Variant report

Variant	rs2525085
Chromosome Location	chr17:46048858-46048859
allele	C/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	MAX	chr17:46047601-46049109	NB4	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
2	E2F6	chr17:46048038-46049058	H1-hESC	embryonic stem cell:	n/a	chr17:46048715-46048726 chr17:46048296-46048308 chr17:46048717-46048724 chr17:46048373-46048382 chr17:46048717-46048724 chr17:46048716-46048725 chr17:46048717-46048724
3	ELF1	chr17:46048149-46048949	A549	lung:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
4	POLR2A	chr17:46047860-46049148	PANC-1	pancreas:	n/a	n/a
5	MAX	chr17:46047943-46049094	K562	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
6	NFIC	chr17:46048364-46049112	GM12878	blood:	n/a	n/a
7	HEY1	chr17:46048317-46048948	K562	blood:	n/a	chr17:46048783-46048798
8	IRF1	chr17:46048010-46048879	K562	blood:	n/a	chr17:46048335-46048349 chr17:46048373-46048382
9	POLR2A	chr17:46048326-46048896	SK-N-SH	brain:	n/a	n/a
10	ELF1	chr17:46048006-46048933	K562	blood:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
11	MAX	chr17:46047776-46049210	HCT-116	colon:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
12	MAX	chr17:46047898-46049065	GM12878	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
13	CBX3	chr17:46048527-46049040	K562	blood:	n/a	n/a
14	JUND	chr17:46047955-46048923	K562	blood:	n/a	chr17:46048467-46048476 chr17:46048371-46048380
15	TAF1	chr17:46047972-46048901	HepG2	liver:	n/a	n/a
16	SMARCB1	chr17:46047953-46049191	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr17:46048079-46049174	IMR90	lung:	n/a	n/a
18	E2F6	chr17:46048035-46049015	K562	blood:	n/a	chr17:46048715-46048726 chr17:46048296-46048308 chr17:46048717-46048724 chr17:46048373-46048382 chr17:46048717-46048724 chr17:46048716-46048725 chr17:46048717-46048724
19	GTF2F1	chr17:46048004-46048939	K562	blood:	n/a	n/a
20	ELF1	chr17:46047860-46048985	GM12878	blood:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
21	CBX3	chr17:46047908-46049109	K562	blood:	n/a	n/a
22	SP1	chr17:46047685-46049130	A549	lung:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
23	NR2F2	chr17:46048683-46049113	K562	blood:	n/a	n/a
24	POLR2A	chr17:46048291-46048977	GM12891	blood:	n/a	n/a
25	USF2	chr17:46048594-46048895	K562	blood:	n/a	chr17:46048792-46048808
26	ELF1	chr17:46047954-46049020	SK-N-SH	brain:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
27	POLR2A	chr17:46048346-46049057	K562	blood:	n/a	n/a
28	POLR2A	chr17:46047890-46048934	ECC-1	luminal epithelium:	n/a	n/a
29	E2F6	chr17:46048045-46049055	A549	lung:	n/a	chr17:46048715-46048726 chr17:46048296-46048308 chr17:46048717-46048724 chr17:46048373-46048382 chr17:46048717-46048724 chr17:46048716-46048725 chr17:46048717-46048724
30	POLR2A	chr17:46047909-46049047	HCT-116	colon:	n/a	n/a
31	TBL1XR1	chr17:46047952-46049041	K562	blood:	n/a	n/a
32	PAX5	chr17:46048027-46048878	GM12892	blood:	n/a	chr17:46048495-46048504
33	BCL3	chr17:46047711-46049097	A549	lung:	n/a	chr17:46048226-46048239 chr17:46048495-46048504
34	ZNF263	chr17:46047886-46048920	HEK293-T-REx	kidney:	n/a	n/a
35	POLR2A	chr17:46047957-46048991	GM12878	blood:	n/a	n/a
36	MBD4	chr17:46047816-46048986	HepG2	liver:	n/a	n/a
37	YY1	chr17:46048019-46049036	A549	lung:	n/a	n/a
38	MYC	chr17:46048073-46048975	MCF-7	breast:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
39	TAF1	chr17:46047940-46048888	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr17:46047904-46049016	H1-neurons	neurons:	n/a	n/a
41	KAP1	chr17:46047778-46048909	HEK293	kidney:	n/a	n/a
42	BCLAF1	chr17:46048267-46048984	K562	blood:	n/a	chr17:46048495-46048504
43	POLR2A	chr17:46048083-46048923	GM12878	blood:	n/a	n/a
44	EGR1	chr17:46047940-46048889	H1-hESC	embryonic stem cell:	n/a	chr17:46048335-46048345 chr17:46048495-46048504 chr17:46048336-46048346 chr17:46048777-46048787
45	MAX	chr17:46047941-46049070	A549	lung:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
46	UBTF	chr17:46048079-46049001	K562	blood:	n/a	n/a
47	POLR2A	chr17:46048208-46048901	GM12892	blood:	n/a	n/a
48	MAX	chr17:46047955-46048963	HepG2	liver:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
49	PML	chr17:46047903-46049056	MCF-7	breast:	n/a	n/a
50	MXI1	chr17:46048265-46048991	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:46048822-46048872	HNPCEpiC	eye:	n/a
2	chr17:46048822-46048872	HCF	heart:	n/a
3	chr17:46048822-46048872	MCF10A-Er-Src	breast:	n/a
4	chr17:46048822-46048872	HMEC	breast:	n/a
5	chr17:46048822-46048872	PFSK-1	brain:	n/a
6	chr17:46048822-46048872	GM12891	blood:	n/a
7	chr17:46048822-46048872	BJ	skin:	n/a
8	chr17:46048822-46048872	ECC-1	luminal epithelium:	n/a
9	chr17:46048822-46048872	HEEpiC	esophagus:	n/a
10	chr17:46048822-46048872	RPTEC	kidney:	n/a
11	chr17:46048822-46048872	AG09309	skin:	n/a
12	chr17:46048822-46048872	BE2_C	brain:	n/a
13	chr17:46048822-46048872	T-47D	breast:	n/a
14	chr17:46048822-46048872	AG04450	lung:	fetal
15	chr17:46048822-46048872	HCT-116	colon:	n/a
16	chr17:46048822-46048872	Hela-S3	cervix:	n/a
17	chr17:46048822-46048872	AG10803	skin:	n/a
18	chr17:46048822-46048872	GM12892	blood:	n/a
19	chr17:46048822-46048872	ovcar-3	ovarian:	n/a
20	chr17:46048822-46048872	IMR90	lung:	fetal
21	chr17:46048822-46048872	HRE	kidney:	n/a
22	chr17:46048822-46048872	ProgFib	skin:	n/a
23	chr17:46048822-46048872	PrEC	prostate:	n/a
24	chr17:46048822-46048872	H1-hESC	embryonic stem cell:	embryo
25	chr17:46048822-46048872	NT2-D1	testis:	n/a
26	chr17:46048822-46048872	Hepatocyte	liver:	n/a
27	chr17:46048822-46048872	HCM	heart:	n/a
28	chr17:46048822-46048872	U87	brain:	n/a
29	chr17:46048822-46048872	NH-A	brain:	n/a
30	chr17:46048822-46048872	K562	blood:	n/a
31	chr17:46048822-46048872	A549	lung:	n/a
32	chr17:46048822-46048872	NHBE	bronchial:	n/a
33	chr17:46048822-46048872	CMK	blood:	n/a
34	chr17:46048822-46048872	HL-60	blood:	n/a
35	chr17:46048822-46048872	SK-N-SH_RA	brain:	n/a
36	chr17:46048822-46048872	SK-N-SH	brain:	n/a
37	chr17:46048822-46048872	HEK293	kidney:	embryo
38	chr17:46048822-46048872	LNCaP	prostate:	n/a
39	chr17:46048822-46048872	MCF-7	breast:	n/a
40	chr17:46048822-46048872	GM06990	blood:	n/a
41	chr17:46048822-46048872	SKMC	muscle:	n/a
42	chr17:46048822-46048872	HRPEpiC	eye:	n/a
43	chr17:46048822-46048872	HCPEpiC	choroid plexus:	n/a
44	chr17:46048822-46048872	HUVEC	blood vessel:	n/a
45	chr17:46048822-46048872	NB4	blood:	n/a
46	chr17:46048822-46048872	AG09319	gingival:	n/a
47	chr17:46048822-46048872	PANC-1	pancreas:	n/a
48	chr17:46048822-46048872	HepG2	liver:	n/a
49	chr17:46048822-46048872	GM19239	blood:	n/a
50	chr17:46048822-46048872	HPAEpiC	pulmonary alveolar:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
2	chr17:45932084..45934510-chr17:46047359..46049635,2	K562	blood:
3	chr17:45915738..45918906-chr17:46047433..46049662,3	K562	blood:
4	chr17:46048621..46050545-chr17:46057076..46059668,3	K562	blood:
5	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
6	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
7	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
8	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
9	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
10	chr17:45727256..45728937-chr17:46047807..46049675,2	K562	blood:
11	chr17:46048432..46050374-chr17:46050535..46053358,3	MCF-7	breast:
12	chr17:46048551..46050173-chr17:46123931..46126830,2	MCF-7	breast:
13	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
14	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:
15	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
16	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
17	chr17:46048370..46050701-chr17:46124898..46126529,2	K562	blood:
18	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
19	chr17:46048142..46050112-chr17:46183426..46185210,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
CDK5RAP3	CpG island
ENSG00000263412	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1476578	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476579	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2003477	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003478	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255697	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255815	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525084	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525087	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525088	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525090	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525091	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525092	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525093	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525094	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525096	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525098	0.97[ASN][1000 genomes]
rs2597161	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597165	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597168	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597171	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597172	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597173	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597174	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597179	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597180	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597181	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875746	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905845	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905848	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905849	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905850	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905851	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905852	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905853	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34190379	0.94[ASN][1000 genomes]
rs35653190	0.83[ASN][1000 genomes]
rs62064873	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6503949	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729785	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729786	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737130	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739853	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7406338	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7503584	0.94[ASN][1000 genomes]
rs8076314	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885634	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46047000-46049400	Active TSS	Rectal Smooth Muscle	rectum
2	chr17:46047400-46049200	Active TSS	Fetal Kidney	kidney
3	chr17:46047600-46049400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:46047600-46049600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:46047800-46049000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr17:46047800-46049000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46047800-46049000	Active TSS	Aorta	Aorta
8	chr17:46047800-46049000	Active TSS	Fetal Brain Female	brain
9	chr17:46047800-46049000	Active TSS	Gastric	stomach
10	chr17:46047800-46049200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr17:46047800-46049200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr17:46047800-46049200	Active TSS	Psoas Muscle	Psoas
13	chr17:46047800-46049200	Active TSS	Right Atrium	heart
14	chr17:46047800-46049400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:46047800-46049400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr17:46047800-46050000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:46048000-46049000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:46048000-46049000	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr17:46048000-46049000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:46048000-46049000	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr17:46048000-46049000	Active TSS	Brain Anterior Caudate	brain
22	chr17:46048000-46049000	Active TSS	Brain Germinal Matrix	brain
23	chr17:46048000-46049000	Active TSS	Brain Hippocampus Middle	brain
24	chr17:46048000-46049000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:46048000-46049000	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr17:46048000-46049000	Active TSS	Right Ventricle	heart
27	chr17:46048000-46049000	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr17:46048000-46049000	Active TSS	Stomach Mucosa	stomach
29	chr17:46048000-46049000	Active TSS	Spleen	Spleen
30	chr17:46048000-46049000	Active TSS	NH-A	brain
31	chr17:46048000-46049200	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr17:46048000-46049200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:46048000-46049200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:46048000-46049200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr17:46048000-46049200	Active TSS	Brain Angular Gyrus	brain
36	chr17:46048000-46049200	Active TSS	Brain Substantia Nigra	brain
37	chr17:46048000-46049200	Active TSS	Colon Smooth Muscle	Colon
38	chr17:46048000-46049200	Active TSS	Esophagus	oesophagus
39	chr17:46048000-46049200	Active TSS	Fetal Intestine Large	intestine
40	chr17:46048000-46049200	Active TSS	Fetal Intestine Small	intestine
41	chr17:46048000-46049200	Active TSS	Left Ventricle	heart
42	chr17:46048000-46049200	Active TSS	Lung	lung
43	chr17:46048000-46049200	Active TSS	NHLF	lung
44	chr17:46048000-46049400	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr17:46048000-46049400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:46048000-46049400	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr17:46048000-46049400	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr17:46048000-46049400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:46048000-46049400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:46048000-46049400	Active TSS	Colonic Mucosa	Colon

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