Variant report

Variant	rs3914868
Chromosome Location	chr3:180001583-180001584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10513771	0.81[ASN][1000 genomes]
rs10755138	0.83[ASN][1000 genomes]
rs10937030	0.81[ASN][1000 genomes]
rs12486206	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491089	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12497420	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12638851	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12638877	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13322790	0.81[ASN][1000 genomes]
rs1357904	0.81[ASN][1000 genomes]
rs1464358	0.81[ASN][1000 genomes]
rs1464845	0.81[ASN][1000 genomes]
rs1520613	0.81[ASN][1000 genomes]
rs1525276	0.81[ASN][1000 genomes]
rs1589858	0.83[ASN][1000 genomes]
rs16831288	0.86[ASN][1000 genomes]
rs16831406	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2091273	0.85[ASN][1000 genomes]
rs2178582	0.87[CEU][hapmap]
rs2337367	0.81[ASN][1000 genomes]
rs2337368	0.86[ASN][1000 genomes]
rs2337369	0.83[ASN][1000 genomes]
rs2878951	0.81[ASN][1000 genomes]
rs2878954	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849424	0.83[ASN][1000 genomes]
rs3849425	0.83[ASN][1000 genomes]
rs3849426	0.83[ASN][1000 genomes]
rs3906013	0.87[ASN][1000 genomes]
rs3906014	0.88[ASN][1000 genomes]
rs3914867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3914869	0.83[ASN][1000 genomes]
rs3914871	0.83[ASN][1000 genomes]
rs4108253	0.84[ASN][1000 genomes]
rs4241377	0.88[ASN][1000 genomes]
rs4568133	0.83[ASN][1000 genomes]
rs4854903	0.81[ASN][1000 genomes]
rs4854966	0.82[ASN][1000 genomes]
rs4854969	0.82[ASN][1000 genomes]
rs4854970	0.93[ASN][1000 genomes]
rs55996463	0.82[ASN][1000 genomes]
rs56234136	0.82[ASN][1000 genomes]
rs57131411	0.96[EUR][1000 genomes]
rs62292283	0.80[ASN][1000 genomes]
rs62292284	0.80[ASN][1000 genomes]
rs62292290	0.82[ASN][1000 genomes]
rs62292291	0.81[ASN][1000 genomes]
rs62292292	0.85[ASN][1000 genomes]
rs62292326	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769259	0.82[ASN][1000 genomes]
rs7622125	0.87[ASN][1000 genomes]
rs7622865	0.86[ASN][1000 genomes]
rs7636890	0.82[ASN][1000 genomes]
rs7639931	0.88[ASN][1000 genomes]
rs7643438	0.92[ASN][1000 genomes]
rs7644566	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7652322	0.81[ASN][1000 genomes]
rs7652473	0.88[ASN][1000 genomes]
rs939440	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs939441	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs939442	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9682110	0.83[ASN][1000 genomes]
rs9683358	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9713189	0.81[ASN][1000 genomes]
rs9713891	0.81[ASN][1000 genomes]
rs9818172	0.82[ASN][1000 genomes]
rs9819178	0.87[ASN][1000 genomes]
rs9824544	0.81[ASN][1000 genomes]
rs9860910	0.83[ASN][1000 genomes]
rs9864534	0.83[ASN][1000 genomes]
rs9867767	0.90[ASN][1000 genomes]
rs9869873	0.88[ASN][1000 genomes]
rs9871936	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3914868	CAMK2N2	cis	parietal	SCAN
rs3914868	ABCC5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179993000-180002000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:179998800-180001600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:179998800-180002400	Weak transcription	HMEC	breast
4	chr3:179998800-180002600	Weak transcription	NHLF	lung
5	chr3:180000000-180002000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:180000200-180003600	Enhancers	NHDF-Ad	bronchial
7	chr3:180001200-180002200	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr3:180001200-180002600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr3:180001400-180001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:180001400-180001800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:180001400-180002800	Enhancers	Osteobl	bone

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