Variant report

Variant	rs1872409
Chromosome Location	chr3:154920562-154920563
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:154893479..154895537-chr3:154919660..154921908,2	MCF-7	breast:
2	chr3:154913287..154916042-chr3:154917763..154920645,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1021215	0.84[AMR][1000 genomes]
rs1117032	0.84[AMR][1000 genomes]
rs12633611	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1385483	0.84[AMR][1000 genomes]
rs1485241	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1485243	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1485245	0.83[AMR][1000 genomes]
rs17386464	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865865	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1982761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062373	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2171016	0.84[AMR][1000 genomes]
rs2171017	0.84[AMR][1000 genomes]
rs2315043	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2315045	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2315046	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3846024	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3846025	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4542981	0.84[AMR][1000 genomes]
rs4680155	0.91[AMR][1000 genomes]
rs58249938	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6763127	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6770273	0.81[AMR][1000 genomes]
rs6779750	0.84[AMR][1000 genomes]
rs723604	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs724381	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7610296	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7614556	0.88[AMR][1000 genomes]
rs7626407	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7643411	0.86[AMR][1000 genomes]
rs9713914	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984920	0.84[AMR][1000 genomes]
rs9869815	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534289	chr3:154535584-154987166	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv532663	chr3:154561578-154960353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv1000753	chr3:154848433-155207022	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv536773	chr3:154848433-155207022	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv829762	chr3:154879350-155052986	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:154915400-154925600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:154918600-154923000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:154920200-154920800	Enhancers	NHDF-Ad	bronchial
4	chr3:154920200-154921600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:154920400-154920600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:154920400-154920800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:154920400-154921000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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