Variant report

Variant	rs4952901
Chromosome Location	chr2:48211454-48211455
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48210960..48212858-chr2:48213095..48216637,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSH6-6	chr2:48211369-48212166	l_1832_chr2:48211368-48231778_testes

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10196696	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125157	0.98[ASN][1000 genomes]
rs1471680	0.92[ASN][1000 genomes]
rs1471681	0.89[ASN][1000 genomes]
rs1483213	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1483221	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1825320	0.87[ASN][1000 genomes]
rs1878079	0.86[ASN][1000 genomes]
rs1878081	0.86[ASN][1000 genomes]
rs2056138	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2128716	0.86[ASN][1000 genomes]
rs2128718	0.92[ASN][1000 genomes]
rs2220075	0.80[EUR][1000 genomes]
rs28460586	0.86[ASN][1000 genomes]
rs4146021	0.89[ASN][1000 genomes]
rs4953534	1.00[ASN][1000 genomes]
rs4953544	0.92[ASN][1000 genomes]
rs4953546	0.88[ASN][1000 genomes]
rs6545011	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6545017	0.83[ASN][1000 genomes]
rs6545018	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6545021	0.81[AMR][1000 genomes]
rs6706664	0.83[ASN][1000 genomes]
rs6718037	0.81[AMR][1000 genomes]
rs6720994	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6749276	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6750246	0.86[ASN][1000 genomes]
rs7584401	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7584493	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7609066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs922903	0.81[AMR][1000 genomes]
rs963134	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs968888	0.86[ASN][1000 genomes]
rs999036	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv874000	chr2:48078838-48291582	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv519761	chr2:48146122-48248101	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4952901	MSH6	cis	cerebellum	SCAN
rs4952901	MSH6	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48211000-48211600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:48211200-48211600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr2:48211200-48211600	Enhancers	Adipose Nuclei	Adipose
4	chr2:48211200-48211600	Enhancers	Left Ventricle	heart
5	chr2:48211200-48211600	Enhancers	Right Atrium	heart
6	chr2:48211200-48211800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:48211400-48211800	Enhancers	GM12878-XiMat	blood

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