Variant report

Variant	rs1516601
Chromosome Location	chr3:95019357-95019358
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:95018524..95019390-chr9:5887461..5888104,2	MCF-7	breast:

Extended variants
information (count: 144 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1012061	0.94[ASN][1000 genomes]
rs10428145	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10428241	0.84[ASN][1000 genomes]
rs10511151	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10933932	0.89[ASN][1000 genomes]
rs10933940	0.96[ASN][1000 genomes]
rs10933941	0.97[ASN][1000 genomes]
rs10933955	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11914749	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11916841	0.81[EUR][1000 genomes]
rs11918082	1.00[ASN][1000 genomes]
rs11918166	0.88[ASN][1000 genomes]
rs11920130	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11923227	0.81[EUR][1000 genomes]
rs11923257	0.81[EUR][1000 genomes]
rs11923716	0.89[ASN][1000 genomes]
rs11924111	0.99[ASN][1000 genomes]
rs11928664	0.99[ASN][1000 genomes]
rs12486859	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495920	0.91[ASN][1000 genomes]
rs12496724	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12497708	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12630013	0.97[ASN][1000 genomes]
rs12630859	0.97[ASN][1000 genomes]
rs12631889	0.81[EUR][1000 genomes]
rs12639003	0.94[ASN][1000 genomes]
rs12695188	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064413	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065008	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065369	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13066378	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13070939	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13071522	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13073991	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13074154	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13076586	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078348	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081547	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13087055	0.84[ASN][1000 genomes]
rs13091172	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13097484	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13098931	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1356269	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1356273	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1356276	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1356277	0.84[ASN][1000 genomes]
rs1400296	0.84[ASN][1000 genomes]
rs1400301	0.84[ASN][1000 genomes]
rs1400302	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1400303	0.84[ASN][1000 genomes]
rs1476323	0.97[ASN][1000 genomes]
rs1516605	1.00[ASN][1000 genomes]
rs1516606	1.00[ASN][1000 genomes]
rs1516607	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1516608	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1516609	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1519160	0.99[ASN][1000 genomes]
rs1607487	0.81[ASN][1000 genomes]
rs1607488	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1607489	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17383687	0.97[ASN][1000 genomes]
rs17383861	0.97[ASN][1000 genomes]
rs17384029	0.96[ASN][1000 genomes]
rs17384064	0.97[ASN][1000 genomes]
rs17442941	0.97[ASN][1000 genomes]
rs1914063	0.98[ASN][1000 genomes]
rs1914064	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1968016	0.97[ASN][1000 genomes]
rs2048861	0.97[ASN][1000 genomes]
rs2048863	0.96[ASN][1000 genomes]
rs2176276	0.96[ASN][1000 genomes]
rs2310403	0.89[ASN][1000 genomes]
rs2310406	0.88[ASN][1000 genomes]
rs2311285	1.00[ASN][1000 genomes]
rs2311287	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849443	0.82[EUR][1000 genomes]
rs3905401	0.84[ASN][1000 genomes]
rs3907753	0.82[EUR][1000 genomes]
rs3926894	0.97[ASN][1000 genomes]
rs4535228	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4610223	0.89[ASN][1000 genomes]
rs478095	0.93[ASN][1000 genomes]
rs479964	0.93[ASN][1000 genomes]
rs4857157	0.97[ASN][1000 genomes]
rs4857159	0.97[ASN][1000 genomes]
rs4857160	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs490921	0.83[ASN][1000 genomes]
rs509321	0.99[ASN][1000 genomes]
rs511189	0.99[ASN][1000 genomes]
rs533453	0.99[ASN][1000 genomes]
rs542297	0.81[ASN][1000 genomes]
rs56233996	0.97[ASN][1000 genomes]
rs57291530	0.97[ASN][1000 genomes]
rs575436	0.81[ASN][1000 genomes]
rs58743887	0.80[EUR][1000 genomes]
rs58823483	0.96[ASN][1000 genomes]
rs58977036	0.82[EUR][1000 genomes]
rs59007421	0.97[ASN][1000 genomes]
rs59469832	0.96[ASN][1000 genomes]
rs60875944	0.98[ASN][1000 genomes]
rs61446477	0.97[ASN][1000 genomes]
rs62269419	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774134	0.97[ASN][1000 genomes]
rs6786697	0.99[ASN][1000 genomes]
rs6807708	1.00[ASN][1000 genomes]
rs6810229	0.97[ASN][1000 genomes]
rs72615787	0.82[ASN][1000 genomes]
rs72615791	0.89[ASN][1000 genomes]
rs72618497	0.96[ASN][1000 genomes]
rs72618498	0.97[ASN][1000 genomes]
rs72618499	0.97[ASN][1000 genomes]
rs72618500	0.97[ASN][1000 genomes]
rs72620004	0.97[ASN][1000 genomes]
rs72620005	0.97[ASN][1000 genomes]
rs72620006	0.98[ASN][1000 genomes]
rs72620007	0.98[ASN][1000 genomes]
rs7429603	1.00[ASN][1000 genomes]
rs7619484	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7627614	1.00[ASN][1000 genomes]
rs7634250	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639829	0.97[ASN][1000 genomes]
rs7653792	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs953342	0.84[ASN][1000 genomes]
rs9809394	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9813568	1.00[ASN][1000 genomes]
rs9826288	0.93[ASN][1000 genomes]
rs9832182	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838302	1.00[ASN][1000 genomes]
rs9847352	0.81[EUR][1000 genomes]
rs9855077	0.99[ASN][1000 genomes]
rs9868858	0.81[EUR][1000 genomes]
rs9878073	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013680	chr3:94777881-95538336	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv536653	chr3:94777881-95538336	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv877170	chr3:94790666-95564838	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv999347	chr3:94832290-95177750	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv877175	chr3:94869561-95210873	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1011235	chr3:94870789-95238299	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv428091	chr3:94942642-95393754	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv428744	chr3:94960533-95145238	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv834767	chr3:94972069-95148035	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1002952	chr3:94972310-95025749	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv536654	chr3:94972310-95025749	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv967260	chr3:95001173-95021114	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:95009200-95020000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:95017000-95020600	Weak transcription	NH-A	brain
3	chr3:95019200-95020200	Enhancers	Fetal Intestine Small	intestine

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