Variant report

Variant	rs778496
Chromosome Location	chr3:23480144-23480145
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	chr3:23477379..23479456-chr3:23479836..23482736,2	MCF-7	breast:

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs11129119	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708160	0.89[ASN][1000 genomes]
rs11715841	0.89[ASN][1000 genomes]
rs11718082	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11916411	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11918529	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12715047	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13064035	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13321359	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13326048	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1498809	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1498811	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1692612	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1692617	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1692620	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692622	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1692650	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1692651	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1692652	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1695170	0.87[EUR][1000 genomes]
rs1695171	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1695181	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1695200	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17194786	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1874235	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1908773	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2036226	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2055310	0.88[ASN][1000 genomes]
rs2133331	0.88[ASN][1000 genomes]
rs2173460	0.89[ASN][1000 genomes]
rs2359759	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2359763	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3104243	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3104244	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3111311	0.91[ASN][1000 genomes]
rs34080387	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3817002	0.89[ASN][1000 genomes]
rs4241512	0.80[EUR][1000 genomes]
rs4383458	0.82[ASN][1000 genomes]
rs4456808	0.82[ASN][1000 genomes]
rs4484143	0.81[ASN][1000 genomes]
rs4513393	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4635650	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858071	0.86[EUR][1000 genomes]
rs4858072	0.85[EUR][1000 genomes]
rs4858077	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4858504	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4858506	0.92[EUR][1000 genomes]
rs4858508	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4858511	0.83[EUR][1000 genomes]
rs57137870	0.88[ASN][1000 genomes]
rs58748418	0.88[ASN][1000 genomes]
rs60430884	0.84[ASN][1000 genomes]
rs60581845	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62256993	0.87[ASN][1000 genomes]
rs62256994	0.87[ASN][1000 genomes]
rs6550756	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6550767	0.80[ASN][1000 genomes]
rs6763329	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6763535	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6767599	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769173	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6770079	0.81[ASN][1000 genomes]
rs6775232	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6776424	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6780723	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780787	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784195	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6795470	0.81[ASN][1000 genomes]
rs6796840	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6797907	0.88[ASN][1000 genomes]
rs6798153	0.91[ASN][1000 genomes]
rs6798328	0.89[ASN][1000 genomes]
rs6808513	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6810100	0.87[ASN][1000 genomes]
rs704533	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs704534	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs716457	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73043614	0.86[ASN][1000 genomes]
rs7612666	0.89[ASN][1000 genomes]
rs7613091	0.91[ASN][1000 genomes]
rs7614146	0.81[ASN][1000 genomes]
rs7631334	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7634117	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7636826	0.81[ASN][1000 genomes]
rs7640308	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7644666	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7645209	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648443	0.87[ASN][1000 genomes]
rs7651893	0.81[ASN][1000 genomes]
rs778459	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778460	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778461	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs778462	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs778467	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778468	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778470	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778475	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778476	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778480	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778482	0.89[ASN][1000 genomes]
rs778484	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778485	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778486	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs778487	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778488	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs778494	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs778499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs778500	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778501	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778503	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778506	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778507	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778508	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778510	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778514	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778523	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778526	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815921	0.84[ASN][1000 genomes]
rs9824359	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9825778	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9826089	0.91[EUR][1000 genomes]
rs9826647	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9827507	0.86[EUR][1000 genomes]
rs9830388	0.86[ASN][1000 genomes]
rs9830742	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9836574	0.81[AFR][1000 genomes]
rs9840820	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9849424	0.90[EUR][1000 genomes]
rs9856169	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9859515	0.93[EUR][1000 genomes]
rs9859651	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9873317	0.93[EUR][1000 genomes]
rs9874519	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv876624	chr3:23385877-23483536	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23472800-23484400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:23472800-23488000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:23473000-23480600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:23473800-23494000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:23476800-23481800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:23477200-23481400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:23477400-23480800	Weak transcription	Dnd41	blood
8	chr3:23477400-23482600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:23477800-23487800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:23478000-23484000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:23478400-23481000	Enhancers	Fetal Heart	heart
12	chr3:23478600-23483400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:23478600-23485800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:23478600-23489400	Weak transcription	Left Ventricle	heart
15	chr3:23478800-23482600	Weak transcription	Psoas Muscle	Psoas
16	chr3:23479400-23483800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:23479400-23484800	Weak transcription	Adipose Nuclei	Adipose
18	chr3:23479600-23480800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:23479600-23481200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr3:23479600-23481200	Enhancers	HUVEC	blood vessel
21	chr3:23479600-23482200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:23479600-23482400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:23479600-23483600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:23479600-23483600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:23479600-23484200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:23479800-23480400	Weak transcription	Primary B cells from cord blood	blood
27	chr3:23479800-23480600	Weak transcription	Brain Angular Gyrus	brain
28	chr3:23479800-23482800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:23479800-23483800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:23479800-23485600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:23479800-23490200	Weak transcription	Brain Substantia Nigra	brain
32	chr3:23480000-23481600	Enhancers	GM12878-XiMat	blood

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