Variant report

Variant	rs56076618
Chromosome Location	chr3:61168916-61168917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:61167426..61169661-chr3:61171203..61172847,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1001788	0.96[ASN][1000 genomes]
rs10049007	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10049287	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10049452	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10049454	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130821	0.87[EUR][1000 genomes]
rs11130822	0.86[EUR][1000 genomes]
rs11130826	0.82[EUR][1000 genomes]
rs11707984	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11712122	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11720254	0.81[EUR][1000 genomes]
rs12053817	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492551	0.82[EUR][1000 genomes]
rs12492939	0.93[EUR][1000 genomes]
rs12635622	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13099397	0.80[ASN][1000 genomes]
rs13320646	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13323296	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1371095	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1470035	0.87[EUR][1000 genomes]
rs1473644	0.83[ASN][1000 genomes]
rs1550343	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554599	0.85[EUR][1000 genomes]
rs1554601	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17064630	0.86[EUR][1000 genomes]
rs1866433	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1866434	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1880213	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1916800	0.86[EUR][1000 genomes]
rs1916801	0.86[EUR][1000 genomes]
rs1916802	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1969420	0.97[ASN][1000 genomes]
rs1980308	0.85[EUR][1000 genomes]
rs1980309	0.85[EUR][1000 genomes]
rs1980310	0.85[EUR][1000 genomes]
rs1980311	0.83[EUR][1000 genomes]
rs2118811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886377	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34045993	0.81[ASN][1000 genomes]
rs35198002	0.86[EUR][1000 genomes]
rs4296587	0.80[ASN][1000 genomes]
rs4309721	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4535219	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4605537	0.82[EUR][1000 genomes]
rs4688295	0.96[ASN][1000 genomes]
rs4688310	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688334	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4688354	0.80[EUR][1000 genomes]
rs4688355	0.80[EUR][1000 genomes]
rs4688379	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61275795	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445196	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6787292	0.86[EUR][1000 genomes]
rs6787313	0.84[EUR][1000 genomes]
rs6787511	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6807748	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6809031	0.82[ASN][1000 genomes]
rs71296711	0.82[EUR][1000 genomes]
rs753661	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7631101	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7631246	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7636682	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7641177	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647122	0.84[ASN][1000 genomes]
rs7653719	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9811478	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9814044	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816087	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9819588	0.87[AFR][1000 genomes]
rs9832387	0.81[EUR][1000 genomes]
rs9832404	0.80[EUR][1000 genomes]
rs9839082	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844741	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846073	0.86[EUR][1000 genomes]
rs9850114	0.82[EUR][1000 genomes]
rs9850125	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851485	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857606	0.88[ASN][1000 genomes]
rs9861713	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9871451	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9871598	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9882800	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv948633	chr3:60993915-61171279	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv590425	chr3:61132698-61186550	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1012435	chr3:61136874-61181318	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1014142	chr3:61136874-61184782	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61151200-61188000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61158800-61172000	Weak transcription	Pancreas	Pancrea
3	chr3:61159600-61172000	Weak transcription	Gastric	stomach
4	chr3:61161000-61186000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:61161400-61169400	Weak transcription	Ovary	ovary
6	chr3:61166200-61170200	Weak transcription	Fetal Lung	lung
7	chr3:61166400-61177800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:61167000-61169000	Enhancers	Brain Hippocampus Middle	brain
9	chr3:61167400-61172000	Weak transcription	Psoas Muscle	Psoas
10	chr3:61167800-61169000	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:61168200-61169000	Enhancers	Brain Cingulate Gyrus	brain
12	chr3:61168200-61169000	Enhancers	Fetal Heart	heart
13	chr3:61168200-61169200	Enhancers	Brain Substantia Nigra	brain
14	chr3:61168400-61179000	Weak transcription	HepG2	liver
15	chr3:61168600-61169200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:61168600-61180600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:61168800-61169200	Enhancers	GM12878-XiMat	blood
18	chr3:61168800-61169400	Enhancers	Brain Angular Gyrus	brain
19	chr3:61168800-61170000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:61168800-61170800	Weak transcription	Brain Anterior Caudate	brain

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