Variant report

Variant	rs58440244
Chromosome Location	chr4:100378680-100378681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100360736..100361324-chr4:100378145..100379030,2	MCF-7	breast:
2	chr4:100008427..100010318-chr4:100377413..100380370,2	MCF-7	breast:
3	chr4:100039119..100039756-chr4:100378505..100379028,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246090	Chromatin interaction
ENSG00000197894	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12499297	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12499621	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12499625	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12499683	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12501931	0.99[ASN][1000 genomes]
rs12502381	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503219	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504511	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505135	0.93[ASN][1000 genomes]
rs12505224	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12509626	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12510523	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12510823	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510825	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510954	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512792	0.93[ASN][1000 genomes]
rs1354367	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1442477	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2903200	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147549	1.00[ASN][1000 genomes]
rs4699750	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57441592	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60003800	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60156573	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6831961	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853853	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72904927	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72904928	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72904929	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72905000	0.93[ASN][1000 genomes]
rs7670511	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7678920	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7690269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692423	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs930478	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs971074	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3353320	chr4:100147870-100425701	Genic enhancers ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3394995	chr4:100147890-100425671	Enhancers Genic enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv879660	chr4:100284199-100380148	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1847619	chr4:100321443-100430924	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3584519	chr4:100323870-100477462	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv3584520	chr4:100324071-100400696	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100377800-100379400	Enhancers	NHEK	skin
2	chr4:100377800-100379600	Enhancers	HMEC	breast
3	chr4:100378000-100379600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:100378000-100379800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:100378600-100381000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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