Variant report

Variant	rs34593533
Chromosome Location	chr3:23988952-23988953
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	TCF7L2	chr3:23988923-23989506	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr3:23988647-23989955	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:23988782-23989327	SK-N-SH	brain:	n/a	n/a
4	MYC	chr3:23988765-23989282	K562	blood:	n/a	n/a
5	NFIC	chr3:23988733-23989420	ECC-1	luminal epithelium:	n/a	n/a
6	MAFK	chr3:23988848-23989313	IMR90	lung:	n/a	n/a
7	MYC	chr3:23988783-23989296	MCF10A-Er-Src	breast:	n/a	n/a
8	RXRA	chr3:23988783-23989298	SK-N-SH	brain:	n/a	n/a
9	CHD1	chr3:23987669-23989094	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:23988850-23989284	U87	brain:	n/a	n/a
11	RFX5	chr3:23988280-23989331	K562	blood:	n/a	chr3:23988706-23988723
12	BACH1	chr3:23988883-23989248	H1-hESC	embryonic stem cell:	n/a	n/a
13	BHLHE40	chr3:23988803-23989327	K562	blood:	n/a	n/a
14	JUN	chr3:23988695-23989298	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr3:23988929-23989129	MCF10A-Er-Src	breast:	n/a	n/a
16	ARID3A	chr3:23988644-23989296	K562	blood:	n/a	n/a
17	TAF1	chr3:23988758-23989157	H1-hESC	embryonic stem cell:	n/a	n/a
18	CEBPB	chr3:23988884-23989342	IMR90	lung:	n/a	n/a
19	STAT3	chr3:23988893-23989282	MCF10A-Er-Src	breast:	n/a	n/a
20	MAX	chr3:23988632-23989179	K562	blood:	n/a	n/a
21	TAF1	chr3:23988802-23989161	SK-N-SH	brain:	n/a	n/a
22	FOS	chr3:23988827-23989334	MCF10A-Er-Src	breast:	n/a	chr3:23989083-23989094
23	MAX	chr3:23988804-23989258	Hela-S3	cervix:	n/a	n/a
24	E2F4	chr3:23988933-23989220	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:23988733-23989170	GM12878	blood:	n/a	n/a
26	FOS	chr3:23988780-23989316	HUVEC	blood vessel:	n/a	chr3:23989083-23989094
27	MAZ	chr3:23986016-23989986	IMR90	lung:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
28	FOS	chr3:23988840-23989338	MCF10A-Er-Src	breast:	n/a	chr3:23989083-23989094
29	TCF12	chr3:23988687-23989530	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr3:23988852-23989306	HCT-116	colon:	n/a	n/a
31	POLR2A	chr3:23988855-23989284	U87	brain:	n/a	n/a
32	POLR2A	chr3:23988774-23992252	A549	lung:	n/a	n/a
33	POLR2A	chr3:23988626-23989318	H1-hESC	embryonic stem cell:	n/a	n/a
34	USF2	chr3:23988852-23989196	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:23988708-23989134	H1-hESC	embryonic stem cell:	n/a	n/a
36	PBX3	chr3:23988841-23989364	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr3:23988838-23989639	Hela-S3	cervix:	n/a	n/a
38	TEAD4	chr3:23988757-23989457	K562	blood:	n/a	n/a
39	KAP1	chr3:23988333-23988954	K562	blood:	n/a	n/a
40	JUND	chr3:23988711-23989325	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr3:23985541-23990663	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr3:23988745-23989346	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr3:23988915-23989233	MCF10A-Er-Src	breast:	n/a	n/a
44	STAT3	chr3:23988949-23989179	MCF10A-Er-Src	breast:	n/a	n/a
45	TEAD4	chr3:23988818-23989342	ECC-1	luminal epithelium:	n/a	n/a
46	SIN3AK20	chr3:23988849-23989156	PFSK-1	brain:	n/a	n/a
47	MAFF	chr3:23988737-23989275	K562	blood:	n/a	n/a
48	STAT3	chr3:23988688-23989276	MCF10A-Er-Src	breast:	n/a	chr3:23988824-23988832
49	NR2F2	chr3:23988625-23989867	K562	blood:	n/a	n/a
50	EP300	chr3:23988709-23989360	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23988282..23990131-chr3:24033697..24035885,2	MCF-7	breast:
2	chr3:23846531..23848270-chr3:23987055..23988984,2	MCF-7	breast:
3	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
4	chr3:23988541..23991177-chr3:24537846..24539360,2	K562	blood:
5	chr3:23988335..23991846-chr3:24002543..24006084,3	K562	blood:
6	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
7	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NKIRAS1	TF binding region
ENSG00000197885	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000170142	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10084748	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11129128	0.87[EUR][1000 genomes]
rs13087250	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13316457	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13317815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533141	0.87[EUR][1000 genomes]
rs1567579	0.92[EUR][1000 genomes]
rs1567580	0.92[EUR][1000 genomes]
rs2360020	0.87[ASN][1000 genomes]
rs28524116	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34036067	0.83[EUR][1000 genomes]
rs34058540	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34082882	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34866549	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35136361	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35457462	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35755171	0.84[EUR][1000 genomes]
rs35755253	0.84[EUR][1000 genomes]
rs36063721	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36089963	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3762775	0.83[EUR][1000 genomes]
rs3935253	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4131404	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4132595	0.93[ASN][1000 genomes]
rs4300960	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4490300	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4602333	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4858096	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4858564	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59090179	0.83[ASN][1000 genomes]
rs6550808	0.83[EUR][1000 genomes]
rs66609380	0.87[EUR][1000 genomes]
rs67002637	0.81[EUR][1000 genomes]
rs67465878	0.83[ASN][1000 genomes]
rs67606949	0.85[EUR][1000 genomes]
rs6770052	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778577	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790140	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6803587	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324126	0.87[EUR][1000 genomes]
rs72627028	0.80[ASN][1000 genomes]
rs72627029	0.80[ASN][1000 genomes]
rs72627030	0.80[ASN][1000 genomes]
rs72627031	0.80[ASN][1000 genomes]
rs72627032	0.80[ASN][1000 genomes]
rs72627033	0.80[ASN][1000 genomes]
rs72627034	0.80[ASN][1000 genomes]
rs72627035	0.80[ASN][1000 genomes]
rs72627036	0.80[ASN][1000 genomes]
rs72627037	0.80[ASN][1000 genomes]
rs72627038	0.80[ASN][1000 genomes]
rs72627039	0.80[ASN][1000 genomes]
rs72627040	0.80[ASN][1000 genomes]
rs72627043	0.80[ASN][1000 genomes]
rs72627044	0.87[ASN][1000 genomes]
rs72627046	0.87[ASN][1000 genomes]
rs72627047	0.83[ASN][1000 genomes]
rs72627048	0.83[ASN][1000 genomes]
rs72627049	0.83[ASN][1000 genomes]
rs72627050	0.83[ASN][1000 genomes]
rs72627051	0.87[ASN][1000 genomes]
rs72627052	0.87[ASN][1000 genomes]
rs72627053	0.87[ASN][1000 genomes]
rs72627055	0.87[ASN][1000 genomes]
rs72627056	0.87[ASN][1000 genomes]
rs72627057	0.87[ASN][1000 genomes]
rs72627058	0.87[ASN][1000 genomes]
rs72627059	0.87[ASN][1000 genomes]
rs72627060	0.87[ASN][1000 genomes]
rs72627061	0.87[ASN][1000 genomes]
rs72627062	0.87[ASN][1000 genomes]
rs72627063	0.87[ASN][1000 genomes]
rs72627064	0.87[ASN][1000 genomes]
rs72627065	0.87[ASN][1000 genomes]
rs72627067	0.87[ASN][1000 genomes]
rs72627068	0.87[ASN][1000 genomes]
rs72627069	0.87[ASN][1000 genomes]
rs72627070	0.87[ASN][1000 genomes]
rs72627071	0.87[ASN][1000 genomes]
rs72627072	0.87[ASN][1000 genomes]
rs72627073	0.87[ASN][1000 genomes]
rs72627074	0.87[ASN][1000 genomes]
rs72627075	0.87[ASN][1000 genomes]
rs72627076	0.87[ASN][1000 genomes]
rs72627078	0.86[ASN][1000 genomes]
rs72627079	0.87[ASN][1000 genomes]
rs72627080	0.87[ASN][1000 genomes]
rs72627081	0.87[ASN][1000 genomes]
rs72627082	0.87[ASN][1000 genomes]
rs72627083	0.87[ASN][1000 genomes]
rs72627084	0.87[ASN][1000 genomes]
rs72627085	0.87[ASN][1000 genomes]
rs72627086	0.87[ASN][1000 genomes]
rs72627087	0.87[ASN][1000 genomes]
rs72627088	0.87[ASN][1000 genomes]
rs72627089	0.87[ASN][1000 genomes]
rs72627090	0.87[ASN][1000 genomes]
rs72627091	0.90[ASN][1000 genomes]
rs72627094	0.92[AMR][1000 genomes]
rs72627096	0.97[ASN][1000 genomes]
rs72627097	0.97[ASN][1000 genomes]
rs72627098	0.97[ASN][1000 genomes]
rs72627099	0.97[ASN][1000 genomes]
rs72627100	0.90[ASN][1000 genomes]
rs72627101	0.90[ASN][1000 genomes]
rs72627102	0.90[ASN][1000 genomes]
rs72628103	0.90[ASN][1000 genomes]
rs72628104	0.90[ASN][1000 genomes]
rs72628105	0.90[ASN][1000 genomes]
rs72628106	0.90[ASN][1000 genomes]
rs72628107	0.90[ASN][1000 genomes]
rs72628108	0.90[ASN][1000 genomes]
rs72628109	0.90[ASN][1000 genomes]
rs72628111	0.90[ASN][1000 genomes]
rs72628112	0.87[ASN][1000 genomes]
rs72628113	0.87[ASN][1000 genomes]
rs72628114	0.87[ASN][1000 genomes]
rs72628115	0.87[ASN][1000 genomes]
rs72628116	0.87[ASN][1000 genomes]
rs72628119	0.83[ASN][1000 genomes]
rs72628123	0.83[ASN][1000 genomes]
rs72628124	0.83[ASN][1000 genomes]
rs72628126	0.87[ASN][1000 genomes]
rs73150266	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73150299	0.90[EUR][1000 genomes]
rs954748	0.94[EUR][1000 genomes]
rs9809225	0.85[EUR][1000 genomes]
rs9812870	0.83[EUR][1000 genomes]
rs9817923	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853954	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9855481	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9863176	0.85[EUR][1000 genomes]
rs9883834	0.83[EUR][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23987800-23989000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:23987800-23989000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:23987800-23989000	Active TSS	Right Atrium	heart
4	chr3:23987800-23989000	Flanking Active TSS	Osteobl	bone
5	chr3:23987800-23989200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:23987800-23989200	Flanking Active TSS	NH-A	brain
7	chr3:23987800-23990000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:23987800-23991200	Enhancers	Fetal Heart	heart
9	chr3:23988000-23989000	Flanking Active TSS	HMEC	breast
10	chr3:23988000-23989000	Flanking Active TSS	HUVEC	blood vessel
11	chr3:23988000-23989000	Flanking Active TSS	NHEK	skin
12	chr3:23988000-23989000	Flanking Active TSS	NHLF	lung
13	chr3:23988000-23989200	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:23988000-23989200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr3:23988000-23989200	Flanking Active TSS	Hela-S3	cervix
16	chr3:23988000-23989400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:23988000-23989400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:23988000-23989400	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr3:23988000-23990000	Flanking Active TSS	K562	blood
20	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
21	chr3:23988200-23989000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:23988200-23989000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr3:23988200-23989000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:23988200-23989000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr3:23988200-23989000	Flanking Active TSS	HepG2	liver
26	chr3:23988200-23989200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr3:23988200-23989200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:23988200-23989400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:23988200-23989400	Weak transcription	Gastric	stomach
30	chr3:23988200-23989400	Weak transcription	Lung	lung
31	chr3:23988200-23990000	Enhancers	Left Ventricle	heart
32	chr3:23988200-23990000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr3:23988200-23990400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:23988200-23991000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:23988200-23992200	Enhancers	Small Intestine	intestine
36	chr3:23988200-23992200	Enhancers	Stomach Mucosa	stomach
37	chr3:23988200-23993800	Enhancers	Brain Substantia Nigra	brain
38	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
39	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:23988400-23989000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr3:23988400-23989000	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr3:23988400-23989000	Enhancers	Primary B cells from peripheral blood	blood
43	chr3:23988400-23989000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:23988400-23989000	Enhancers	Brain Germinal Matrix	brain
45	chr3:23988400-23989000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:23988400-23989000	Enhancers	Fetal Intestine Large	intestine
47	chr3:23988400-23989000	Enhancers	Fetal Stomach	stomach
48	chr3:23988400-23989200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:23988400-23989200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr3:23988400-23989400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links