Variant report

Variant	rs62256977
Chromosome Location	chr3:23609196-23609197
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23594511..23597259-chr3:23606854..23610185,3	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10510539	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11129120	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11706875	0.95[ASN][1000 genomes]
rs11712991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713090	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11715736	0.99[ASN][1000 genomes]
rs11717508	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11718111	0.99[ASN][1000 genomes]
rs13316118	0.97[ASN][1000 genomes]
rs1391756	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1498810	0.99[ASN][1000 genomes]
rs1498812	0.92[ASN][1000 genomes]
rs1692621	0.93[ASN][1000 genomes]
rs1692646	0.97[ASN][1000 genomes]
rs1692648	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1692649	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1695183	0.97[ASN][1000 genomes]
rs1695185	0.97[ASN][1000 genomes]
rs1695197	0.97[ASN][1000 genomes]
rs17013268	0.93[ASN][1000 genomes]
rs17013425	1.00[ASN][1000 genomes]
rs17194751	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1995173	0.99[ASN][1000 genomes]
rs1995174	0.99[ASN][1000 genomes]
rs2055307	1.00[ASN][1000 genomes]
rs28367247	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858517	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56034809	0.99[ASN][1000 genomes]
rs58130044	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58618629	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59012069	0.99[ASN][1000 genomes]
rs60028742	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60137984	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255784	1.00[ASN][1000 genomes]
rs62255785	1.00[ASN][1000 genomes]
rs62255789	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62256025	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62256972	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62256973	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256974	0.84[EUR][1000 genomes]
rs62256975	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256982	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256990	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62256991	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66864142	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6774454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807859	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs68093882	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139773	0.97[ASN][1000 genomes]
rs73140507	0.94[ASN][1000 genomes]
rs73140523	0.98[ASN][1000 genomes]
rs73140544	0.99[ASN][1000 genomes]
rs7430428	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614195	1.00[ASN][1000 genomes]
rs7636705	1.00[ASN][1000 genomes]
rs778465	0.98[ASN][1000 genomes]
rs778473	0.91[ASN][1000 genomes]
rs778483	0.97[ASN][1000 genomes]
rs778489	0.95[ASN][1000 genomes]
rs778492	0.93[ASN][1000 genomes]
rs778497	0.92[ASN][1000 genomes]
rs778502	0.92[ASN][1000 genomes]
rs778511	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs778512	1.00[ASN][1000 genomes]
rs778513	1.00[ASN][1000 genomes]
rs778516	1.00[ASN][1000 genomes]
rs778517	1.00[ASN][1000 genomes]
rs778518	1.00[ASN][1000 genomes]
rs778519	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs778522	1.00[ASN][1000 genomes]
rs778525	0.94[ASN][1000 genomes]
rs778527	0.94[ASN][1000 genomes]
rs809640	1.00[ASN][1000 genomes]
rs875443	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23583400-23615200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:23585600-23609400	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:23591400-23611600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:23597400-23613600	Weak transcription	Liver	Liver
5	chr3:23599600-23609400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:23606000-23643000	Weak transcription	Primary T cells from cord blood	blood
7	chr3:23606600-23609200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:23606800-23609200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:23607000-23609200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:23607000-23609200	Weak transcription	NHLF	lung
11	chr3:23607000-23640400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:23607600-23609800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:23608200-23609800	Enhancers	Aorta	Aorta
14	chr3:23608400-23609600	Enhancers	Right Ventricle	heart
15	chr3:23608400-23610000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:23608600-23609600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:23608600-23609800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:23608600-23609800	Enhancers	Fetal Heart	heart
19	chr3:23608600-23609800	Enhancers	GM12878-XiMat	blood
20	chr3:23608600-23610000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:23608600-23634400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:23608800-23610000	Enhancers	HMEC	breast
23	chr3:23609000-23609400	Flanking Active TSS	HSMMtube	muscle
24	chr3:23609000-23609800	Enhancers	Psoas Muscle	Psoas
25	chr3:23609000-23609800	Enhancers	HSMM	muscle
26	chr3:23609000-23609800	Enhancers	NHEK	skin
27	chr3:23609000-23609800	Enhancers	Osteobl	bone
28	chr3:23609000-23610000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:23609000-23610000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:23609000-23610000	Enhancers	NH-A	brain

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