Variant report

Variant	rs4652524
Chromosome Location	chr1:180600970-180600971
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	CTCF	chr1:180600830-180601137	Lung_OC	lung:	n/a	n/a
2	REST	chr1:180600887-180601726	K562	blood:	n/a	n/a
3	MAX	chr1:180600961-180601382	GM12878	blood:	n/a	chr1:180601114-180601123
4	CTCF	chr1:180600926-180601077	MCF-7	breast:	n/a	n/a
5	REST	chr1:180600744-180601566	A549	lung:	n/a	n/a
6	SIN3A	chr1:180600944-180602107	H1-hESC	embryonic stem cell:	n/a	chr1:180600971-180600979 chr1:180601797-180601810 chr1:180601722-180601735
7	CTCF	chr1:180600940-180601090	Caco-2	colon:	n/a	n/a
8	ELF1	chr1:180600802-180601604	K562	blood:	n/a	chr1:180601522-180601531 chr1:180601568-180601580 chr1:180601285-180601294 chr1:180601206-180601215
9	CTCF	chr1:180600898-180601081	Gliobla	brain:	n/a	n/a
10	GTF2F1	chr1:180600924-180601365	H1-hESC	embryonic stem cell:	n/a	n/a
11	SP1	chr1:180600711-180601753	A549	lung:	n/a	chr1:180601136-180601145 chr1:180601140-180601152 chr1:180601147-180601156 chr1:180601142-180601151 chr1:180601040-180601052 chr1:180601588-180601597 chr1:180601140-180601152 chr1:180601146-180601155 chr1:180601069-180601080 chr1:180601145-180601157 chr1:180601040-180601052 chr1:180601147-180601156 chr1:180601069-180601081 chr1:180601142-180601156 chr1:180601145-180601157 chr1:180601146-180601156 chr1:180601040-180601051 chr1:180601070-180601080 chr1:180601135-180601147 chr1:180601070-180601079 chr1:180601146-180601156 chr1:180601141-180601150
12	POLR2A	chr1:180600803-180601361	U87	brain:	n/a	n/a
13	POLR2A	chr1:180600829-180601729	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr1:180600892-180601087	NHEK	skin:	n/a	n/a
15	TAF1	chr1:180600881-180601985	ECC-1	luminal epithelium:	n/a	n/a
16	NRF1	chr1:180600860-180601445	GM12878	blood:	n/a	n/a
17	FOS	chr1:180600840-180601127	MCF10A-Er-Src	breast:	n/a	chr1:180600987-180600998
18	POLR2A	chr1:180600775-180601806	K562	blood:	n/a	n/a
19	POLR2A	chr1:180600772-180601579	SK-N-MC	brain:	n/a	n/a
20	CTCF	chr1:180600901-180601039	GM13977	blood:	n/a	n/a
21	CTCF	chr1:180600920-180601070	SAEC	small airway:	n/a	n/a
22	CTCF	chr1:180600886-180601063	GM10248	blood:	n/a	n/a
23	POLR2A	chr1:180600776-180601532	K562	blood:	n/a	n/a
24	POLR2A	chr1:180600801-180601622	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:180600769-180601518	HCT-116	colon:	n/a	n/a
26	HEY1	chr1:180600840-180601062	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:180600793-180601540	PFSK-1	brain:	n/a	n/a
28	CTCF	chr1:180600820-180600970	GM12864	blood:	n/a	n/a
29	MAZ	chr1:180600834-180601994	K562	blood:	n/a	chr1:180601114-180601123
30	POLR2A	chr1:180600788-180601769	GM18526	blood:	n/a	n/a
31	RFX5	chr1:180600956-180601313	HepG2	liver:	n/a	chr1:180601110-180601125 chr1:180601113-180601128 chr1:180601113-180601128 chr1:180601113-180601128 chr1:180601112-180601129
32	PML	chr1:180600336-180601941	GM12878	blood:	n/a	chr1:180601875-180601883
33	MAX	chr1:180600821-180602115	ECC-1	luminal epithelium:	n/a	chr1:180601114-180601123
34	CTCF	chr1:180600880-180601030	GM06990	blood:	n/a	n/a
35	CTCF	chr1:180600920-180601070	GM12875	blood:	n/a	n/a
36	CTCF	chr1:180600900-180601050	SK-N-SH_RA	brain:	n/a	n/a
37	CTCF	chr1:180600960-180601110	HRE	kidney:	n/a	n/a
38	MAX	chr1:180600852-180601809	NB4	blood:	n/a	chr1:180601114-180601123
39	POLR2A	chr1:180600824-180601458	K562	blood:	n/a	n/a
40	UBTF	chr1:180600896-180602112	K562	blood:	n/a	n/a
41	POLR2A	chr1:180600798-180601817	GM12892	blood:	n/a	n/a
42	POLR2A	chr1:180600772-180601425	HCT-116	colon:	n/a	n/a
43	TAF1	chr1:180600908-180601831	HepG2	liver:	n/a	n/a
44	EP300	chr1:180600968-180602059	ECC-1	luminal epithelium:	n/a	chr1:180601520-180601536 chr1:180601287-180601303 chr1:180601550-180601566 chr1:180601551-180601567 chr1:180601205-180601214 chr1:180601594-180601610 chr1:180601283-180601292
45	CTCF	chr1:180600846-180601233	T-47D	breast:	n/a	n/a
46	FOS	chr1:180600926-180601130	MCF10A-Er-Src	breast:	n/a	chr1:180600987-180600998
47	ZNF143	chr1:180600925-180601085	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr1:180600940-180601090	GM12868	blood:	n/a	n/a
49	POLR2A	chr1:180600895-180601815	A549	lung:	n/a	n/a
50	POLR2A	chr1:180600872-180601701	ProgFib	skin:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:180600963-180601013	HL-60	blood:	n/a
2	chr1:180600963-180601013	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:180600963-180601013	IMR90	lung:	fetal
4	chr1:180600963-180601013	HRE	kidney:	n/a
5	chr1:180600963-180601013	SKMC	muscle:	n/a
6	chr1:180600963-180601013	H1-hESC	embryonic stem cell:	embryo
7	chr1:180600963-180601013	HAEpiC	amniotic membrane:	n/a
8	chr1:180600963-180601013	NHDF-neo	bronchial:	n/a
9	chr1:180600963-180601013	BJ	skin:	n/a
10	chr1:180600963-180601013	K562	blood:	n/a
11	chr1:180600963-180601013	Hela-S3	cervix:	n/a
12	chr1:180600963-180601013	LNCaP	prostate:	n/a
13	chr1:180600963-180601013	HUVEC	blood vessel:	n/a
14	chr1:180600963-180601013	HCF	heart:	n/a
15	chr1:180600963-180601013	HRCEpiC	kidney:	n/a
16	chr1:180600963-180601013	SAEC	small airway:	n/a
17	chr1:180600963-180601013	AG09319	gingival:	n/a
18	chr1:180600963-180601013	ovcar-3	ovarian:	n/a
19	chr1:180600963-180601013	NHBE	bronchial:	n/a
20	chr1:180600963-180601013	HMEC	breast:	n/a
21	chr1:180600963-180601013	MCF-7	breast:	n/a
22	chr1:180600963-180601013	AG04450	lung:	fetal
23	chr1:180600963-180601013	AG04449	skin:	fetal
24	chr1:180600963-180601013	ECC-1	luminal epithelium:	n/a
25	chr1:180600963-180601013	RPTEC	kidney:	n/a
26	chr1:180600963-180601013	PFSK-1	brain:	n/a
27	chr1:180600963-180601013	MCF10A-Er-Src	breast:	n/a
28	chr1:180600963-180601013	SK-N-SH	brain:	n/a
29	chr1:180600963-180601013	HCM	heart:	n/a
30	chr1:180600963-180601013	Jurkat	blood:	n/a
31	chr1:180600963-180601013	GM12891	blood:	n/a
32	chr1:180600963-180601013	HCT-116	colon:	n/a
33	chr1:180600963-180601013	HEEpiC	esophagus:	n/a
34	chr1:180600963-180601013	T-47D	breast:	n/a
35	chr1:180600963-180601013	CMK	blood:	n/a
36	chr1:180600963-180601013	PrEC	prostate:	n/a
37	chr1:180600963-180601013	SK-N-SH_RA	brain:	n/a
38	chr1:180600963-180601013	Caco-2	colon:	n/a
39	chr1:180600963-180601013	AoSMC	blood vessel:	n/a
40	chr1:180600963-180601013	GM12878	blood:	n/a
41	chr1:180600963-180601013	HCPEpiC	choroid plexus:	n/a
42	chr1:180600963-180601013	AG10803	skin:	n/a
43	chr1:180600963-180601013	HEK293	kidney:	embryo
44	chr1:180600963-180601013	BE2_C	brain:	n/a
45	chr1:180600963-180601013	HepG2	liver:	n/a
46	chr1:180600963-180601013	HIPEpiC	eye:	n/a
47	chr1:180600963-180601013	HNPCEpiC	eye:	n/a
48	chr1:180600963-180601013	HRPEpiC	eye:	n/a
49	chr1:180600963-180601013	GM12892	blood:	n/a
50	chr1:180600963-180601013	GM06990	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180486117..180489431-chr1:180599413..180603700,5	MCF-7	breast:
2	chr1:180599642..180602569-chr1:180990925..180993189,3	MCF-7	breast:
3	chr1:180599613..180601233-chr1:180805149..180807716,2	K562	blood:
4	chr1:180470531..180473320-chr1:180599332..180602016,2	K562	blood:
5	chr1:180470493..180473506-chr1:180597830..180602116,4	MCF-7	breast:

Variant related genes	Relation type
XPR1	TF binding region
XPR1	CpG island
ENSG00000135823	Chromatin interaction
ENSG00000135847	Chromatin interaction
ENSG00000143324	Chromatin interaction
ENSG00000206905	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10157637	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737349	0.93[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331546	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331753	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs3903980	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3908502	0.93[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4589068	0.81[AMR][1000 genomes]
rs4651074	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651075	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425648	0.93[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656378	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664826	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180593200-180601000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:180599400-180601000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:180599400-180601000	Enhancers	Osteobl	bone
4	chr1:180599600-180601000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:180599600-180601200	Weak transcription	Right Atrium	heart
6	chr1:180599600-180601200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr1:180599800-180601000	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:180600000-180601000	Enhancers	Fetal Intestine Large	intestine
9	chr1:180600000-180601200	Enhancers	Primary B cells from cord blood	blood
10	chr1:180600200-180601000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:180600200-180601000	Enhancers	Stomach Mucosa	stomach
12	chr1:180600200-180601200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:180600200-180601200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:180600400-180601000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr1:180600400-180601000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:180600400-180601000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:180600400-180601000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr1:180600400-180601000	Enhancers	Liver	Liver
19	chr1:180600400-180601000	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr1:180600400-180601000	Enhancers	Fetal Intestine Small	intestine
21	chr1:180600400-180601000	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr1:180600400-180601000	Flanking Active TSS	Dnd41	blood
23	chr1:180600400-180601200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:180600400-180601200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:180600400-180601200	Enhancers	Brain Angular Gyrus	brain
26	chr1:180600600-180601000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:180600600-180601000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:180600600-180601000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr1:180600600-180601000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:180600600-180601000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:180600600-180601000	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr1:180600600-180601000	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr1:180600600-180601000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:180600600-180601000	Weak transcription	Esophagus	oesophagus
35	chr1:180600600-180601000	Enhancers	Fetal Heart	heart
36	chr1:180600600-180601000	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr1:180600600-180601000	Enhancers	Rectal Smooth Muscle	rectum
38	chr1:180600600-180601000	Enhancers	Hela-S3	cervix
39	chr1:180600600-180601000	Enhancers	HSMM	muscle
40	chr1:180600600-180601200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:180600600-180601200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:180600600-180601200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:180600600-180601200	Weak transcription	Fetal Thymus	thymus
44	chr1:180600600-180601200	Weak transcription	Left Ventricle	heart
45	chr1:180600600-180601200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:180600600-180601200	Weak transcription	Spleen	Spleen
47	chr1:180600600-180601200	Enhancers	HUVEC	blood vessel
48	chr1:180600600-180601200	Enhancers	NHEK	skin
49	chr1:180600600-180602200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:180600600-180602600	Active TSS	Skeletal Muscle Female	skeletal muscle

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