Variant report

Variant	rs4651075
Chromosome Location	chr1:180601006-180601007
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	MAX	chr1:180600975-180601664	ECC-1	luminal epithelium:	n/a	chr1:180601114-180601123
11	GTF2F1	chr1:180600924-180601365	H1-hESC	embryonic stem cell:	n/a	n/a
12	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
13	POLR2A	chr1:180600803-180601361	U87	brain:	n/a	n/a
14	TAF1	chr1:180600982-180601429	PFSK-1	brain:	n/a	n/a
15	TAF1	chr1:180601006-180601446	GM12891	blood:	n/a	n/a
16	POLR2A	chr1:180600829-180601729	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr1:180600892-180601087	NHEK	skin:	n/a	n/a
18	TAF1	chr1:180600881-180601985	ECC-1	luminal epithelium:	n/a	n/a
19	NRF1	chr1:180600860-180601445	GM12878	blood:	n/a	n/a
20	FOS	chr1:180600840-180601127	MCF10A-Er-Src	breast:	n/a	chr1:180600987-180600998
21	POLR2A	chr1:180600775-180601806	K562	blood:	n/a	n/a
22	POLR2A	chr1:180600772-180601579	SK-N-MC	brain:	n/a	n/a
23	CTCF	chr1:180600901-180601039	GM13977	blood:	n/a	n/a
24	CTCF	chr1:180600920-180601070	SAEC	small airway:	n/a	n/a
25	CTCF	chr1:180600886-180601063	GM10248	blood:	n/a	n/a
26	POLR2A	chr1:180600776-180601532	K562	blood:	n/a	n/a
27	POLR2A	chr1:180600801-180601622	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:180600769-180601518	HCT-116	colon:	n/a	n/a
29	HEY1	chr1:180600840-180601062	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:180600793-180601540	PFSK-1	brain:	n/a	n/a
31	MAZ	chr1:180600834-180601994	K562	blood:	n/a	chr1:180601114-180601123
32	POLR2A	chr1:180600788-180601769	GM18526	blood:	n/a	n/a
33	RFX5	chr1:180600956-180601313	HepG2	liver:	n/a	chr1:180601110-180601125 chr1:180601113-180601128 chr1:180601113-180601128 chr1:180601113-180601128 chr1:180601112-180601129
34	PML	chr1:180600336-180601941	GM12878	blood:	n/a	chr1:180601875-180601883
35	MAX	chr1:180600821-180602115	ECC-1	luminal epithelium:	n/a	chr1:180601114-180601123
36	CTCF	chr1:180600880-180601030	GM06990	blood:	n/a	n/a
37	YY1	chr1:180600995-180601775	K562	blood:	n/a	chr1:180601552-180601561 chr1:180601602-180601613 chr1:180601174-180601182 chr1:180601550-180601564 chr1:180601207-180601218 chr1:180601285-180601294 chr1:180601277-180601291 chr1:180601553-180601567 chr1:180601206-180601215 chr1:180601173-180601183 chr1:180601594-180601605
38	CTCF	chr1:180600920-180601070	GM12875	blood:	n/a	n/a
39	CTCF	chr1:180600900-180601050	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr1:180600960-180601110	HRE	kidney:	n/a	n/a
41	MAX	chr1:180600852-180601809	NB4	blood:	n/a	chr1:180601114-180601123
42	POLR2A	chr1:180600824-180601458	K562	blood:	n/a	n/a
43	UBTF	chr1:180600896-180602112	K562	blood:	n/a	n/a
44	POLR2A	chr1:180600798-180601817	GM12892	blood:	n/a	n/a
45	POLR2A	chr1:180600772-180601425	HCT-116	colon:	n/a	n/a
46	YY1	chr1:180600995-180601398	A549	lung:	n/a	chr1:180601174-180601182 chr1:180601207-180601218 chr1:180601285-180601294 chr1:180601277-180601291 chr1:180601206-180601215 chr1:180601173-180601183
47	TAF1	chr1:180600908-180601831	HepG2	liver:	n/a	n/a
48	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
49	CTCF	chr1:180600846-180601233	T-47D	breast:	n/a	n/a
50	FOS	chr1:180600926-180601130	MCF10A-Er-Src	breast:	n/a	chr1:180600987-180600998

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
ENSG00000143324	Chromatin interaction
ENSG00000206905	Chromatin interaction
ENSG00000135847	Chromatin interaction
ENSG00000135823	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10157637	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737349	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331546	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903980	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903981	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3908502	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651074	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652524	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425648	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656378	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664826	0.93[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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180599600-180601200	Weak transcription	Right Atrium	heart
2	chr1:180599600-180601200	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr1:180600000-180601200	Enhancers	Primary B cells from cord blood	blood
4	chr1:180600200-180601200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:180600200-180601200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:180600400-180601200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:180600400-180601200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:180600400-180601200	Enhancers	Brain Angular Gyrus	brain
9	chr1:180600600-180601200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:180600600-180601200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:180600600-180601200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:180600600-180601200	Weak transcription	Fetal Thymus	thymus
13	chr1:180600600-180601200	Weak transcription	Left Ventricle	heart
14	chr1:180600600-180601200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:180600600-180601200	Weak transcription	Spleen	Spleen
16	chr1:180600600-180601200	Enhancers	HUVEC	blood vessel
17	chr1:180600600-180601200	Enhancers	NHEK	skin
18	chr1:180600600-180602200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:180600600-180602600	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr1:180600800-180601200	Enhancers	Primary T cells from cord blood	blood
21	chr1:180600800-180601200	Active TSS	Brain Germinal Matrix	brain
22	chr1:180600800-180601200	Enhancers	HMEC	breast
23	chr1:180600800-180601600	Active TSS	HepG2	liver
24	chr1:180600800-180601800	Active TSS	Primary hematopoietic stem cells	blood
25	chr1:180600800-180601800	Active TSS	Fetal Brain Female	brain
26	chr1:180600800-180602000	Active TSS	Colon Smooth Muscle	Colon
27	chr1:180600800-180602000	Active TSS	NH-A	brain
28	chr1:180600800-180602200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:180600800-180602200	Active TSS	Fetal Stomach	stomach
30	chr1:180600800-180602400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr1:180600800-180602400	Active TSS	Fetal Muscle Leg	muscle
32	chr1:180600800-180602600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:180600800-180602600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr1:180600800-180602600	Active TSS	A549	lung
35	chr1:180600800-180603000	Active TSS	GM12878-XiMat	blood
36	chr1:180600800-180603400	Active TSS	Brain Anterior Caudate	brain
37	chr1:180600800-180603600	Active TSS	Thymus	Thymus
38	chr1:180600800-180603800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:180600800-180604400	Active TSS	Fetal Brain Male	brain
40	chr1:180601000-180601200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:180601000-180601200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:180601000-180601200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr1:180601000-180601200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:180601000-180601200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:180601000-180601200	Weak transcription	Fetal Intestine Large	intestine
46	chr1:180601000-180601200	Weak transcription	Stomach Mucosa	stomach
47	chr1:180601000-180601400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:180601000-180601600	Weak transcription	Fetal Heart	heart
49	chr1:180601000-180601800	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr1:180601000-180601800	Active TSS	Primary neutrophils fromperipheralblood	blood

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