Variant report

Variant	rs6050390
Chromosome Location	chr20:25146781-25146782
allele	A/G
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	FOSL2	chr20:25146715-25147067	HepG2	liver:	n/a	n/a
2	HNF4A	chr20:25146718-25147022	HepG2	liver:	n/a	n/a
3	JUND	chr20:25146740-25147031	HepG2	liver:	n/a	n/a
4	FOXA2	chr20:25146755-25147275	A549	lung:	n/a	n/a
5	FOXA1	chr20:25146679-25147202	HepG2	liver:	n/a	chr20:25146935-25146950
6	FOXA2	chr20:25146677-25147116	A549	lung:	n/a	n/a
7	FOXA1	chr20:25146649-25147213	HepG2	liver:	n/a	chr20:25146935-25146950
8	HNF4A	chr20:25146756-25147019	HepG2	liver:	n/a	n/a
9	TCF12	chr20:25146758-25146986	HepG2	liver:	n/a	n/a
10	FOXA2	chr20:25146533-25147345	HepG2	liver:	n/a	n/a
11	YY1	chr20:25146658-25147100	HepG2	liver:	n/a	n/a
12	EP300	chr20:25146758-25147006	HepG2	liver:	n/a	n/a
13	RXRA	chr20:25146763-25146977	HepG2	liver:	n/a	n/a
14	SP1	chr20:25146664-25147156	HepG2	liver:	n/a	n/a
15	HNF4G	chr20:25146702-25147026	HepG2	liver:	n/a	n/a
16	FOXA1	chr20:25146642-25147074	HepG2	liver:	n/a	chr20:25146935-25146950

Variant related genes	Relation type
ENSG00000225344	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1108810	0.83[ASN][1000 genomes]
rs1108811	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11698226	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11699149	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11699219	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11699614	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12625069	0.83[ASN][1000 genomes]
rs13036626	0.93[ASN][1000 genomes]
rs13037201	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13037374	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13039237	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13041051	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13043355	0.81[ASN][1000 genomes]
rs13043906	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13045280	0.82[ASN][1000 genomes]
rs13045481	0.84[EUR][1000 genomes]
rs2038182	0.94[ASN][1000 genomes]
rs2103715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179639	0.87[ASN][1000 genomes]
rs2235770	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2892314	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34631700	0.82[ASN][1000 genomes]
rs35047430	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35231728	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36115891	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815388	0.94[ASN][1000 genomes]
rs4815389	0.94[ASN][1000 genomes]
rs6037025	0.81[ASN][1000 genomes]
rs6037028	0.83[ASN][1000 genomes]
rs6037029	0.83[ASN][1000 genomes]
rs6037030	0.82[ASN][1000 genomes]
rs6037031	0.81[ASN][1000 genomes]
rs6037038	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6037049	0.94[ASN][1000 genomes]
rs6037052	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6050341	0.82[ASN][1000 genomes]
rs6050351	0.82[ASN][1000 genomes]
rs6050397	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6050399	0.94[ASN][1000 genomes]
rs6050400	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050403	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050404	0.93[ASN][1000 genomes]
rs6050406	0.91[ASN][1000 genomes]
rs6050408	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6050409	0.83[ASN][1000 genomes]
rs6050410	0.86[ASN][1000 genomes]
rs6050411	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6050412	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6050413	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6050415	0.87[ASN][1000 genomes]
rs6050418	0.87[ASN][1000 genomes]
rs6050419	0.87[ASN][1000 genomes]
rs6050421	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6107013	0.84[ASN][1000 genomes]
rs6115069	0.94[ASN][1000 genomes]
rs6132804	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6132810	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6132812	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132816	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138492	0.88[EUR][1000 genomes]
rs6138493	0.90[EUR][1000 genomes]
rs6138496	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138504	0.83[ASN][1000 genomes]
rs6138506	0.83[ASN][1000 genomes]
rs6138510	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138511	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138519	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138520	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138521	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138528	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138530	0.93[ASN][1000 genomes]
rs6138531	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138532	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6138533	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6515614	0.87[ASN][1000 genomes]
rs7261718	0.82[ASN][1000 genomes]
rs7270433	0.82[ASN][1000 genomes]
rs7270464	0.83[ASN][1000 genomes]
rs7272141	0.81[ASN][1000 genomes]
rs8119777	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs910101	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
13	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
17	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25146000-25148000	Enhancers	HepG2	liver
2	chr20:25146400-25146800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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