.84[AFR][1000 genomes]
rs12522386	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13168504	0.87[AFR][1000 genomes]
rs13184050	0.87[AFR][1000 genomes]
rs13188849	0.87[AFR][1000 genomes]
rs16888201	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17709855	0.88[AFR][1000 genomes]
rs17710502	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17710615	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17767072	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2201293	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2220785	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2408946	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2408947	0.85[AMR][1000 genomes]
rs33921924	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34150563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34974449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4699926	0.87[AFR][1000 genomes]
rs4700289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55827457	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56010771	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs56286824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56318521	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs59135347	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs62366360	0.88[AFR][1000 genomes]
rs6450474	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6879330	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6882289	0.88[AFR][1000 genomes]
rs6890785	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72758173	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72758189	0.80[AMR][1000 genomes]
rs7701530	0.87[AFR][1000 genomes]
rs7706545	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7708381	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs7725097	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7736949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs929818	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]

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	esv3332078	chr5:57754795-57756793	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
2	esv3437453	chr5:57755020-57757568	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57750000-57756800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr5:57750800-57756800	Active TSS	Right Atrium	heart
3	chr5:57751000-57756800	Active TSS	Brain Angular Gyrus	brain
4	chr5:57751600-57756800	Active TSS	Rectal Smooth Muscle	rectum
5	chr5:57751600-57756800	Active TSS	Right Ventricle	heart
6	chr5:57751600-57757000	Active TSS	Brain Hippocampus Middle	brain
7	chr5:57751800-57756800	Active TSS	Brain Cingulate Gyrus	brain
8	chr5:57752000-57756600	Active TSS	Aorta	Aorta
9	chr5:57752200-57756800	Active TSS	Fetal Stomach	stomach
10	chr5:57752200-57756800	Active TSS	Lung	lung
11	chr5:57752200-57756800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr5:57753000-57756800	Active TSS	Esophagus	oesophagus
13	chr5:57753400-57756600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr5:57753400-57756600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:57753400-57756800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:57753400-57756800	Active TSS	Psoas Muscle	Psoas
17	chr5:57753600-57756800	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr5:57753600-57756800	Active TSS	NHDF-Ad	bronchial
19	chr5:57753600-57757000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:57753800-57756800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:57753800-57756800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr5:57754000-57756800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:57754200-57756600	Active TSS	Gastric	stomach
24	chr5:57754200-57756600	Active TSS	Stomach Mucosa	stomach
25	chr5:57754200-57756800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:57754200-57756800	Active TSS	H9 Cell Line	embryonic stem cell
27	chr5:57754200-57756800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:57754200-57756800	Active TSS	Colon Smooth Muscle	Colon
29	chr5:57754200-57757000	Active TSS	Pancreas	Pancrea
30	chr5:57754400-57756800	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr5:57754400-57756800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:57754400-57756800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:57754400-57756800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:57754400-57756800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr5:57754400-57756800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr5:57754400-57756800	Active TSS	Fetal Muscle Leg	muscle
37	chr5:57754400-57756800	Active TSS	Left Ventricle	heart
38	chr5:57754400-57756800	Active TSS	Ovary	ovary
39	chr5:57754400-57756800	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr5:57754400-57756800	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr5:57754400-57756800	Active TSS	Small Intestine	intestine
42	chr5:57754400-57757000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:57754400-57757000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:57754600-57756600	Active TSS	Brain Substantia Nigra	brain
45	chr5:57754600-57756600	Active TSS	Placenta	Placenta
46	chr5:57754600-57756800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:57754600-57756800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:57754600-57756800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:57754600-57756800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:57754600-57756800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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