Variant report

Variant	rs336549
Chromosome Location	chr3:161114968-161114969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10804790	0.81[EUR][1000 genomes]
rs1382427	0.81[EUR][1000 genomes]
rs1382428	0.81[EUR][1000 genomes]
rs1478565	0.81[EUR][1000 genomes]
rs1600209	0.81[EUR][1000 genomes]
rs163328	0.86[EUR][1000 genomes]
rs189270	0.82[EUR][1000 genomes]
rs1993891	0.81[EUR][1000 genomes]
rs28515190	0.80[EUR][1000 genomes]
rs336541	0.81[EUR][1000 genomes]
rs336543	0.81[EUR][1000 genomes]
rs336548	0.81[EUR][1000 genomes]
rs336551	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs336561	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs336567	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336569	0.86[EUR][1000 genomes]
rs336570	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336577	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs336579	0.85[EUR][1000 genomes]
rs336583	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336585	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336586	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336589	0.86[EUR][1000 genomes]
rs336590	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336591	0.86[EUR][1000 genomes]
rs336593	0.86[EUR][1000 genomes]
rs339101	0.81[EUR][1000 genomes]
rs339114	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs455386	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs456611	0.87[EUR][1000 genomes]
rs457272	0.86[EUR][1000 genomes]
rs459697	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs460165	0.81[EUR][1000 genomes]
rs460508	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs461638	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs462413	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs463928	0.82[EUR][1000 genomes]
rs464766	0.85[EUR][1000 genomes]
rs465985	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs466399	0.81[EUR][1000 genomes]
rs466626	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62279921	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6441373	0.81[EUR][1000 genomes]
rs7638668	0.81[EUR][1000 genomes]
rs975323	0.80[EUR][1000 genomes]
rs9863590	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9872514	0.81[EUR][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	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
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs336549	SPTSSB	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161113400-161115000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr3:161113600-161118000	Weak transcription	Liver	Liver
3	chr3:161113600-161118000	Weak transcription	HepG2	liver
4	chr3:161113600-161127600	Weak transcription	NHEK	skin
5	chr3:161114000-161116000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:161114000-161116200	Weak transcription	Primary T cells from cord blood	blood
7	chr3:161114400-161116000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:161114600-161115800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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