Variant report

Variant	rs6554065
Chromosome Location	chr4:53971011-53971012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10013152	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs10024057	0.90[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs10033650	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10517278	0.94[ASW][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs11941906	0.90[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs13142315	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13340297	1.00[CEU][hapmap]
rs1384696	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17082301	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17082330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2062185	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs2062186	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs28688668	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28713187	0.81[AMR][1000 genomes]
rs28882784	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864445	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864712	0.90[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs4864715	0.90[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs4864717	0.83[GIH][hapmap]
rs56259272	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62338998	0.93[EUR][1000 genomes]
rs6822707	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6855010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7658716	0.90[CHB][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap]
rs7671836	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7694940	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7698034	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9312635	0.80[EUR][1000 genomes]
rs9790561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999433	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53965800-53971200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:53965800-53971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:53965800-53986000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:53966000-53975000	Weak transcription	Fetal Stomach	stomach
5	chr4:53968000-53975200	Weak transcription	Fetal Heart	heart
6	chr4:53968200-53979200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:53968400-53983200	Weak transcription	NHEK	skin
8	chr4:53968400-53984600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:53969200-53983200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:53969400-53979400	Weak transcription	Osteobl	bone
11	chr4:53969600-53979600	Weak transcription	NHDF-Ad	bronchial
12	chr4:53970200-53971400	Enhancers	Fetal Lung	lung
13	chr4:53970600-53971400	Enhancers	HepG2	liver
14	chr4:53970800-53971200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr4:53970800-53972000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr4:53971000-53971200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:53971000-53971200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr4:53971000-53971400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr4:53971000-53971400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr4:53971000-53971400	Enhancers	Ovary	ovary

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