Variant report

Variant	rs6543280
Chromosome Location	chr2:98701043-98701044
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	FOXA2	chr2:98700954-98701957	HepG2	liver:	n/a	n/a
2	RUNX3	chr2:98701025-98701354	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:98610350..98614892-chr2:98700211..98704879,10	MCF-7	breast:
2	chr2:98687875..98690748-chr2:98700886..98703566,2	MCF-7	breast:
3	chr2:98687924..98689825-chr2:98699366..98701312,2	K562	blood:
4	chr2:98640904..98642915-chr2:98701010..98703488,2	MCF-7	breast:

Variant related genes	Relation type
VWA3B	TF binding region
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10169441	0.94[ASN][1000 genomes]
rs10200560	0.94[ASN][1000 genomes]
rs10204649	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10207101	0.94[ASN][1000 genomes]
rs10211067	0.92[MEX][hapmap]
rs11695490	0.81[ASN][1000 genomes]
rs13417459	0.94[ASN][1000 genomes]
rs1699023	0.85[JPT][hapmap]
rs298902	0.85[JPT][hapmap]
rs298904	0.85[JPT][hapmap]
rs298905	0.85[JPT][hapmap]
rs298906	0.85[JPT][hapmap]
rs298917	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs58097088	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60884498	0.94[ASN][1000 genomes]
rs6729411	0.94[ASN][1000 genomes]
rs6756742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72946920	0.94[ASN][1000 genomes]
rs7355475	1.00[ASN][1000 genomes]
rs7591591	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs921423	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv834309	chr2:98643304-98793838	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv527817	chr2:98701043-98791433	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6543280	CNNM4	cis	cerebellum	SCAN
rs6543280	ACTR1B	cis	Artery Tibial	GTEx
rs6543280	ACTR1B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98695400-98702800	Weak transcription	Fetal Brain Female	brain
2	chr2:98697400-98702200	Weak transcription	Aorta	Aorta
3	chr2:98698800-98702800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:98698800-98703000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:98698800-98703000	Weak transcription	Spleen	Spleen
6	chr2:98699000-98702800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:98699000-98702800	Weak transcription	Primary B cells from cord blood	blood
8	chr2:98700000-98702800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:98700400-98701800	Enhancers	Colonic Mucosa	Colon
10	chr2:98700400-98701800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr2:98700600-98701600	Flanking Active TSS	Stomach Mucosa	stomach
12	chr2:98700600-98702600	Enhancers	HepG2	liver
13	chr2:98700800-98701200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr2:98701000-98701200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:98701000-98701400	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr2:98701000-98701600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr2:98701000-98702200	Enhancers	Fetal Intestine Large	intestine
18	chr2:98701000-98702400	Enhancers	Gastric	stomach
19	chr2:98701000-98702800	Enhancers	Liver	Liver
20	chr2:98701000-98703000	Enhancers	Fetal Intestine Small	intestine
21	chr2:98701000-98703200	Enhancers	Pancreas	Pancrea

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