Variant report

Variant	rs56960576
Chromosome Location	chr3:52553167-52553168
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	MYC	chr3:52552604-52553713	K562	blood:	n/a	n/a
2	MAX	chr3:52552484-52553519	H1-hESC	embryonic stem cell:	n/a	n/a
3	YY1	chr3:52552693-52553172	K562	blood:	n/a	chr3:52553106-52553115
4	SP1	chr3:52552931-52553337	H1-hESC	embryonic stem cell:	n/a	chr3:52553134-52553145 chr3:52553267-52553277 chr3:52553105-52553114 chr3:52553104-52553116 chr3:52553104-52553116 chr3:52553267-52553277 chr3:52553105-52553114 chr3:52553135-52553145 chr3:52553122-52553133 chr3:52553134-52553146 chr3:52553134-52553146 chr3:52553136-52553145 chr3:52553106-52553115 chr3:52553104-52553115 chr3:52553135-52553144 chr3:52553266-52553278 chr3:52553268-52553277 chr3:52553135-52553145 chr3:52553267-52553276 chr3:52553266-52553278 chr3:52553105-52553115 chr3:52553135-52553144 chr3:52553046-52553059 chr3:52553105-52553115 chr3:52553105-52553119 chr3:52553267-52553276
5	HMGN3	chr3:52552594-52553398	K562	blood:	n/a	n/a
6	POLR2A	chr3:52552717-52553325	K562	blood:	n/a	n/a
7	MAX	chr3:52553137-52553415	K562	blood:	n/a	n/a
8	CTCF	chr3:52552795-52553168	K562	blood:	n/a	chr3:52552993-52553003 chr3:52553001-52553014
9	MAX	chr3:52552574-52553902	K562	blood:	n/a	chr3:52553734-52553744 chr3:52553752-52553762
10	E2F6	chr3:52552606-52553637	K562	blood:	n/a	chr3:52553106-52553115 chr3:52553268-52553277
11	RCOR1	chr3:52552908-52553183	K562	blood:	n/a	n/a
12	CEBPB	chr3:52553161-52553318	K562	blood:	n/a	n/a
13	POLR2A	chr3:52553115-52553991	HUVEC	blood vessel:	n/a	n/a
14	CCNT2	chr3:52552915-52553206	K562	blood:	n/a	chr3:52553106-52553115
15	SIN3A	chr3:52552586-52553454	H1-hESC	embryonic stem cell:	n/a	n/a
16	EGR1	chr3:52552775-52553210	K562	blood:	n/a	chr3:52553107-52553120 chr3:52553105-52553115 chr3:52553136-52553146
17	E2F6	chr3:52553134-52553544	K562	blood:	n/a	chr3:52553268-52553277
18	MAZ	chr3:52552763-52553404	K562	blood:	n/a	n/a
19	MYC	chr3:52552695-52553881	K562	blood:	n/a	chr3:52553734-52553744 chr3:52553752-52553762
20	EP300	chr3:52552949-52553199	K562	blood:	n/a	n/a
21	IRF1	chr3:52552914-52553360	K562	blood:	n/a	chr3:52553264-52553278 chr3:52553102-52553116 chr3:52553132-52553146
22	MAX	chr3:52552644-52553483	K562	blood:	n/a	n/a
23	MAX	chr3:52552408-52553551	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52553167-52553217	AG09309	skin:	n/a
2	chr3:52553167-52553217	GM12891	blood:	n/a
3	chr3:52553167-52553217	HIPEpiC	eye:	n/a
4	chr3:52553167-52553217	MCF10A-Er-Src	breast:	n/a
5	chr3:52553167-52553217	ECC-1	luminal epithelium:	n/a
6	chr3:52553167-52553217	BJ	skin:	n/a
7	chr3:52553167-52553217	BE2_C	brain:	n/a
8	chr3:52553167-52553217	GM06990	blood:	n/a
9	chr3:52553167-52553217	AoSMC	blood vessel:	n/a
10	chr3:52553167-52553217	HEEpiC	esophagus:	n/a
11	chr3:52553167-52553217	HRE	kidney:	n/a
12	chr3:52553167-52553217	Hela-S3	cervix:	n/a
13	chr3:52553167-52553217	ovcar-3	ovarian:	n/a
14	chr3:52553167-52553217	H1-hESC	embryonic stem cell:	embryo
15	chr3:52553167-52553217	SKMC	muscle:	n/a
16	chr3:52553167-52553217	IMR90	lung:	fetal
17	chr3:52553167-52553217	NHBE	bronchial:	n/a
18	chr3:52553167-52553217	SK-N-SH_RA	brain:	n/a
19	chr3:52553167-52553217	NH-A	brain:	n/a
20	chr3:52553167-52553217	HRCEpiC	kidney:	n/a
21	chr3:52553167-52553217	PANC-1	pancreas:	n/a
22	chr3:52553167-52553217	HCF	heart:	n/a
23	chr3:52553167-52553217	AG04449	skin:	fetal
24	chr3:52553167-52553217	Hepatocyte	liver:	n/a
25	chr3:52553167-52553217	HCPEpiC	choroid plexus:	n/a
26	chr3:52553167-52553217	PFSK-1	brain:	n/a
27	chr3:52553167-52553217	K562	blood:	n/a
28	chr3:52553167-52553217	HCM	heart:	n/a
29	chr3:52553167-52553217	AG10803	skin:	n/a
30	chr3:52553167-52553217	HEK293	kidney:	embryo
31	chr3:52553167-52553217	GM19239	blood:	n/a
32	chr3:52553167-52553217	HAEpiC	amniotic membrane:	n/a
33	chr3:52553167-52553217	ProgFib	skin:	n/a
34	chr3:52553167-52553217	CMK	blood:	n/a
35	chr3:52553167-52553217	Caco-2	colon:	n/a
36	chr3:52553167-52553217	A549	lung:	n/a
37	chr3:52553167-52553217	NHDF-neo	bronchial:	n/a
38	chr3:52553167-52553217	NB4	blood:	n/a
39	chr3:52553167-52553217	PrEC	prostate:	n/a
40	chr3:52553167-52553217	HUVEC	blood vessel:	n/a
41	chr3:52553167-52553217	HL-60	blood:	n/a
42	chr3:52553167-52553217	U87	brain:	n/a
43	chr3:52553167-52553217	LNCaP	prostate:	n/a
44	chr3:52553167-52553217	HRPEpiC	eye:	n/a
45	chr3:52553167-52553217	SK-N-SH	brain:	n/a
46	chr3:52553167-52553217	HCT-116	colon:	n/a
47	chr3:52553167-52553217	Jurkat	blood:	n/a
48	chr3:52553167-52553217	MCF-7	breast:	n/a
49	chr3:52553167-52553217	RPTEC	kidney:	n/a
50	chr3:52553167-52553217	HPAEpiC	pulmonary alveolar:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52551111..52554473-chr3:52556873..52560591,3	MCF-7	breast:
2	chr3:52550660..52553610-chr3:52725143..52727667,2	K562	blood:
3	chr3:52551484..52554158-chr3:52567066..52569157,2	MCF-7	breast:
4	chr3:52552118..52554542-chr3:52561235..52564270,3	MCF-7	breast:

Variant related genes	Relation type
STAB1	TF binding region
STAB1	CpG island
ENSG00000163938	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000222345	Chromatin interaction
ENSG00000212452	Chromatin interaction
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10510759	1.00[EUR][1000 genomes]
rs1987234	1.00[EUR][1000 genomes]
rs35920544	1.00[EUR][1000 genomes]
rs56259931	1.00[EUR][1000 genomes]
rs57246324	1.00[EUR][1000 genomes]
rs57319306	1.00[EUR][1000 genomes]
rs57560655	1.00[EUR][1000 genomes]
rs58100002	1.00[EUR][1000 genomes]
rs58409398	1.00[AMR][1000 genomes]
rs58725214	1.00[EUR][1000 genomes]
rs60040519	0.89[AMR][1000 genomes]
rs60256157	0.89[AMR][1000 genomes]
rs60415551	1.00[EUR][1000 genomes]
rs60823713	1.00[EUR][1000 genomes]
rs60830326	0.89[AMR][1000 genomes]
rs60916588	1.00[EUR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	1.00[EUR][1000 genomes]
rs73837804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839126	0.89[AMR][1000 genomes]
rs7648016	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:52533400-52559800	Weak transcription	Liver	Liver
4	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:52540000-52553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:52542000-52557400	Weak transcription	Thymus	Thymus
11	chr3:52544000-52557400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:52549800-52553600	Weak transcription	Right Ventricle	heart
13	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:52550800-52558400	Strong transcription	HUVEC	blood vessel
15	chr3:52551000-52554600	Genic enhancers	Spleen	Spleen
16	chr3:52552000-52553400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
17	chr3:52552000-52553400	Enhancers	Fetal Brain Male	brain
18	chr3:52552000-52560800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:52552400-52553400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:52552400-52559200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:52552600-52553200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr3:52552600-52553200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:52552600-52553200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:52552600-52553200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:52552600-52553200	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
26	chr3:52552600-52553200	ZNF genes & repeats	Fetal Intestine Large	intestine
27	chr3:52552600-52553200	Genic enhancers	Gastric	stomach
28	chr3:52552600-52553400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr3:52552600-52553400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr3:52552600-52553400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:52552600-52553400	Genic enhancers	Adipose Nuclei	Adipose
32	chr3:52552600-52558200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:52552800-52553200	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:52552800-52553200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:52552800-52553200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:52552800-52553200	Active TSS	Brain Anterior Caudate	brain
37	chr3:52552800-52553200	Active TSS	Brain Germinal Matrix	brain
38	chr3:52552800-52553200	Active TSS	Duodenum Mucosa	Duodenum
39	chr3:52552800-52553200	Flanking Active TSS	Ovary	ovary
40	chr3:52552800-52553200	Active TSS	Psoas Muscle	Psoas
41	chr3:52552800-52553200	Active TSS	Right Atrium	heart
42	chr3:52552800-52553200	Active TSS	Stomach Smooth Muscle	stomach
43	chr3:52552800-52553400	Active TSS	H1 Cell Line	embryonic stem cell
44	chr3:52552800-52553400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr3:52552800-52553400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:52552800-52553400	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr3:52552800-52553400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:52552800-52553400	Active TSS	Fetal Brain Female	brain
49	chr3:52552800-52553400	Active TSS	Fetal Intestine Small	intestine
50	chr3:52552800-52553400	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links