Variant report

Variant	rs12575840
Chromosome Location	chr7:55645323-55645324
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	chr7:55638719..55641008-chr7:55642505..55645934,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223475	Chromatin interaction
ENSG00000154978	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10741703	0.80[AFR][1000 genomes]
rs10741709	0.83[AMR][1000 genomes]
rs10766329	0.84[EUR][1000 genomes]
rs10766331	0.85[EUR][1000 genomes]
rs10766337	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10766343	0.84[AMR][1000 genomes]
rs10832622	0.83[EUR][1000 genomes]
rs10832627	0.84[EUR][1000 genomes]
rs10832628	0.84[EUR][1000 genomes]
rs10832629	0.85[EUR][1000 genomes]
rs10832635	0.85[EUR][1000 genomes]
rs10832637	0.85[EUR][1000 genomes]
rs10832639	0.85[EUR][1000 genomes]
rs10832640	0.85[EUR][1000 genomes]
rs10832642	0.87[EUR][1000 genomes]
rs10832643	0.87[EUR][1000 genomes]
rs10832647	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832648	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10832668	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832671	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10832672	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10832674	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11023962	0.83[EUR][1000 genomes]
rs11023981	0.85[EUR][1000 genomes]
rs11023988	0.91[EUR][1000 genomes]
rs11024012	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11024033	0.85[AMR][1000 genomes]
rs11529132	0.84[EUR][1000 genomes]
rs11529582	0.83[EUR][1000 genomes]
rs12270317	0.85[EUR][1000 genomes]
rs12271656	0.84[EUR][1000 genomes]
rs12276256	0.84[EUR][1000 genomes]
rs12283896	0.90[EUR][1000 genomes]
rs12289091	0.94[EUR][1000 genomes]
rs12289093	0.91[EUR][1000 genomes]
rs12289098	0.81[EUR][1000 genomes]
rs12295506	0.81[EUR][1000 genomes]
rs12574185	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12576360	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12794400	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12806064	0.82[EUR][1000 genomes]
rs34840028	0.91[EUR][1000 genomes]
rs35223308	0.84[EUR][1000 genomes]
rs36002981	0.83[AMR][1000 genomes]
rs4492775	0.83[EUR][1000 genomes]
rs4511252	0.89[EUR][1000 genomes]
rs4525190	0.85[EUR][1000 genomes]
rs4536174	0.84[EUR][1000 genomes]
rs4603269	0.91[EUR][1000 genomes]
rs56965201	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57248274	0.84[EUR][1000 genomes]
rs60439454	0.84[EUR][1000 genomes]
rs6486296	0.93[EUR][1000 genomes]
rs6486298	0.94[EUR][1000 genomes]
rs6486300	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7103094	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7109995	0.85[AMR][1000 genomes]
rs7111016	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7115099	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7116121	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7117636	0.84[EUR][1000 genomes]
rs7118181	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7126577	0.83[EUR][1000 genomes]
rs7127280	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7128876	0.84[AMR][1000 genomes]
rs7129286	0.85[EUR][1000 genomes]
rs7924787	0.85[EUR][1000 genomes]
rs7927904	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7928885	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7935041	0.94[EUR][1000 genomes]
rs7937139	0.85[EUR][1000 genomes]
rs7942856	0.89[EUR][1000 genomes]
rs7943712	0.84[EUR][1000 genomes]
rs7945295	0.87[EUR][1000 genomes]
rs7945898	0.83[EUR][1000 genomes]
rs7951676	0.85[AMR][1000 genomes]
rs9988855	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv1016349	chr7:55618646-55724541	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1019204	chr7:55620604-55724518	Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv916996	chr7:55628517-55728507	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv469822	chr7:55630280-55792932	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv482409	chr7:55630280-55792932	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1020959	chr7:55632524-55668503	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55642600-55649800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:55642600-55650600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:55643200-55649800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr7:55643400-55649800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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