Variant report

Variant	rs59972445
Chromosome Location	chr3:159725002-159725003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159479933..159482326-chr3:159723100..159725647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12486839	1.00[EUR][1000 genomes]
rs12487209	1.00[EUR][1000 genomes]
rs12487614	0.88[ASN][1000 genomes]
rs12488038	1.00[EUR][1000 genomes]
rs12489264	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12492679	0.88[ASN][1000 genomes]
rs12492730	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12496176	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16830996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831029	0.83[EUR][1000 genomes]
rs2115174	0.88[ASN][1000 genomes]
rs34842858	0.88[ASN][1000 genomes]
rs35321606	0.88[ASN][1000 genomes]
rs59249997	0.83[EUR][1000 genomes]
rs6771983	0.88[ASN][1000 genomes]
rs6784758	0.88[ASN][1000 genomes]
rs7427782	0.84[ASN][1000 genomes]
rs7427801	0.84[ASN][1000 genomes]
rs7427807	0.88[ASN][1000 genomes]
rs7429852	0.84[ASN][1000 genomes]
rs7625648	0.88[ASN][1000 genomes]
rs9283612	0.88[ASN][1000 genomes]
rs9290052	0.88[ASN][1000 genomes]
rs9290053	0.88[ASN][1000 genomes]
rs9812698	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812995	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813028	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9816860	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9827531	0.88[ASN][1000 genomes]
rs9830969	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834418	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9835467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838248	0.86[ASN][1000 genomes]
rs9850910	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9851355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9857045	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862350	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871440	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9872678	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873090	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883287	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968092	0.88[ASN][1000 genomes]
rs9968093	0.88[ASN][1000 genomes]
rs9968095	0.96[ASN][1000 genomes]
rs9968097	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1806743	chr3:159723529-159744022	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159712000-159729600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:159713000-159734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:159721000-159730000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:159724600-159726000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:159724600-159726600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:159724800-159726800	Weak transcription	GM12878-XiMat	blood
7	chr3:159724800-159729800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:159724800-159729800	Weak transcription	Osteobl	bone
9	chr3:159725000-159728600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:159725000-159729000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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