Variant report

Variant	rs10078892
Chromosome Location	chr5:52833190-52833191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10065003	0.92[ASN][1000 genomes]
rs10940322	0.83[ASN][1000 genomes]
rs10940323	0.86[ASN][1000 genomes]
rs12514280	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs12515137	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12657948	0.93[ASN][1000 genomes]
rs13177321	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1532162	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs16881474	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1844697	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1873426	0.86[JPT][hapmap]
rs187658	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs189849	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2124950	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs256081	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs256082	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs256093	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs256098	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs256111	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs256118	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2607478	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2607485	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2607506	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs2607508	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2637002	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs2637003	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2637029	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs31308	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs365358	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs366313	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs368461	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs372215	0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs377077	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs381575	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs392169	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs404838	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4147732	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4147734	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs417550	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs425880	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs432020	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs445347	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs451881	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4865547	0.86[ASN][1000 genomes]
rs4865548	0.87[ASN][1000 genomes]
rs524289	0.86[JPT][hapmap]
rs535277	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs58889983	0.95[ASN][1000 genomes]
rs6450142	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6450143	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7701972	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7702077	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7711180	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7717681	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs7736747	0.86[ASN][1000 genomes]
rs786334	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs918625	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs923610	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9292024	0.82[CHD][hapmap]
rs9790964	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9791019	0.91[ASN][1000 genomes]
rs9791152	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10078892	NDUFS4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52809200-52833600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links