Variant report

Variant	rs4342427
Chromosome Location	chr6:55819077-55819078
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	chr6:55309906..55311058-chr6:55817976..55819297,5	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1883703	0.87[ASN][1000 genomes]
rs1900528	0.81[ASN][1000 genomes]
rs2009726	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206681	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250848	0.86[ASN][1000 genomes]
rs2745739	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2745741	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2745742	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2745744	0.82[ASN][1000 genomes]
rs2745745	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745746	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2745747	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2843539	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843540	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2843541	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843542	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2843543	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4130775	0.81[ASN][1000 genomes]
rs4299832	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341007	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432971	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4712110	0.81[ASN][1000 genomes]
rs4715569	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56232118	0.82[ASN][1000 genomes]
rs6459119	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6459120	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6911711	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6925035	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72870667	0.81[ASN][1000 genomes]
rs72872205	0.81[ASN][1000 genomes]
rs9357881	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370474	0.81[ASN][1000 genomes]
rs9370475	0.96[ASN][1000 genomes]
rs9370476	0.81[ASN][1000 genomes]
rs9382569	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396164	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464306	0.80[AMR][1000 genomes]
rs9464316	0.81[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	nsv1024174	chr6:55713889-55829936	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1029301	chr6:55713889-55834480	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv830665	chr6:55755560-55920219	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv5312	chr6:55784991-55830051	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 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	chr6:55816600-55820600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:55818400-55822200	Weak transcription	Fetal Lung	lung
3	chr6:55818400-55823000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:55818600-55819400	Weak transcription	Fetal Heart	heart
5	chr6:55818600-55822600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:55818600-55822800	Weak transcription	NHDF-Ad	bronchial
7	chr6:55818600-55827600	Weak transcription	Colon Smooth Muscle	Colon

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