Variant report

Variant	rs4617171
Chromosome Location	chr8:20557530-20557531
allele	A/C
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	ZNF143	chr8:20557523-20557723	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr8:20557184-20557838	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr8:20557350-20557821	H1-neurons	neurons:	n/a	n/a
4	REST	chr8:20556815-20558111	H1-neurons	neurons:	n/a	chr8:20557955-20557975 chr8:20556926-20556944
5	MAX	chr8:20557447-20557654	H1-hESC	embryonic stem cell:	n/a	chr8:20557545-20557554
6	POLR2A	chr8:20557307-20557806	H1-neurons	neurons:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LZTS1-1	chr8:20557261-20557645	ENSG00000253300

Variant related genes	Relation type
ENSG00000253300	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10097713	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10503684	0.95[EUR][1000 genomes]
rs10503686	0.85[EUR][1000 genomes]
rs10503687	0.85[EUR][1000 genomes]
rs11997151	0.95[EUR][1000 genomes]
rs12335299	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376004	0.95[EUR][1000 genomes]
rs1376006	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1376007	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092933	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092968	0.88[AFR][1000 genomes]
rs17092972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092979	0.88[AFR][1000 genomes]
rs17092986	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092995	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17093077	0.83[EUR][1000 genomes]
rs17421224	0.95[EUR][1000 genomes]
rs17421273	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493314	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493335	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17603878	0.95[EUR][1000 genomes]
rs17603885	0.95[EUR][1000 genomes]
rs17604003	0.89[EUR][1000 genomes]
rs1839454	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839455	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167173	0.95[EUR][1000 genomes]
rs4412388	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5019271	1.00[JPT][hapmap]
rs55848611	0.83[EUR][1000 genomes]
rs56332110	0.83[EUR][1000 genomes]
rs57680857	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57870062	0.95[EUR][1000 genomes]
rs731067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73667856	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73667857	0.88[AFR][1000 genomes]
rs73667859	0.91[AFR][1000 genomes]
rs73667860	0.91[AFR][1000 genomes]
rs7813612	0.81[EUR][1000 genomes]
rs7823002	0.92[EUR][1000 genomes]
rs7845060	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033511	chr8:19751299-20625091	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv530877	chr8:19873053-20593254	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS 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	nsv1027535	chr8:20506377-20613664	Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1032450	chr8:20514995-21033577	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv539524	chr8:20514995-21033577	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2761417	chr8:20523767-20669443	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20552200-20559800	Weak transcription	Fetal Kidney	kidney
2	chr8:20555600-20558400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:20555600-20558800	Enhancers	Fetal Brain Male	brain
4	chr8:20555800-20559600	Enhancers	Fetal Brain Female	brain
5	chr8:20557000-20557800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr8:20557000-20558200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:20557200-20557600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr8:20557200-20557800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:20557200-20557800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:20557200-20558400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr8:20557200-20558400	Enhancers	Brain Germinal Matrix	brain
12	chr8:20557400-20557600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr8:20557400-20557800	Enhancers	HUES6 Cell Line	embryonic stem cell

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