Variant report

Variant	rs9872514
Chromosome Location	chr3:161042833-161042834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
2	chr3:160942925..160944989-chr3:161039772..161043116,3	MCF-7	breast:
3	chr3:160940058..160942666-chr3:161042036..161044035,3	MCF-7	breast:
4	chr3:161009978..161012586-chr3:161040587..161043038,3	MCF-7	breast:
5	chr3:161040559..161042979-chr3:161133154..161135842,2	MCF-7	breast:
6	chr3:161040460..161042970-chr3:161125296..161126963,2	MCF-7	breast:
7	chr3:161006869..161011120-chr3:161039575..161043501,7	MCF-7	breast:
8	chr3:161041936..161043684-chr3:161128783..161133001,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPTSSB-3	chr3:161042701-161044007	NONHSAT093013

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1017799	0.90[JPT][hapmap]
rs10804790	0.99[EUR][1000 genomes]
rs1154701	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12487002	0.80[JPT][hapmap]
rs12490149	0.89[JPT][hapmap]
rs13083229	0.82[CEU][hapmap]
rs13319558	0.90[JPT][hapmap]
rs13319771	0.88[JPT][hapmap]
rs1382427	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1382428	0.99[EUR][1000 genomes]
rs1478565	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1478568	0.82[CEU][hapmap]
rs1600209	0.99[EUR][1000 genomes]
rs163327	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs163328	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs189270	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1993891	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2306209	0.89[JPT][hapmap]
rs2404340	0.94[EUR][1000 genomes]
rs28515190	0.98[EUR][1000 genomes]
rs336541	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs336543	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs336548	0.99[EUR][1000 genomes]
rs336549	0.81[EUR][1000 genomes]
rs336567	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs336568	0.81[EUR][1000 genomes]
rs336569	0.95[EUR][1000 genomes]
rs336570	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs336572	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs336577	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs336579	0.94[EUR][1000 genomes]
rs336580	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs336582	0.81[EUR][1000 genomes]
rs336583	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs336585	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs336586	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs336589	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs336590	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs336591	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs336593	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs339101	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3849524	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4273380	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4290817	0.83[CEU][hapmap]
rs4350933	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4352387	0.89[JPT][hapmap]
rs4370045	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4414866	0.89[CEU][hapmap]
rs4468992	0.90[JPT][hapmap]
rs4493448	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4493449	1.00[CEU][hapmap]
rs4518145	0.82[EUR][1000 genomes]
rs455386	0.84[EUR][1000 genomes]
rs456611	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs457272	0.93[EUR][1000 genomes]
rs459697	0.94[EUR][1000 genomes]
rs4597724	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs460165	0.90[EUR][1000 genomes]
rs460508	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs461638	0.84[EUR][1000 genomes]
rs462413	0.84[EUR][1000 genomes]
rs462514	0.85[CEU][hapmap]
rs463928	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs464766	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs465985	0.85[EUR][1000 genomes]
rs466399	0.90[EUR][1000 genomes]
rs4856714	0.83[CEU][hapmap]
rs4856739	0.85[EUR][1000 genomes]
rs4856767	0.83[CEU][hapmap]
rs62279921	0.93[EUR][1000 genomes]
rs6441370	0.86[EUR][1000 genomes]
rs6441371	0.84[EUR][1000 genomes]
rs6441373	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6441375	0.89[JPT][hapmap]
rs6762645	0.92[EUR][1000 genomes]
rs6765269	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6774276	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6775446	0.89[JPT][hapmap]
rs6775627	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6775931	0.89[JPT][hapmap]
rs6782415	0.89[JPT][hapmap]
rs6782518	0.89[JPT][hapmap]
rs6785714	0.84[JPT][hapmap]
rs6789388	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs6791213	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs6794601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7611367	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7613358	0.83[CEU][hapmap]
rs7615592	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7623206	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7626773	0.90[JPT][hapmap]
rs7629987	0.94[EUR][1000 genomes]
rs7631479	0.88[CEU][hapmap]
rs7632797	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7633186	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7634299	0.90[JPT][hapmap]
rs7638668	0.99[EUR][1000 genomes]
rs7647327	0.96[EUR][1000 genomes]
rs7651924	0.90[JPT][hapmap]
rs7652267	0.82[CEU][hapmap]
rs7653233	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653361	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs899275	0.80[EUR][1000 genomes]
rs9290073	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9290074	0.92[EUR][1000 genomes]
rs975323	0.97[EUR][1000 genomes]
rs9790314	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9815222	0.83[CEU][hapmap]
rs9819793	0.86[JPT][hapmap]
rs9821201	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9822916	0.89[JPT][hapmap]
rs9824805	0.90[JPT][hapmap]
rs9835530	0.90[JPT][hapmap]
rs9846756	0.93[EUR][1000 genomes]
rs9847842	0.89[JPT][hapmap]
rs9850455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9859641	0.89[JPT][hapmap]
rs9860980	0.88[JPT][hapmap]
rs9862867	0.90[JPT][hapmap]
rs9863590	0.83[EUR][1000 genomes]
rs9870059	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs9877309	0.86[JPT][hapmap]
rs9880536	0.90[JPT][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161042200-161043800	Enhancers	HepG2	liver

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