Variant report

Variant	rs4955802
Chromosome Location	chr3:178672902-178672903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11711320	0.91[EUR][1000 genomes]
rs11720081	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13092881	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4245914	0.91[EUR][1000 genomes]
rs4279147	0.91[EUR][1000 genomes]
rs4280676	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4315724	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4337680	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4377525	0.90[EUR][1000 genomes]
rs4395442	0.91[EUR][1000 genomes]
rs4417911	0.91[EUR][1000 genomes]
rs4469018	0.89[EUR][1000 genomes]
rs4501160	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4505756	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4522816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4525914	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4552405	0.91[EUR][1000 genomes]
rs4579062	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs4607155	0.85[EUR][1000 genomes]
rs4626139	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4637331	0.94[CEU][hapmap]
rs4955796	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4955807	0.94[CEU][hapmap]
rs4955810	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs56115013	0.91[EUR][1000 genomes]
rs56154408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443607	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443614	0.91[EUR][1000 genomes]
rs6772028	0.94[CEU][hapmap]
rs6789706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790867	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6793769	0.91[EUR][1000 genomes]
rs6793893	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs6794956	0.85[EUR][1000 genomes]
rs6795238	0.85[EUR][1000 genomes]
rs6800015	0.89[CEU][hapmap]
rs6804084	0.94[CEU][hapmap]
rs7429173	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7612363	0.91[EUR][1000 genomes]
rs7633318	0.94[CEU][hapmap]
rs7639391	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs7643052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651510	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7652668	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7652946	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9846511	0.91[EUR][1000 genomes]
rs9860318	0.88[EUR][1000 genomes]
rs9860749	0.89[EUR][1000 genomes]
rs9879637	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9880749	0.89[EUR][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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1010148	chr3:178650949-178691377	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' 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
5	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178666000-178677800	Weak transcription	HSMMtube	muscle
2	chr3:178668800-178683000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:178669400-178685000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:178671400-178676000	Strong transcription	HSMM	muscle
5	chr3:178671400-178684000	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links