Variant report

Variant	rs6445506
Chromosome Location	chr3:52528292-52528293
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	MAX	chr3:52528108-52528309	NB4	blood:	n/a	chr3:52528214-52528223 chr3:52528215-52528222
2	POLR2A	chr3:52526972-52528773	K562	blood:	n/a	n/a
3	POLR2A	chr3:52527697-52528396	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:52527455-52528368	U87	brain:	n/a	n/a
5	POLR2A	chr3:52528064-52528307	HCT-116	colon:	n/a	n/a
6	MYC	chr3:52528111-52528403	NB4	blood:	n/a	chr3:52528214-52528223 chr3:52528215-52528222
7	POLR2A	chr3:52527490-52528414	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr3:52527145-52528307	K562	blood:	n/a	n/a
9	POLR2A	chr3:52527473-52528327	U87	brain:	n/a	n/a
10	POLR2A	chr3:52528094-52528310	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr3:52527443-52528313	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52525356..52528300-chr3:52566814..52568456,2	MCF-7	breast:
2	chr3:52527250..52529955-chr3:52567199..52569414,2	MCF-7	breast:
3	chr3:52527621..52529302-chr3:52531817..52533690,2	K562	blood:

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

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1011062	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1011063	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1011064	0.82[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs1035002	0.91[EUR][1000 genomes]
rs1035003	0.93[EUR][1000 genomes]
rs1077142	1.00[JPT][hapmap]
rs10865972	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123598	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs123602	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs13074649	0.93[EUR][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13089892	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[JPT][hapmap]
rs1541495	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2109557	0.81[EUR][1000 genomes]
rs2109558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159607	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2215466	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335928	0.91[EUR][1000 genomes]
rs2335929	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2878549	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs34261027	1.00[ASN][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs35860312	1.00[JPT][hapmap]
rs3755810	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs3774409	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs390802	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs409803	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs419050	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs419604	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs419752	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4312651	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4687541	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4687543	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687544	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687614	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4687616	0.84[EUR][1000 genomes]
rs4687617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687618	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687619	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687621	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs498778	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs498946	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs575476	0.81[EUR][1000 genomes]
rs613519	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes]
rs634382	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6414568	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445483	0.81[EUR][1000 genomes]
rs6445484	0.93[EUR][1000 genomes]
rs6445485	0.93[EUR][1000 genomes]
rs6445486	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6782162	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6784615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787493	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6810027	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs728408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758800	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7620015	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887515	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs929528	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs929529	0.91[EUR][1000 genomes]
rs9846089	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9847332	0.93[EUR][1000 genomes]
rs9850471	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9855470	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9863753	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9867823	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
3	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
4	chr3:52508000-52532200	Weak transcription	K562	blood
5	chr3:52510600-52528600	Weak transcription	Fetal Brain Male	brain
6	chr3:52513400-52541400	Weak transcription	A549	lung
7	chr3:52513600-52530000	Weak transcription	Fetal Kidney	kidney
8	chr3:52514600-52534200	Weak transcription	Small Intestine	intestine
9	chr3:52515600-52528400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:52519000-52528600	Weak transcription	Fetal Heart	heart
11	chr3:52519400-52530000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:52521000-52529800	Weak transcription	Hela-S3	cervix
13	chr3:52522600-52529400	Weak transcription	Psoas Muscle	Psoas
14	chr3:52523600-52528400	Genic enhancers	Lung	lung
15	chr3:52523600-52528800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:52524400-52529400	Weak transcription	NHDF-Ad	bronchial
17	chr3:52524800-52528400	Strong transcription	NHLF	lung
18	chr3:52525000-52528400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:52525600-52528400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:52526000-52530200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:52526200-52529000	Enhancers	HUVEC	blood vessel
22	chr3:52526800-52528400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:52526800-52528600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:52526800-52529400	Weak transcription	HepG2	liver
25	chr3:52527000-52528400	Weak transcription	Right Atrium	heart
26	chr3:52527000-52528600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:52527000-52528600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:52527000-52528600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:52527000-52529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:52527000-52529000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:52527000-52529200	Weak transcription	NH-A	brain
32	chr3:52527000-52529400	Weak transcription	HMEC	breast
33	chr3:52527000-52529600	Weak transcription	Fetal Lung	lung
34	chr3:52527000-52530000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:52527000-52530200	Weak transcription	HSMMtube	muscle
36	chr3:52527000-52532400	Weak transcription	GM12878-XiMat	blood
37	chr3:52527000-52538000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:52527000-52540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:52527200-52528600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:52527200-52528600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:52527200-52528800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:52527200-52528800	Weak transcription	NHEK	skin
43	chr3:52527200-52529000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:52527200-52529000	Enhancers	Placenta	Placenta
45	chr3:52527200-52529600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:52527200-52529600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:52527200-52530400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:52527200-52531200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:52527400-52528400	Enhancers	Adipose Nuclei	Adipose
50	chr3:52527400-52528600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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