Variant report

Variant	rs9396140
Chromosome Location	chr6:55579345-55579346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:55573574..55576320-chr6:55577711..55581469,3	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10948951	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11970729	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173380	0.97[ASN][1000 genomes]
rs17732188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17732224	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17732324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17732451	1.00[ASN][1000 genomes]
rs2065026	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228139	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs228152	1.00[ASW][hapmap]
rs28654252	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756991	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6915090	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72865341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72865350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349789	0.91[ASN][1000 genomes]
rs9349791	0.97[ASN][1000 genomes]
rs9357875	0.97[ASN][1000 genomes]
rs9367652	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367653	1.00[ASN][1000 genomes]
rs9367654	1.00[ASN][1000 genomes]
rs9367655	1.00[ASN][1000 genomes]
rs9367661	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370450	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370451	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370452	1.00[ASN][1000 genomes]
rs9370453	1.00[ASN][1000 genomes]
rs9370454	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370456	0.97[ASN][1000 genomes]
rs9382529	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382531	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382532	1.00[ASN][1000 genomes]
rs9382535	1.00[ASN][1000 genomes]
rs9382536	1.00[ASN][1000 genomes]
rs9382537	1.00[ASN][1000 genomes]
rs9382538	1.00[ASN][1000 genomes]
rs9382540	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382549	0.97[ASN][1000 genomes]
rs9382550	0.97[ASN][1000 genomes]
rs9382551	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9396138	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396141	1.00[ASN][1000 genomes]
rs9396142	1.00[ASN][1000 genomes]
rs9396143	0.97[ASN][1000 genomes]
rs9396144	1.00[ASN][1000 genomes]
rs9396145	1.00[ASN][1000 genomes]
rs9396148	0.97[ASN][1000 genomes]
rs9396149	0.97[ASN][1000 genomes]
rs9396150	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9396151	0.97[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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1026411	chr6:55372845-55653498	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885905	chr6:55539010-55596618	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv885906	chr6:55539010-55612431	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv885907	chr6:55539010-55621377	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885908	chr6:55539010-55625041	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv885909	chr6:55539010-55674338	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr6:55577600-55580200	Enhancers	Fetal Lung	lung
2	chr6:55579000-55579400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:55579200-55579600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:55579200-55579600	Enhancers	Fetal Muscle Leg	muscle
5	chr6:55579200-55584800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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