Variant report

Variant	rs462514
Chromosome Location	chr3:161092809-161092810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr10:32635339..32635985-chr3:161092789..161093738,2	MCF-7	breast:
4	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
5	chr3:161090533..161094064-chr8:101963094..101965869,3	MCF-7	breast:
6	chr17:48942183..48944855-chr3:161092802..161095476,2	MCF-7	breast:
7	chr21:41709121..41711584-chr3:161091853..161094106,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120616	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000233825	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000222309	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10804790	0.83[AMR][1000 genomes]
rs1154701	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12632686	0.88[JPT][hapmap]
rs12634006	0.88[JPT][hapmap]
rs12634319	0.88[JPT][hapmap]
rs13083229	0.96[CEU][hapmap]
rs1382427	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs1382428	0.82[AMR][1000 genomes]
rs1478565	0.85[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs1478568	0.96[CEU][hapmap]
rs1600209	0.83[AMR][1000 genomes]
rs163328	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs189270	0.85[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs1993891	0.85[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs28515190	0.83[AMR][1000 genomes]
rs336541	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs336543	0.85[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs336548	0.83[AMR][1000 genomes]
rs336567	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336569	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336570	0.85[CEU][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336572	0.81[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs336577	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336579	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336580	1.00[CEU][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336582	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336583	0.85[CEU][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336585	0.85[CEU][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336586	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336589	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336590	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336591	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336593	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs339101	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3849524	0.85[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs4273380	0.85[CEU][hapmap]
rs4290817	0.96[CEU][hapmap]
rs4370045	0.85[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs4493449	0.85[CEU][hapmap]
rs4518145	0.83[EUR][1000 genomes]
rs456611	0.85[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs457272	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs459515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459697	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4597724	0.85[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs460165	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs460508	0.85[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs463928	0.85[CEU][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs464766	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs466399	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4856714	0.96[CEU][hapmap]
rs4856739	0.85[EUR][1000 genomes]
rs4856767	0.96[CEU][hapmap]
rs62279921	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6441370	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6441371	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441373	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs6765269	0.85[CEU][hapmap]
rs6774276	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6775627	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs6789388	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs6791213	0.96[CEU][hapmap]
rs6794601	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs7611367	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7613358	0.96[CEU][hapmap]
rs7615592	0.85[CEU][hapmap]
rs7623206	0.85[CEU][hapmap]
rs7629987	0.81[AMR][1000 genomes]
rs7632797	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7633186	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7638668	0.83[AMR][1000 genomes]
rs7647327	0.82[AMR][1000 genomes]
rs7652267	0.96[CEU][hapmap]
rs7653361	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs873183	0.85[JPT][hapmap]
rs896080	0.88[JPT][hapmap]
rs9290074	0.81[AMR][1000 genomes]
rs975323	0.83[AMR][1000 genomes]
rs9815222	0.96[CEU][hapmap]
rs9821201	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs9850455	0.85[CEU][hapmap]
rs9864752	0.85[CEU][hapmap]
rs9870059	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs9872514	0.85[CEU][hapmap]

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
rs462514	SPTSSB	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161091200-161093200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:161091200-161096800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:161091400-161093000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:161091400-161102800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:161092800-161093600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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