Variant report

Variant	rs6508904
Chromosome Location	chr19:40186517-40186518
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	chr19:40186332-40186848	HepG2	liver:	n/a	n/a
2	RXRA	chr19:40186323-40186789	HepG2	liver:	n/a	n/a
3	SP1	chr19:40186267-40186871	HepG2	liver:	n/a	n/a
4	EP300	chr19:40186342-40186856	HepG2	liver:	n/a	chr19:40186841-40186855 chr19:40186598-40186608 chr19:40186546-40186556
5	SMC3	chr19:40186463-40186587	HepG2	liver:	n/a	n/a
6	NFIC	chr19:40186355-40186825	HepG2	liver:	n/a	n/a
7	HNF4A	chr19:40186420-40186787	HepG2	liver:	n/a	chr19:40186549-40186557
8	FOXA1	chr19:40186259-40186804	HepG2	liver:	n/a	n/a
9	FOXA2	chr19:40186154-40187603	HepG2	liver:	n/a	n/a
10	HNF4A	chr19:40186498-40186762	HepG2	liver:	n/a	chr19:40186549-40186557
11	ARID3A	chr19:40186329-40186749	HepG2	liver:	n/a	n/a
12	FOXA1	chr19:40186263-40186872	HepG2	liver:	n/a	n/a
13	HDAC2	chr19:40186394-40186806	HepG2	liver:	n/a	chr19:40186599-40186608 chr19:40186547-40186556
14	MYBL2	chr19:40186283-40186872	HepG2	liver:	n/a	n/a
15	FOXA2	chr19:40186369-40186837	HepG2	liver:	n/a	n/a
16	FOXA1	chr19:40186288-40186857	HepG2	liver:	n/a	n/a
17	EP300	chr19:40186374-40186787	HepG2	liver:	n/a	chr19:40186598-40186608 chr19:40186546-40186556
18	BHLHE40	chr19:40186478-40186798	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000240320	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10407647	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409279	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10410864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10755	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1126158	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17608	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2159169	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159170	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286759	0.82[AFR][1000 genomes]
rs35837917	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs364911	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs367529	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs367788	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs372081	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs372902	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs373449	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs375867	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs378917	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs383768	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs384138	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs385240	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs385288	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs385520	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs388648	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs391646	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs391660	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs395892	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs396854	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs399641	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4028673	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412884	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4132248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414423	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs416255	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs418664	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs425218	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs425265	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs428007	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs431329	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs437780	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs439881	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs440191	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs440334	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs44048	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs44049	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs444817	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs444963	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs446425	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs447034	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs453827	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4802054	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4803286	0.81[AFR][1000 genomes]
rs4830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58602176	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61213408	0.82[AFR][1000 genomes]
rs6508903	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249368	0.82[AFR][1000 genomes]
rs7249415	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7249575	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250681	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253094	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7254368	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254761	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255025	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7255040	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7258833	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3355956	chr19:40135051-40188792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3998	chr19:40135120-40188646	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3397881	chr19:40150495-40199437	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv3332670	chr19:40181720-40297955	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr19:40171200-40189000	Weak transcription	Psoas Muscle	Psoas
2	chr19:40184400-40188000	Enhancers	HepG2	liver
3	chr19:40186400-40186800	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr19:40186400-40187400	Enhancers	GM12878-XiMat	blood
5	chr19:40186400-40188400	Enhancers	Placenta	Placenta

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