Variant report

Variant	rs28515190
Chromosome Location	chr3:161028605-161028606
allele	A/G
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:0)
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	chr3:161025819..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	chr3:161027478..161029275-chr3:161031278..161032778,2	MCF-7	breast:
5	chr3:160995856..160997723-chr3:161026666..161029126,2	MCF-7	breast:
6	chr3:161025866..161029285-chr3:161088973..161091892,6	MCF-7	breast:
7	chr3:160472534..160474749-chr3:161027522..161029214,2	MCF-7	breast:
8	chr3:161026928..161036306-chr3:161081784..161094254,31	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction
ENSG00000260572	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10804790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1154701	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12493960	0.82[AMR][1000 genomes]
rs1382427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1382428	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1478565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599374	0.82[AMR][1000 genomes]
rs1599376	0.82[AMR][1000 genomes]
rs1599378	0.82[AMR][1000 genomes]
rs1600209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1609688	0.82[AMR][1000 genomes]
rs163327	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs163328	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs189270	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1993891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2404340	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs336541	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336543	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336548	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336549	0.80[EUR][1000 genomes]
rs336567	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336568	0.83[AMR][1000 genomes]
rs336569	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336570	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336572	0.82[EUR][1000 genomes]
rs336577	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336579	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336580	0.83[AMR][1000 genomes]
rs336582	0.84[AMR][1000 genomes]
rs336583	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336585	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336586	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336589	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336590	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336591	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336593	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339101	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3849524	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4273380	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4350933	0.93[EUR][1000 genomes]
rs4370045	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4414866	0.85[AMR][1000 genomes]
rs4493448	0.92[EUR][1000 genomes]
rs4518145	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs455386	0.83[EUR][1000 genomes]
rs456611	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs457272	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs459515	0.83[AMR][1000 genomes]
rs459697	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4597724	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs460165	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs460508	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs461638	0.83[EUR][1000 genomes]
rs462413	0.83[EUR][1000 genomes]
rs462514	0.83[AMR][1000 genomes]
rs463928	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs464766	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs465985	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs466399	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4856739	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62279921	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6441370	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6441371	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441373	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6762645	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6765269	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6765270	0.82[AMR][1000 genomes]
rs6774276	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6775627	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6789388	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6794601	0.91[EUR][1000 genomes]
rs7611367	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7615592	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7623206	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7629987	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7632797	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7633186	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7638668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7647327	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7653233	0.95[EUR][1000 genomes]
rs7653361	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9290073	0.90[EUR][1000 genomes]
rs9290074	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs975323	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9790314	0.96[EUR][1000 genomes]
rs9821201	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9846756	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850455	0.96[EUR][1000 genomes]
rs9863590	0.82[EUR][1000 genomes]
rs9870059	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9872514	0.98[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	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:27 , 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	chr3:161025400-161031800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:161026400-161031600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:161026600-161032400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr3:161027000-161029200	Enhancers	Primary T cells from cord blood	blood
7	chr3:161027000-161032000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:161027000-161032600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:161027000-161032800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:161027200-161029000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr3:161027200-161031200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:161027200-161032600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:161027800-161029800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:161027800-161031800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:161028000-161029200	Enhancers	GM12878-XiMat	blood
16	chr3:161028000-161030800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:161028000-161031200	Enhancers	Dnd41	blood
18	chr3:161028200-161031400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr3:161028400-161028800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:161028400-161029000	Enhancers	Thymus	Thymus
21	chr3:161028400-161029200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:161028400-161029200	Enhancers	Fetal Thymus	thymus
23	chr3:161028400-161029400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:161028400-161029600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:161028600-161029400	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:161028600-161031800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr3:161028600-161032600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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