Variant report

Variant	rs4260404
Chromosome Location	chr3:141581203-141581204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141580131..141582651-chr3:141594440..141596950,2	MCF-7	breast:
2	chr3:141577387..141581642-chr3:141595422..141599021,5	K562	blood:
3	chr3:141581084..141582668-chr3:141665975..141668647,2	K562	blood:
4	chr3:141578935..141581204-chr3:141581944..141585535,3	K562	blood:

Variant related genes	Relation type
ENSG00000269905	Chromatin interaction
ENSG00000228398	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1073464	0.81[CEU][hapmap];0.80[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12386355	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13059220	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13061474	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13067998	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13069329	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082115	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13086153	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1897139	0.81[CEU][hapmap];0.80[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35681935	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5013124	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7636902	0.89[YRI][hapmap]
rs8179925	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8179994	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9810380	0.81[CEU][hapmap];0.80[CHB][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9822066	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9827902	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9836116	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850595	0.81[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9855878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9858477	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9873028	0.82[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9878540	1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.81[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv965218	chr3:141580574-141584429	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141573000-141582000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:141579400-141583200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:141579800-141582000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:141579800-141582000	Weak transcription	Left Ventricle	heart
5	chr3:141579800-141583800	Weak transcription	Lung	lung
6	chr3:141580000-141584000	Weak transcription	Right Ventricle	heart
7	chr3:141580200-141582400	Weak transcription	Adipose Nuclei	Adipose
8	chr3:141580400-141581800	Enhancers	K562	blood
9	chr3:141580600-141582000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:141580600-141582200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:141580800-141588600	Weak transcription	HUVEC	blood vessel
12	chr3:141581000-141581400	Weak transcription	Monocytes-CD14+_RO01746	blood

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