Variant report

Variant	rs55930543
Chromosome Location	chr4:87450560-87450561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87450415..87452912-chr4:87515354..87517183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163629	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10023787	0.81[ASN][1000 genomes]
rs10031843	0.84[ASN][1000 genomes]
rs11097115	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11947775	0.93[ASN][1000 genomes]
rs1481833	0.82[ASN][1000 genomes]
rs17011924	0.87[ASN][1000 genomes]
rs17418221	0.88[ASN][1000 genomes]
rs17418531	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17418801	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17418878	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17419295	0.82[ASN][1000 genomes]
rs17452467	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17452556	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28483710	0.82[ASN][1000 genomes]
rs28485273	0.82[ASN][1000 genomes]
rs28529445	0.84[ASN][1000 genomes]
rs28534599	0.82[ASN][1000 genomes]
rs28663376	0.82[ASN][1000 genomes]
rs28678816	0.81[ASN][1000 genomes]
rs28735881	0.82[ASN][1000 genomes]
rs4235081	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4277747	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4404513	0.89[ASN][1000 genomes]
rs4405982	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4407468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452393	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4466012	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4511966	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4513526	0.82[ASN][1000 genomes]
rs4529013	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4552430	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4607180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622964	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4640633	0.94[ASN][1000 genomes]
rs4693147	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693772	0.93[ASN][1000 genomes]
rs4693776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693777	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55653332	0.93[ASN][1000 genomes]
rs55654230	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55660529	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55722156	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55746316	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55757426	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55773619	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55814693	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55842318	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55872468	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55879246	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55881335	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55908925	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55969415	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55982489	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56009992	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56150118	0.84[ASN][1000 genomes]
rs56164000	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56178389	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56222033	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56296936	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56348925	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56353461	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59644743	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61152200	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6531932	0.81[ASN][1000 genomes]
rs66669421	0.82[ASN][1000 genomes]
rs67274037	0.82[ASN][1000 genomes]
rs67341369	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs67523832	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67928053	0.82[ASN][1000 genomes]
rs6822396	0.91[ASN][1000 genomes]
rs6838659	0.93[ASN][1000 genomes]
rs6847139	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72664002	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665711	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665712	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665714	0.93[ASN][1000 genomes]
rs72665719	0.94[ASN][1000 genomes]
rs72665722	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72665724	0.96[ASN][1000 genomes]
rs72665725	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72665729	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665740	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665744	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665746	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665752	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665753	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665756	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665759	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72665762	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72665769	0.85[ASN][1000 genomes]
rs72665771	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72665772	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs72665777	0.82[ASN][1000 genomes]
rs7435744	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673698	0.93[ASN][1000 genomes]
rs7675845	0.85[ASN][1000 genomes]
rs7694723	0.82[ASN][1000 genomes]
rs7695011	0.93[ASN][1000 genomes]
rs7697819	0.90[ASN][1000 genomes]
rs9307020	0.82[ASN][1000 genomes]
rs9683663	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9993042	0.84[ASN][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	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 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	chr4:87432000-87464800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:87438000-87465200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:87443200-87468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:87445200-87458000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:87448400-87463400	Weak transcription	Lung	lung
6	chr4:87450000-87450600	Enhancers	Fetal Lung	lung
7	chr4:87450400-87450600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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