Variant report

Variant	rs6868833
Chromosome Location	chr5:29162813-29162814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr5:29162343-29162841	HepG2	liver:	n/a	chr5:29162581-29162596 chr5:29162596-29162611
2	FOXA1	chr5:29162440-29162838	HepG2	liver:	n/a	chr5:29162581-29162596 chr5:29162596-29162611

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDH6-2	chr5:29162522-29162847	NONHSAT100838

Variant related genes	Relation type
ENSG00000259786	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10940780	0.89[EUR][1000 genomes]
rs10940782	0.89[EUR][1000 genomes]
rs10940783	0.89[EUR][1000 genomes]
rs12518840	0.89[EUR][1000 genomes]
rs1390658	0.88[EUR][1000 genomes]
rs1390659	0.88[EUR][1000 genomes]
rs1390661	0.88[EUR][1000 genomes]
rs1496417	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs160304	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs160305	0.91[EUR][1000 genomes]
rs160306	0.93[EUR][1000 genomes]
rs160326	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1687612	0.88[EUR][1000 genomes]
rs1687613	0.88[EUR][1000 genomes]
rs1692342	0.88[EUR][1000 genomes]
rs1692345	0.87[EUR][1000 genomes]
rs1692348	0.88[EUR][1000 genomes]
rs177935	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs251062	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs251070	0.81[EUR][1000 genomes]
rs2618418	0.88[EUR][1000 genomes]
rs2644937	0.91[EUR][1000 genomes]
rs2644949	0.88[EUR][1000 genomes]
rs2932806	0.93[EUR][1000 genomes]
rs309667	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309668	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309669	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309674	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs309683	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309685	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309686	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309689	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309694	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4507498	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs474325	0.89[EUR][1000 genomes]
rs477865	0.89[EUR][1000 genomes]
rs480650	0.88[EUR][1000 genomes]
rs484786	0.91[EUR][1000 genomes]
rs489449	0.91[EUR][1000 genomes]
rs506533	0.91[EUR][1000 genomes]
rs506623	0.89[EUR][1000 genomes]
rs508549	0.91[EUR][1000 genomes]
rs509431	0.88[EUR][1000 genomes]
rs509455	0.91[EUR][1000 genomes]
rs514676	0.88[EUR][1000 genomes]
rs515977	0.93[EUR][1000 genomes]
rs516107	0.88[EUR][1000 genomes]
rs516178	0.93[EUR][1000 genomes]
rs516480	0.88[EUR][1000 genomes]
rs519037	0.88[EUR][1000 genomes]
rs520652	0.93[EUR][1000 genomes]
rs520670	0.88[EUR][1000 genomes]
rs521714	0.88[EUR][1000 genomes]
rs523336	0.93[EUR][1000 genomes]
rs533948	0.91[EUR][1000 genomes]
rs534864	0.91[EUR][1000 genomes]
rs535850	0.91[EUR][1000 genomes]
rs536846	0.91[EUR][1000 genomes]
rs537697	0.91[EUR][1000 genomes]
rs547220	0.87[EUR][1000 genomes]
rs547299	0.87[EUR][1000 genomes]
rs557997	0.88[EUR][1000 genomes]
rs583745	0.91[EUR][1000 genomes]
rs593372	0.87[EUR][1000 genomes]
rs594211	0.88[EUR][1000 genomes]
rs594297	0.88[EUR][1000 genomes]
rs594842	0.91[EUR][1000 genomes]
rs595097	0.86[EUR][1000 genomes]
rs596766	0.91[EUR][1000 genomes]
rs597694	0.91[EUR][1000 genomes]
rs602489	0.88[EUR][1000 genomes]
rs603756	0.88[EUR][1000 genomes]
rs603837	0.88[EUR][1000 genomes]
rs605997	0.87[EUR][1000 genomes]
rs607286	0.88[EUR][1000 genomes]
rs610094	0.91[EUR][1000 genomes]
rs613237	0.82[EUR][1000 genomes]
rs617084	0.88[EUR][1000 genomes]
rs644330	0.91[EUR][1000 genomes]
rs656260	0.93[EUR][1000 genomes]
rs658439	0.93[EUR][1000 genomes]
rs700897	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs824326	0.94[EUR][1000 genomes]
rs824327	0.94[EUR][1000 genomes]
rs824329	0.92[EUR][1000 genomes]
rs824331	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs824342	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs824343	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023990	chr5:28917253-29220447	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3528360	chr5:29069255-29548659	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv3528361	chr5:29069255-29548659	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1022253	chr5:29076460-29195987	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1016603	chr5:29102713-29843965	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv537712	chr5:29102713-29843965	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv1030526	chr5:29125802-29204186	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv964827	chr5:29138557-29198352	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:29161200-29163200	Enhancers	Liver	Liver

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