Variant report

Variant	rs6809256
Chromosome Location	chr3:161026513-161026514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161025819..161030681-chr3:161030815..161036788,8	MCF-7	breast:
2	chr3:161026332..161029255-chr3:161034425..161036502,2	MCF-7	breast:
3	chr3:161023364..161025630-chr3:161026423..161028838,2	MCF-7	breast:
4	chr3:161024510..161027943-chr3:161039749..161042505,4	MCF-7	breast:
5	chr3:161024873..161027806-chr3:161085286..161087243,2	MCF-7	breast:
6	chr3:161025355..161028351-chr3:161131512..161133073,2	MCF-7	breast:
7	chr3:161025866..161029285-chr3:161088973..161091892,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10804790	0.80[EUR][1000 genomes]
rs10936223	0.84[AMR][1000 genomes]
rs10936224	0.87[AMR][1000 genomes]
rs1154701	0.87[EUR][1000 genomes]
rs12486253	0.95[EUR][1000 genomes]
rs12495310	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12631850	0.84[AMR][1000 genomes]
rs13083229	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1382427	0.80[EUR][1000 genomes]
rs1478565	0.81[EUR][1000 genomes]
rs1478568	0.96[EUR][1000 genomes]
rs1600209	0.80[EUR][1000 genomes]
rs1993891	0.80[EUR][1000 genomes]
rs336541	0.80[EUR][1000 genomes]
rs336543	0.80[EUR][1000 genomes]
rs336548	0.80[EUR][1000 genomes]
rs336568	0.81[EUR][1000 genomes]
rs336572	0.82[EUR][1000 genomes]
rs336580	0.81[EUR][1000 genomes]
rs336582	0.81[EUR][1000 genomes]
rs4290817	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4470535	0.95[EUR][1000 genomes]
rs4518145	0.84[EUR][1000 genomes]
rs4560315	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4856714	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4856738	0.95[EUR][1000 genomes]
rs4856739	0.86[EUR][1000 genomes]
rs4856767	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4856768	0.96[EUR][1000 genomes]
rs55688744	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441370	0.87[EUR][1000 genomes]
rs6441371	0.85[EUR][1000 genomes]
rs6441373	0.81[EUR][1000 genomes]
rs6768818	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6774276	0.82[EUR][1000 genomes]
rs6789388	0.86[EUR][1000 genomes]
rs6791213	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611367	0.87[EUR][1000 genomes]
rs7613227	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7613358	0.93[EUR][1000 genomes]
rs7627528	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7632797	0.87[EUR][1000 genomes]
rs7633186	0.86[EUR][1000 genomes]
rs7636941	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638668	0.80[EUR][1000 genomes]
rs7652267	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs899275	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9809522	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9815222	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9834659	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9839527	0.96[EUR][1000 genomes]
rs9864752	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9879687	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6809256	SPTSSB	cis	Heart Left Ventricle	GTEx
rs6809256	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161017000-161033000	Weak transcription	Left Ventricle	heart
2	chr3:161017600-161032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:161023600-161027200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:161025400-161031800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr3:161025600-161026600	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
6	chr3:161025800-161027000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:161026400-161028200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:161026400-161031600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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