Variant report

Variant	rs4646486
Chromosome Location	chr1:47278997-47278998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47274872..47277380-chr1:47277423..47279681,2	K562	blood:
2	chr1:47270918..47272980-chr1:47278589..47280565,2	K562	blood:

Variant related genes	Relation type
ENSG00000142973	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11211366	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs11211369	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11211386	0.85[EUR][1000 genomes]
rs11211387	0.86[EUR][1000 genomes]
rs1122582	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11576162	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11583378	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11584320	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11586184	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12402717	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12410657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12566735	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12569216	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1572603	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1890246	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1890248	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1890249	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1890250	0.93[ASN][1000 genomes]
rs1890251	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2065996	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2185032	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2405335	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs3766195	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766196	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766197	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820080	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3863632	0.81[EUR][1000 genomes]
rs4417002	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs45563134	0.85[ASN][1000 genomes]
rs4560983	0.81[EUR][1000 genomes]
rs4646482	0.82[ASN][1000 genomes]
rs4646487	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646492	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646493	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646495	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4660960	0.96[EUR][1000 genomes]
rs55868139	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55936777	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60430993	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61741519	0.81[EUR][1000 genomes]
rs67678353	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs681840	0.88[CHD][hapmap]
rs72637963	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72681939	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs751027	0.81[ASN][1000 genomes]
rs7553652	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs837395	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs9728536	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1011086	chr1:47259078-47305191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870538	chr1:47259138-47309265	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1010063	chr1:47264205-47285118	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1004143	chr1:47270942-47321982	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1004246	chr1:47274901-47321982	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv947111	chr1:47277189-47308420	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4646486	PTPRF	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47265600-47279200	Weak transcription	Gastric	stomach
2	chr1:47273400-47285600	Weak transcription	Spleen	Spleen
3	chr1:47277000-47286800	Strong transcription	Esophagus	oesophagus
4	chr1:47278200-47279400	Genic enhancers	Left Ventricle	heart
5	chr1:47278400-47279200	Weak transcription	Lung	lung
6	chr1:47278600-47279400	Weak transcription	Right Ventricle	heart
7	chr1:47278800-47279000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
8	chr1:47278800-47285000	Strong transcription	Adipose Nuclei	Adipose

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