Variant report

Variant	rs9290074
Chromosome Location	chr3:160997823-160997824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160980523..160999163-chr3:161073509..161094838,104	MCF-7	breast:
2	chr3:160995830..160998585-chr3:161007446..161010411,2	MCF-7	breast:
3	chr3:160996301..160998461-chr3:161053862..161055519,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1037888	0.80[ASN][1000 genomes]
rs10804790	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1154701	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12493960	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1382427	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1382428	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1478565	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1599374	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1599376	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1599378	0.84[AMR][1000 genomes]
rs1599386	0.80[ASN][1000 genomes]
rs1600209	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1609688	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs163328	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs189270	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1993891	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2404340	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515190	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336541	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336543	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336548	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336567	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336568	0.81[AMR][1000 genomes]
rs336569	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336570	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336577	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336579	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336580	0.81[AMR][1000 genomes]
rs336582	0.82[AMR][1000 genomes]
rs336583	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336585	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336586	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336589	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336590	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336591	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336593	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs339101	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3849524	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273380	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4350933	0.93[EUR][1000 genomes]
rs4370045	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414866	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4493448	0.93[EUR][1000 genomes]
rs4518145	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs455386	0.80[EUR][1000 genomes]
rs456611	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs457272	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs459515	0.81[AMR][1000 genomes]
rs459697	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4597724	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460165	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs460508	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs461638	0.80[EUR][1000 genomes]
rs4616689	0.80[ASN][1000 genomes]
rs462413	0.80[EUR][1000 genomes]
rs462514	0.81[AMR][1000 genomes]
rs463928	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs464766	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs465985	0.81[EUR][1000 genomes]
rs466399	0.86[EUR][1000 genomes]
rs4856739	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62279921	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6441370	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6441371	0.99[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441373	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762645	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765269	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765270	0.84[AMR][1000 genomes]
rs6774276	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6774635	0.80[ASN][1000 genomes]
rs6775627	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789388	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6794601	0.91[EUR][1000 genomes]
rs7611367	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7615592	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622047	0.80[ASN][1000 genomes]
rs7623206	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629987	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632797	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7633186	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7638668	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7647327	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653233	0.95[EUR][1000 genomes]
rs7653361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898680	0.80[ASN][1000 genomes]
rs9290065	0.80[ASN][1000 genomes]
rs9290073	0.90[EUR][1000 genomes]
rs975323	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790314	0.96[EUR][1000 genomes]
rs980975	0.80[ASN][1000 genomes]
rs980976	0.80[ASN][1000 genomes]
rs9821201	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9846756	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848239	0.80[ASN][1000 genomes]
rs9850455	0.96[EUR][1000 genomes]
rs9870059	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872514	0.92[EUR][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	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	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9290074	SPTSSB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160979200-160999800	Weak transcription	Psoas Muscle	Psoas
2	chr3:160984800-161002400	Weak transcription	NHEK	skin
3	chr3:160989000-161000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:160994600-161002200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:160994600-161016800	Weak transcription	Right Ventricle	heart
6	chr3:160997400-161002200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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