Variant report

Variant	rs56234441
Chromosome Location	chr17:20845003-20845004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12051606	0.82[ASN][1000 genomes]
rs12601292	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2886105	0.82[AMR][1000 genomes]
rs4985811	0.82[ASN][1000 genomes]
rs56209912	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56298745	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080341	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs880653	0.82[AMR][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	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv3361931	chr17:20539962-20845258	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv3330516	chr17:20572433-20862663	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv574597	chr17:20802778-20872331	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv527161	chr17:20814766-20872331	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv457706	chr17:20814766-20872331	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv574598	chr17:20814766-20872331	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
11	nsv978393	chr17:20841928-20851802	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs56234441	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs56234441	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs56234441	RP11-344E13.3	cis	Artery Tibial	GTEx
rs56234441	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs56234441	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs56234441	RP11-344E13.3	cis	Thyroid	GTEx
rs56234441	RP11-344E13.3	cis	Whole Blood	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20827200-20856200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:20831000-20846800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr17:20831000-20847200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:20831400-20847000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr17:20831600-20845800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:20832400-20847800	Weak transcription	Gastric	stomach
7	chr17:20834200-20846800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:20834600-20847200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr17:20834600-20847800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:20835600-20869000	Weak transcription	HepG2	liver
11	chr17:20838600-20852400	Weak transcription	K562	blood
12	chr17:20841600-20847400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:20843200-20845400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:20843200-20852200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr17:20844600-20847600	Weak transcription	Placenta	Placenta
16	chr17:20845000-20845400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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