Variant report

Variant	rs6798562
Chromosome Location	chr3:179726524-179726525
allele	G/T
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: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11918999	1.00[ASN][1000 genomes]
rs12107616	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314236	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13433950	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13434137	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13434299	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34523880	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855114	1.00[ASN][1000 genomes]
rs6765550	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770389	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6770956	0.81[AFR][1000 genomes]
rs6773711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778485	0.81[AFR][1000 genomes]
rs6780178	1.00[ASN][1000 genomes]
rs6780400	1.00[ASN][1000 genomes]
rs6781524	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6783759	0.81[AFR][1000 genomes]
rs6804558	1.00[ASN][1000 genomes]
rs6809211	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73883447	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73883448	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73883457	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73883458	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611246	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7618538	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7640403	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7643575	1.00[ASN][1000 genomes]
rs7652816	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824887	1.00[ASN][1000 genomes]
rs9842944	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9853277	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9868787	1.00[ASN][1000 genomes]
rs9870834	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9873975	1.00[ASN][1000 genomes]
rs9880614	1.00[ASN][1000 genomes]
rs9968146	0.87[EUR][1000 genomes];1.00[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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