Variant report

Variant	rs2285860
Chromosome Location	chr17:46048412-46048413
allele	G/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	chr17:46047601-46049109	NB4	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
2	EP300	chr17:46047914-46048560	SK-N-SH_RA	brain:	n/a	n/a
3	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
4	ELF1	chr17:46048149-46048949	A549	lung:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
5	POLR2A	chr17:46047860-46049148	PANC-1	pancreas:	n/a	n/a
6	MAX	chr17:46047943-46049094	K562	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
7	NFIC	chr17:46048364-46049112	GM12878	blood:	n/a	n/a
8	HEY1	chr17:46048317-46048948	K562	blood:	n/a	chr17:46048783-46048798
9	IRF1	chr17:46048010-46048879	K562	blood:	n/a	chr17:46048335-46048349 chr17:46048373-46048382
10	SIN3AK20	chr17:46048277-46048785	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr17:46048326-46048896	SK-N-SH	brain:	n/a	n/a
12	ELF1	chr17:46048006-46048933	K562	blood:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
13	MAX	chr17:46047776-46049210	HCT-116	colon:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
14	MAX	chr17:46047898-46049065	GM12878	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
15	POLR2A	chr17:46048334-46048783	A549	lung:	n/a	n/a
16	JUND	chr17:46047955-46048923	K562	blood:	n/a	chr17:46048467-46048476 chr17:46048371-46048380
17	SP1	chr17:46047927-46048696	HepG2	liver:	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
18	ZNF143	chr17:46047928-46048797	K562	blood:	n/a	n/a
19	TAF1	chr17:46047972-46048901	HepG2	liver:	n/a	n/a
20	SIN3AK20	chr17:46048307-46048840	HepG2	liver:	n/a	n/a
21	SMARCB1	chr17:46047953-46049191	Hela-S3	cervix:	n/a	n/a
22	FOSL1	chr17:46047792-46048669	K562	blood:	n/a	chr17:46048467-46048476 chr17:46048371-46048380
23	POLR2A	chr17:46048079-46049174	IMR90	lung:	n/a	n/a
24	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
25	GTF2F1	chr17:46048004-46048939	K562	blood:	n/a	n/a
26	ELF1	chr17:46047860-46048985	GM12878	blood:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
27	CBX3	chr17:46047908-46049109	K562	blood:	n/a	n/a
28	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
29	POLR2A	chr17:46048291-46048977	GM12891	blood:	n/a	n/a
30	ELF1	chr17:46047954-46049020	SK-N-SH	brain:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
31	POLR2A	chr17:46048346-46049057	K562	blood:	n/a	n/a
32	JUND	chr17:46047983-46048414	HepG2	liver:	n/a	chr17:46048371-46048380
33	POLR2A	chr17:46047890-46048934	ECC-1	luminal epithelium:	n/a	n/a
34	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
35	POLR2A	chr17:46047909-46049047	HCT-116	colon:	n/a	n/a
36	REST	chr17:46047896-46048649	HepG2	liver:	n/a	n/a
37	TBL1XR1	chr17:46047952-46049041	K562	blood:	n/a	n/a
38	PAX5	chr17:46048027-46048878	GM12892	blood:	n/a	chr17:46048495-46048504
39	BCL3	chr17:46047711-46049097	A549	lung:	n/a	chr17:46048226-46048239 chr17:46048495-46048504
40	POLR2A	chr17:46048317-46048725	HepG2	liver:	n/a	n/a
41	ELK1	chr17:46047939-46048749	GM12878	blood:	n/a	n/a
42	ZNF263	chr17:46047886-46048920	HEK293-T-REx	kidney:	n/a	n/a
43	TAF1	chr17:46047893-46048764	GM12878	blood:	n/a	n/a
44	POLR2A	chr17:46047957-46048991	GM12878	blood:	n/a	n/a
45	MBD4	chr17:46047816-46048986	HepG2	liver:	n/a	n/a
46	YY1	chr17:46048019-46049036	A549	lung:	n/a	n/a
47	MYC	chr17:46048073-46048975	MCF-7	breast:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
48	TAF1	chr17:46047940-46048888	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr17:46047904-46049016	H1-neurons	neurons:	n/a	n/a
50	KAP1	chr17:46047778-46048909	HEK293	kidney:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:46048395-46048445	BE2_C	brain:	n/a
2	chr17:46048404-46048454	AoSMC	blood vessel:	n/a
3	chr17:46048395-46048445	HepG2	liver:	n/a
4	chr17:46048392-46048442	HCF	heart:	n/a
5	chr17:46048395-46048445	NHBE	bronchial:	n/a
6	chr17:46048404-46048454	AG09319	gingival:	n/a
7	chr17:46048404-46048454	A549	lung:	n/a
8	chr17:46048392-46048442	NB4	blood:	n/a
9	chr17:46048395-46048445	HCPEpiC	choroid plexus:	n/a
10	chr17:46048385-46048435	HRCEpiC	kidney:	n/a
11	chr17:46048364-46048414	RPTEC	kidney:	n/a
12	chr17:46048395-46048445	SK-N-SH_RA	brain:	n/a
13	chr17:46048404-46048454	HIPEpiC	eye:	n/a
14	chr17:46048385-46048435	HUVEC	blood vessel:	n/a
15	chr17:46048364-46048414	H1-hESC	embryonic stem cell:	embryo
16	chr17:46048395-46048445	HIPEpiC	eye:	n/a
17	chr17:46048364-46048414	ovcar-3	ovarian:	n/a
18	chr17:46048385-46048435	HEEpiC	esophagus:	n/a
19	chr17:46048395-46048445	CMK	blood:	n/a
20	chr17:46048364-46048414	GM12891	blood:	n/a
21	chr17:46048392-46048442	PANC-1	pancreas:	n/a
22	chr17:46048385-46048435	GM12892	blood:	n/a
23	chr17:46048364-46048414	HRE	kidney:	n/a
24	chr17:46048392-46048442	Jurkat	blood:	n/a
25	chr17:46048395-46048445	SKMC	muscle:	n/a
26	chr17:46048395-46048445	ECC-1	luminal epithelium:	n/a
27	chr17:46048364-46048414	SAEC	small airway:	n/a
28	chr17:46048364-46048414	GM19239	blood:	n/a
29	chr17:46048364-46048414	GM12892	blood:	n/a
30	chr17:46048385-46048435	AoSMC	blood vessel:	n/a
31	chr17:46048364-46048414	NH-A	brain:	n/a
32	chr17:46048392-46048442	BJ	skin:	n/a
33	chr17:46048364-46048414	HAEpiC	amniotic membrane:	n/a
34	chr17:46048395-46048445	K562	blood:	n/a
35	chr17:46048404-46048454	H1-hESC	embryonic stem cell:	embryo
36	chr17:46048364-46048414	SKMC	muscle:	n/a
37	chr17:46048385-46048435	NT2-D1	testis:	n/a
38	chr17:46048395-46048445	SAEC	small airway:	n/a
39	chr17:46048395-46048445	NHDF-neo	bronchial:	n/a
40	chr17:46048392-46048442	HPAEpiC	pulmonary alveolar:	n/a
41	chr17:46048385-46048435	Jurkat	blood:	n/a
42	chr17:46048392-46048442	AG04450	lung:	fetal
43	chr17:46048404-46048454	PANC-1	pancreas:	n/a
44	chr17:46048364-46048414	SK-N-SH	brain:	n/a
45	chr17:46048385-46048435	AG04450	lung:	fetal
46	chr17:46048385-46048435	AG09309	skin:	n/a
47	chr17:46048404-46048454	HCT-116	colon:	n/a
48	chr17:46048404-46048454	PFSK-1	brain:	n/a
49	chr17:46048364-46048414	HCT-116	colon:	n/a
50	chr17:46048404-46048454	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr12:125398635..125399328-chr17:46048183..46048815,2	HCT-116	colon:
2	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
3	chr17:45932084..45934510-chr17:46047359..46049635,2	K562	blood:
4	chr17:45915738..45918906-chr17:46047433..46049662,3	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	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
12	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
13	chr17:46048149..46048819-chr5:114879946..114880664,2	NB4	blood:
14	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
15	chr17:46034698..46035465-chr17:46047687..46048504,2	MCF-7	breast:
16	chr17:46048370..46050701-chr17:46124898..46126529,2	K562	blood:
17	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
18	chr17:45973269..45974008-chr17:46047794..46048455,3	K562	blood:
19	chr17:46046859..46048450-chr17:46055513..46058232,2	K562	blood:
20	chr17:46048142..46050112-chr17:46183426..46185210,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
CDK5RAP3	CpG island
ENSG00000167183	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000150991	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000145780	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1133221	0.94[GIH][hapmap]
rs12601350	0.85[EUR][1000 genomes]
rs12602131	0.85[EUR][1000 genomes]
rs12602670	0.85[EUR][1000 genomes]
rs1473117	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16949270	0.94[GIH][hapmap]
rs16951519	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs17616799	0.94[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1986694	0.82[EUR][1000 genomes]
rs2023885	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs208005	0.83[CEU][hapmap];0.94[GIH][hapmap]
rs208008	0.94[GIH][hapmap]
rs208009	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs2229369	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2240119	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[EUR][1000 genomes]
rs2240120	0.91[CEU][hapmap];0.94[GIH][hapmap];0.81[EUR][1000 genomes]
rs2240121	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs2325783	0.81[EUR][1000 genomes]
rs2325804	0.91[CEU][hapmap]
rs2525105	1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs55982711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56402159	0.91[EUR][1000 genomes]
rs57782323	0.94[EUR][1000 genomes]
rs58554000	0.83[EUR][1000 genomes]
rs61396871	0.91[EUR][1000 genomes]
rs7224461	0.82[CEU][hapmap]
rs72823519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823528	0.85[EUR][1000 genomes]
rs72823532	0.85[EUR][1000 genomes]
rs72823533	0.85[EUR][1000 genomes]
rs757353	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[EUR][1000 genomes]
rs8071199	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs8071879	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs978263	0.88[CEU][hapmap]
rs9944405	0.83[GIH][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2285860	CBX1	Cis_1M	lymphoblastoid	RTeQTL
rs2285860	CDK5RAP3	cis	Nerve Tibial	GTEx

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	chr17:46047800-46048800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr17:46047800-46048800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr17:46047800-46049000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr17:46047800-46049000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:46047800-46049000	Active TSS	Aorta	Aorta
10	chr17:46047800-46049000	Active TSS	Fetal Brain Female	brain
11	chr17:46047800-46049000	Active TSS	Gastric	stomach
12	chr17:46047800-46049200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr17:46047800-46049200	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr17:46047800-46049200	Active TSS	Psoas Muscle	Psoas
15	chr17:46047800-46049200	Active TSS	Right Atrium	heart
16	chr17:46047800-46049400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:46047800-46049400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr17:46047800-46050000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr17:46048000-46048600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr17:46048000-46048600	Active TSS	Primary T cells from cord blood	blood
21	chr17:46048000-46048600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr17:46048000-46048600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:46048000-46048600	Bivalent/Poised TSS	HepG2	liver
24	chr17:46048000-46048800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr17:46048000-46048800	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr17:46048000-46048800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:46048000-46048800	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr17:46048000-46048800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr17:46048000-46048800	Active TSS	Brain Cingulate Gyrus	brain
30	chr17:46048000-46048800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr17:46048000-46048800	Active TSS	Duodenum Mucosa	Duodenum
32	chr17:46048000-46048800	Active TSS	Fetal Brain Male	brain
33	chr17:46048000-46048800	Active TSS	Fetal Lung	lung
34	chr17:46048000-46049000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr17:46048000-46049000	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr17:46048000-46049000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr17:46048000-46049000	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr17:46048000-46049000	Active TSS	Brain Anterior Caudate	brain
39	chr17:46048000-46049000	Active TSS	Brain Germinal Matrix	brain
40	chr17:46048000-46049000	Active TSS	Brain Hippocampus Middle	brain
41	chr17:46048000-46049000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr17:46048000-46049000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr17:46048000-46049000	Active TSS	Right Ventricle	heart
44	chr17:46048000-46049000	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr17:46048000-46049000	Active TSS	Stomach Mucosa	stomach
46	chr17:46048000-46049000	Active TSS	Spleen	Spleen
47	chr17:46048000-46049000	Active TSS	NH-A	brain
48	chr17:46048000-46049200	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr17:46048000-46049200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:46048000-46049200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links