Variant report

Variant	rs28542140
Chromosome Location	chr3:101662503-101662504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101655492..101658302-chr3:101660937..101663877,2	MCF-7	breast:
2	chr3:101661155..101664150-chr3:101664624..101666610,2	K562	blood:
3	chr3:101658485..101660497-chr3:101661357..101663143,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214407	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10470501	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1081574	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1081576	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1088047	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1091320	0.87[EUR][1000 genomes]
rs1378838	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1513118	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1672380	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1672386	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1707608	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1707613	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1707618	0.83[EUR][1000 genomes]
rs1707619	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2860329	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2925323	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2925325	0.85[EUR][1000 genomes]
rs2925326	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs797866	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9869373	0.86[EUR][1000 genomes]
rs9881690	0.87[AMR][1000 genomes];0.91[EUR][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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1010762	chr3:101584836-101803821	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101654000-101662800	Enhancers	Primary B cells from peripheral blood	blood
2	chr3:101656200-101662800	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr3:101659800-101662600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:101659800-101662800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr3:101660000-101663800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:101660200-101667800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:101660400-101669200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:101661400-101662800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:101661400-101662800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr3:101661400-101664600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:101661600-101662600	Enhancers	Primary B cells from cord blood	blood
12	chr3:101661600-101662800	Enhancers	GM12878-XiMat	blood
13	chr3:101661600-101663800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:101661600-101669000	Weak transcription	NH-A	brain
15	chr3:101661600-101669400	Weak transcription	HSMM	muscle
16	chr3:101661800-101678000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:101662000-101662800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:101662200-101664800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:101662400-101664800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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