Variant report

Variant	rs4563409
Chromosome Location	chr3:143682122-143682123
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	chr3:143680103..143683758-chr3:143690045..143692584,4	MCF-7	breast:
2	chr3:143679544..143684036-chr3:143688020..143692535,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10513234	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10513235	0.81[ASN][1000 genomes]
rs13064130	0.82[ASN][1000 genomes]
rs13078840	0.81[ASN][1000 genomes]
rs1466941	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16854772	0.80[ASN][1000 genomes]
rs17602500	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1992093	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279856	0.92[ASN][1000 genomes]
rs2885197	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34038325	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34071449	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34402874	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35072578	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35211123	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35362423	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35692092	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35716467	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4315684	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4446205	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4535221	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59287916	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60505453	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62267390	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6768153	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs723491	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3349108	chr3:143676303-143692796	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143680400-143689600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:143682000-143682200	Enhancers	H9 Cell Line	embryonic stem cell

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