Variant report

Variant	rs3802543
Chromosome Location	chr10:46169092-46169093
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	POLR2A	chr10:46167256-46169209	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr10:46167043-46169438	A549	lung:	n/a	n/a
3	MAX	chr10:46167471-46169126	HepG2	liver:	n/a	chr10:46168328-46168337 chr10:46168302-46168312
4	CREB1	chr10:46167581-46169142	HepG2	liver:	n/a	n/a
5	E2F6	chr10:46167430-46169092	H1-hESC	embryonic stem cell:	n/a	chr10:46168306-46168316 chr10:46168302-46168311 chr10:46168344-46168354 chr10:46168226-46168236
6	RFX5	chr10:46167017-46169117	IMR90	lung:	n/a	chr10:46168338-46168347 chr10:46168334-46168349
7	FOXA2	chr10:46168729-46169141	A549	lung:	n/a	n/a
8	POLR2A	chr10:46169069-46169144	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr10:46167570-46169180	HepG2	liver:	n/a	n/a
10	RFX5	chr10:46167020-46169234	SK-N-SH	brain:	n/a	chr10:46168338-46168347 chr10:46168334-46168349
11	FOXA1	chr10:46168631-46169110	HepG2	liver:	n/a	n/a
12	NFIC	chr10:46167506-46169239	ECC-1	luminal epithelium:	n/a	chr10:46168908-46168925 chr10:46168909-46168925
13	MXI1	chr10:46167668-46169106	HepG2	liver:	n/a	chr10:46168338-46168353
14	FOXA1	chr10:46168730-46169117	HepG2	liver:	n/a	n/a
15	NFIC	chr10:46168617-46169109	HepG2	liver:	n/a	chr10:46168908-46168925 chr10:46168909-46168925
16	NFIC	chr10:46167494-46169206	ECC-1	luminal epithelium:	n/a	chr10:46168908-46168925 chr10:46168909-46168925
17	MAX	chr10:46167490-46169137	HepG2	liver:	n/a	chr10:46168328-46168337 chr10:46168302-46168312
18	FOXA1	chr10:46167945-46169100	HepG2	liver:	n/a	n/a
19	MTA3	chr10:46167442-46169256	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ZFAND4	TF binding region

Extended variants
information (count: 171 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs10508896	0.88[ASN][1000 genomes]
rs1060848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12098366	0.88[ASN][1000 genomes]
rs12761573	0.88[ASN][1000 genomes]
rs12762495	0.82[ASN][1000 genomes]
rs12763285	0.88[ASN][1000 genomes]
rs12764693	0.82[ASN][1000 genomes]
rs12765244	0.88[ASN][1000 genomes]
rs12766764	0.88[ASN][1000 genomes]
rs12771659	0.83[EUR][1000 genomes]
rs12772102	0.88[ASN][1000 genomes]
rs12774453	0.88[ASN][1000 genomes]
rs12775527	0.82[ASN][1000 genomes]
rs12776291	0.88[ASN][1000 genomes]
rs12777172	0.88[ASN][1000 genomes]
rs12778143	0.88[ASN][1000 genomes]
rs12779005	0.88[ASN][1000 genomes]
rs12779198	0.82[ASN][1000 genomes]
rs12779204	0.88[ASN][1000 genomes]
rs12779637	0.88[ASN][1000 genomes]
rs12779976	0.88[ASN][1000 genomes]
rs12781186	0.82[ASN][1000 genomes]
rs12781506	0.88[ASN][1000 genomes]
rs12783233	0.82[ASN][1000 genomes]
rs17157859	1.00[AFR][1000 genomes]
rs17157861	1.00[AFR][1000 genomes]
rs17157880	0.82[ASN][1000 genomes]
rs17157884	0.82[ASN][1000 genomes]
rs17157885	0.82[ASN][1000 genomes]
rs17157887	0.82[ASN][1000 genomes]
rs17157890	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17157898	0.88[ASN][1000 genomes]
rs17157919	0.88[ASN][1000 genomes]
rs17157928	0.88[ASN][1000 genomes]
rs17157931	0.88[ASN][1000 genomes]
rs17157941	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17157944	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17157945	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157971	0.89[EUR][1000 genomes]
rs17158898	0.81[EUR][1000 genomes]
rs17159059	0.89[EUR][1000 genomes]
rs17159087	0.89[EUR][1000 genomes]
rs17159090	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17159113	0.94[EUR][1000 genomes]
rs17159119	0.85[EUR][1000 genomes]
rs17451208	0.88[ASN][1000 genomes]
rs17696005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696112	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17768650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17768692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768852	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1868622	0.80[EUR][1000 genomes]
rs2197982	0.92[EUR][1000 genomes]
rs33997730	0.80[ASN][1000 genomes]
rs34011467	0.88[ASN][1000 genomes]
rs34138033	0.88[ASN][1000 genomes]
rs34144887	0.88[ASN][1000 genomes]
rs34163035	0.88[ASN][1000 genomes]
rs34195613	0.88[ASN][1000 genomes]
rs34309840	0.88[ASN][1000 genomes]
rs34383275	0.88[ASN][1000 genomes]
rs34516867	0.88[ASN][1000 genomes]
rs34539215	0.88[ASN][1000 genomes]
rs34574958	0.88[ASN][1000 genomes]
rs34604216	0.88[ASN][1000 genomes]
rs34618850	0.88[ASN][1000 genomes]
rs34670342	0.88[ASN][1000 genomes]
rs34793991	0.88[ASN][1000 genomes]
rs34897497	0.82[ASN][1000 genomes]
rs35001302	0.88[ASN][1000 genomes]
rs35003524	0.88[ASN][1000 genomes]
rs35034867	0.88[ASN][1000 genomes]
rs35036712	0.88[ASN][1000 genomes]
rs35047800	0.88[ASN][1000 genomes]
rs35049879	0.88[ASN][1000 genomes]
rs35070150	0.88[ASN][1000 genomes]
rs35131026	0.82[ASN][1000 genomes]
rs35150810	0.88[ASN][1000 genomes]
rs35183191	0.88[ASN][1000 genomes]
rs35183751	0.88[ASN][1000 genomes]
rs35331393	0.88[ASN][1000 genomes]
rs35506889	0.88[ASN][1000 genomes]
rs35585999	0.88[ASN][1000 genomes]
rs35626777	0.88[ASN][1000 genomes]
rs35629170	0.88[ASN][1000 genomes]
rs35639934	0.88[ASN][1000 genomes]
rs35670420	0.88[ASN][1000 genomes]
rs35713143	0.88[ASN][1000 genomes]
rs35750365	0.82[ASN][1000 genomes]
rs35775604	0.83[ASN][1000 genomes]
rs35824277	0.88[ASN][1000 genomes]
rs35902429	0.82[ASN][1000 genomes]
rs35916836	0.88[ASN][1000 genomes]
rs35934513	0.88[ASN][1000 genomes]
rs35968565	0.88[ASN][1000 genomes]
rs36052429	0.82[ASN][1000 genomes]
rs36053776	0.88[ASN][1000 genomes]
rs36054203	0.88[ASN][1000 genomes]
rs36070535	0.82[ASN][1000 genomes]
rs36074276	0.88[ASN][1000 genomes]
rs36100685	0.88[ASN][1000 genomes]
rs36102549	0.83[ASN][1000 genomes]
rs36109121	0.88[ASN][1000 genomes]
rs41301625	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41301629	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301631	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4418752	1.00[EUR][1000 genomes]
rs4442500	0.88[ASN][1000 genomes]
rs4576771	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55814534	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56034881	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56277479	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56388386	0.94[EUR][1000 genomes]
rs57279747	0.94[EUR][1000 genomes]
rs58849111	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59689764	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60791882	0.88[ASN][1000 genomes]
rs71496608	0.82[ASN][1000 genomes]
rs71496609	0.82[ASN][1000 genomes]
rs71496610	0.82[ASN][1000 genomes]
rs71496611	0.82[ASN][1000 genomes]
rs71496612	0.88[ASN][1000 genomes]
rs71496613	0.88[ASN][1000 genomes]
rs71496614	0.88[ASN][1000 genomes]
rs71496618	0.88[ASN][1000 genomes]
rs71496619	0.88[ASN][1000 genomes]
rs71496620	0.88[ASN][1000 genomes]
rs71496621	0.88[ASN][1000 genomes]
rs71496622	0.88[ASN][1000 genomes]
rs71496623	0.88[ASN][1000 genomes]
rs71496624	0.88[ASN][1000 genomes]
rs71496625	0.88[ASN][1000 genomes]
rs71499567	0.88[ASN][1000 genomes]
rs73291115	0.88[ASN][1000 genomes]
rs73291121	0.88[ASN][1000 genomes]
rs73291122	0.88[ASN][1000 genomes]
rs73291195	0.88[ASN][1000 genomes]
rs73291198	0.88[ASN][1000 genomes]
rs73292811	1.00[EUR][1000 genomes]
rs73292848	1.00[EUR][1000 genomes]
rs74128806	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7898761	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9422439	0.88[ASN][1000 genomes]
rs9422440	0.88[ASN][1000 genomes]
rs9422441	0.88[ASN][1000 genomes]
rs9422442	0.88[ASN][1000 genomes]
rs9422650	0.88[ASN][1000 genomes]
rs9422651	0.88[ASN][1000 genomes]
rs9422652	0.88[ASN][1000 genomes]
rs9422653	0.88[ASN][1000 genomes]
rs9422654	0.88[ASN][1000 genomes]
rs9422655	0.88[ASN][1000 genomes]
rs9422657	0.88[ASN][1000 genomes]
rs9422658	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv3392795	chr10:46147995-46170942	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1045014	chr10:46148750-46814526	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv2754498	chr10:46148750-47136996	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv540591	chr10:46153700-47140487	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1044906	chr10:46153700-47148281	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv540592	chr10:46153700-47148281	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv870020	chr10:46158215-47148490	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1040524	chr10:46160537-47122043	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
13	nsv1038499	chr10:46160537-47140487	Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv540593	chr10:46160537-47140487	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv1055132	chr10:46160537-47148281	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv540594	chr10:46160537-47148281	Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3802543	ZFAND4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46167000-46169200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr10:46167000-46169200	Active TSS	Fetal Kidney	kidney
3	chr10:46168400-46169200	Flanking Active TSS	NHEK	skin
4	chr10:46168600-46169200	Enhancers	Spleen	Spleen
5	chr10:46168600-46169200	Flanking Bivalent TSS/Enh	HepG2	liver
6	chr10:46168800-46169200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:46168800-46169200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr10:46168800-46169200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:46168800-46169200	Enhancers	Right Ventricle	heart
10	chr10:46168800-46169800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:46169000-46169200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr10:46169000-46169200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr10:46169000-46169200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr10:46169000-46169200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:46169000-46169200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:46169000-46169200	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr10:46169000-46169200	Enhancers	Adipose Nuclei	Adipose
18	chr10:46169000-46169200	Flanking Active TSS	Liver	Liver
19	chr10:46169000-46169200	Enhancers	Fetal Heart	heart
20	chr10:46169000-46169200	Enhancers	Fetal Muscle Leg	muscle
21	chr10:46169000-46169200	Enhancers	Stomach Mucosa	stomach

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