Variant report

Variant	rs758800
Chromosome Location	chr3:52529266-52529267
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	CTCF	chr3:52529160-52529310	HBMEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:52528958-52531074	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:52528752-52530368	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:52528796-52530229	NB4	blood:	n/a	n/a
5	FOS	chr3:52529036-52530423	HUVEC	blood vessel:	n/a	chr3:52529953-52529962 chr3:52529949-52529960 chr3:52529952-52529962 chr3:52529952-52529962 chr3:52529952-52529962 chr3:52529951-52529962 chr3:52529952-52529962
6	ZBTB7A	chr3:52529104-52529268	K562	blood:	n/a	n/a
7	MAX	chr3:52529068-52530148	NB4	blood:	n/a	chr3:52529952-52529961 chr3:52529888-52529897 chr3:52529903-52529913
8	POLR2A	chr3:52528298-52530927	HUVEC	blood vessel:	n/a	n/a
9	TAL1	chr3:52529153-52529353	K562	blood:	n/a	n/a
10	POLR2A	chr3:52528361-52531115	HUVEC	blood vessel:	n/a	n/a
11	GATA2	chr3:52528956-52530190	HUVEC	blood vessel:	n/a	chr3:52529954-52529963 chr3:52529951-52529960
12	POLR2A	chr3:52528848-52531039	HUVEC	blood vessel:	n/a	n/a
13	MYC	chr3:52528946-52529619	HUVEC	blood vessel:	n/a	n/a
14	MYC	chr3:52528678-52530130	NB4	blood:	n/a	chr3:52529952-52529961 chr3:52529888-52529897 chr3:52529903-52529913

No.	Distal block	Cell Line	Cell type
1	chr3:52517051..52518693-chr3:52528843..52530538,2	K562	blood:
2	chr12:46777478..46778461-chr3:52529014..52529621,2	NB4	blood:
3	chr3:52488362..52490407-chr3:52528579..52530282,2	K562	blood:
4	chr3:52527250..52529955-chr3:52567199..52569414,2	MCF-7	breast:
5	chr3:52527621..52529302-chr3:52531817..52533690,2	K562	blood:

Variant related genes	Relation type
STAB1	TF binding region
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000257261	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1011062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1011064	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1035002	0.97[EUR][1000 genomes]
rs1035003	1.00[EUR][1000 genomes]
rs10865972	0.82[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs11721286	0.93[EUR][1000 genomes]
rs123598	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs123603	1.00[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs13060192	1.00[ASW][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs13074649	1.00[EUR][1000 genomes]
rs13089892	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs13096571	0.80[EUR][1000 genomes]
rs1541495	0.82[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2070914	1.00[CHB][hapmap]
rs2109557	0.88[EUR][1000 genomes]
rs2109558	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2109559	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2215466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs2240897	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs2335928	0.98[EUR][1000 genomes]
rs2335929	1.00[EUR][1000 genomes]
rs2878549	1.00[ASW][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs3755810	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3774409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs409803	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs419050	1.00[GIH][hapmap];0.92[TSI][hapmap]
rs419604	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs419752	0.83[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4312651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4687541	1.00[EUR][1000 genomes]
rs4687543	0.85[EUR][1000 genomes]
rs4687544	1.00[EUR][1000 genomes]
rs4687614	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs4687616	0.90[EUR][1000 genomes]
rs4687617	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs4687618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs4687619	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4687621	1.00[EUR][1000 genomes]
rs498778	1.00[ASW][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs575476	0.88[EUR][1000 genomes]
rs613519	0.81[EUR][1000 genomes]
rs6414568	1.00[EUR][1000 genomes]
rs6445483	0.87[EUR][1000 genomes]
rs6445484	1.00[EUR][1000 genomes]
rs6445485	1.00[EUR][1000 genomes]
rs6445486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6445506	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs676034	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs6771558	1.00[EUR][1000 genomes]
rs6782162	1.00[EUR][1000 genomes]
rs6784615	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs6787493	0.93[EUR][1000 genomes]
rs6795333	0.81[EUR][1000 genomes]
rs6810027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs728408	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs758803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7620015	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs887514	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs929528	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs929529	0.98[EUR][1000 genomes]
rs9846089	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9847332	1.00[EUR][1000 genomes]
rs9850471	1.00[EUR][1000 genomes]
rs9855470	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9863753	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs9867823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv590304	chr3:52517206-52529266	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52508000-52532200	Weak transcription	K562	blood
2	chr3:52513400-52541400	Weak transcription	A549	lung
3	chr3:52513600-52530000	Weak transcription	Fetal Kidney	kidney
4	chr3:52514600-52534200	Weak transcription	Small Intestine	intestine
5	chr3:52519400-52530000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:52521000-52529800	Weak transcription	Hela-S3	cervix
7	chr3:52522600-52529400	Weak transcription	Psoas Muscle	Psoas
8	chr3:52524400-52529400	Weak transcription	NHDF-Ad	bronchial
9	chr3:52526000-52530200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:52526800-52529400	Weak transcription	HepG2	liver
11	chr3:52527000-52529400	Weak transcription	HMEC	breast
12	chr3:52527000-52529600	Weak transcription	Fetal Lung	lung
13	chr3:52527000-52530000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:52527000-52530200	Weak transcription	HSMMtube	muscle
15	chr3:52527000-52532400	Weak transcription	GM12878-XiMat	blood
16	chr3:52527000-52538000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:52527000-52540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:52527200-52529600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:52527200-52529600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:52527200-52530400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:52527200-52531200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:52527400-52529400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:52527400-52529400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:52527400-52529400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:52527400-52529400	Weak transcription	Brain Anterior Caudate	brain
26	chr3:52527400-52529400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:52527400-52529400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:52527400-52529600	Weak transcription	Brain Substantia Nigra	brain
29	chr3:52527400-52529600	Weak transcription	HSMM	muscle
30	chr3:52527400-52529600	Weak transcription	Osteobl	bone
31	chr3:52527400-52529800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:52527400-52530600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:52527400-52532600	Weak transcription	Stomach Mucosa	stomach
34	chr3:52527600-52529400	Weak transcription	Pancreas	Pancrea
35	chr3:52527600-52530400	Weak transcription	Dnd41	blood
36	chr3:52527800-52529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:52527800-52529400	Weak transcription	Fetal Intestine Large	intestine
38	chr3:52527800-52529400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:52527800-52529600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:52527800-52529600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:52527800-52531600	Weak transcription	Primary B cells from cord blood	blood
42	chr3:52527800-52531800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:52527800-52532800	Weak transcription	Primary T cells from cord blood	blood
44	chr3:52527800-52533200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:52527800-52533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:52528000-52529400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:52528000-52529400	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:52528000-52529400	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:52528000-52529400	Weak transcription	Esophagus	oesophagus
50	chr3:52528000-52529400	Weak transcription	Gastric	stomach

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