Variant report

Variant	rs55647727
Chromosome Location	chr3:179726875-179726876
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179722123..179723923-chr3:179725732..179727617,2	MCF-7	breast:
2	chr3:179721672..179723580-chr3:179725340..179727242,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PEX5L-1	chr3:179725969-179727107	ucscGeneNc_uc003fjb_1

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10513766	0.92[ASN][1000 genomes]
rs12054131	0.92[ASN][1000 genomes]
rs1522123	0.92[ASN][1000 genomes]
rs1568553	0.92[ASN][1000 genomes]
rs2031045	0.92[ASN][1000 genomes]
rs41463648	0.92[ASN][1000 genomes]
rs41513245	0.92[ASN][1000 genomes]
rs55801919	0.92[ASN][1000 genomes]
rs55829880	0.92[ASN][1000 genomes]
rs55856121	0.84[ASN][1000 genomes]
rs55895012	0.84[ASN][1000 genomes]
rs55903935	0.92[ASN][1000 genomes]
rs55952695	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs55996513	0.92[ASN][1000 genomes]
rs56006824	0.92[ASN][1000 genomes]
rs56100025	0.92[ASN][1000 genomes]
rs56116940	0.92[ASN][1000 genomes]
rs56145741	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs56273619	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs56335806	0.92[ASN][1000 genomes]
rs56362569	0.92[ASN][1000 genomes]
rs56378746	0.84[ASN][1000 genomes]
rs57313970	0.84[ASN][1000 genomes]
rs57943546	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6443686	0.92[ASN][1000 genomes]
rs66486754	0.92[ASN][1000 genomes]
rs66810269	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs66906982	0.92[ASN][1000 genomes]
rs66924709	0.92[ASN][1000 genomes]
rs67219312	0.84[ASN][1000 genomes]
rs6771088	0.92[ASN][1000 genomes]
rs6781338	0.92[ASN][1000 genomes]
rs6789142	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs68011865	0.92[ASN][1000 genomes]
rs6804267	0.84[ASN][1000 genomes]
rs6806193	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6809015	0.92[ASN][1000 genomes]
rs68185071	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs68188167	0.92[ASN][1000 genomes]
rs73178101	0.92[ASN][1000 genomes]
rs73180003	0.92[ASN][1000 genomes]
rs73180017	0.92[ASN][1000 genomes]
rs73180024	0.92[ASN][1000 genomes]
rs73180036	0.92[ASN][1000 genomes]
rs73180045	0.92[ASN][1000 genomes]
rs73180054	0.92[ASN][1000 genomes]
rs73180061	0.84[ASN][1000 genomes]
rs73180077	0.84[ASN][1000 genomes]
rs73180081	0.84[ASN][1000 genomes]
rs73180085	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73180087	0.84[ASN][1000 genomes]
rs73180091	0.84[ASN][1000 genomes]
rs73180095	0.84[ASN][1000 genomes]
rs73180097	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7627389	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7645574	0.92[ASN][1000 genomes]
rs9290689	0.92[ASN][1000 genomes]
rs9809837	0.92[ASN][1000 genomes]
rs9816489	0.92[ASN][1000 genomes]
rs9828241	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9828328	0.92[ASN][1000 genomes]
rs9849079	0.92[ASN][1000 genomes]
rs9855659	0.92[ASN][1000 genomes]
rs9861123	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr3:179725200-179727000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:179725800-179727000	ZNF genes & repeats	Dnd41	blood
3	chr3:179726000-179754200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:179726400-179728800	Weak transcription	Brain Hippocampus Middle	brain

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