Variant report

Variant	rs1949481
Chromosome Location	chr11:16259405-16259406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:16258646..16260759-chr11:16262336..16265198,2	K562	blood:
2	chr11:16251614..16253946-chr11:16259376..16260960,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1013304	0.86[JPT][hapmap]
rs10219384	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10500828	0.82[JPT][hapmap]
rs10500829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10741696	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10766303	0.82[JPT][hapmap]
rs10766304	0.85[JPT][hapmap]
rs10832561	0.81[JPT][hapmap]
rs10832565	0.82[JPT][hapmap]
rs10832566	0.82[JPT][hapmap]
rs10832567	0.82[JPT][hapmap]
rs10832569	0.81[JPT][hapmap]
rs10832577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10832580	0.87[ASN][1000 genomes]
rs10832587	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10832591	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10832592	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10832593	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs10832594	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11023875	0.81[JPT][hapmap]
rs11023882	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs11023894	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11023898	0.87[ASN][1000 genomes]
rs11023917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12271339	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12274377	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12281119	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs12420519	0.82[JPT][hapmap]
rs1401454	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs1519123	0.82[JPT][hapmap]
rs1519126	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs1607480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1837095	0.91[JPT][hapmap]
rs190929	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs2118361	0.80[JPT][hapmap]
rs2351964	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs2917899	0.80[ASN][1000 genomes]
rs297342	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs297344	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs297365	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs297366	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4757388	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4757390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4757392	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs588470	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7109206	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs961002	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv897012	chr11:16189326-16283644	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv553563	chr11:16206658-16259405	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv897013	chr11:16206658-16307700	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv897014	chr11:16211343-16283644	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv467710	chr11:16219341-16266740	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv553564	chr11:16219341-16266740	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv553565	chr11:16220289-16307700	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv897015	chr11:16235962-16307700	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1949481	E2F8	cis	cerebellum	SCAN
rs1949481	SERGEF	cis	parietal	SCAN
rs1949481	SPTY2D1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16238600-16260800	Weak transcription	Psoas Muscle	Psoas
2	chr11:16248200-16260600	Weak transcription	Fetal Lung	lung
3	chr11:16248200-16274200	Weak transcription	Pancreas	Pancrea
4	chr11:16248400-16260400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:16256200-16272000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:16257800-16260600	Weak transcription	Right Atrium	heart
7	chr11:16258600-16264200	Enhancers	Fetal Heart	heart
8	chr11:16258800-16260200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:16258800-16260600	Weak transcription	K562	blood
10	chr11:16259000-16260800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:16259200-16259600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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