Variant report

Variant	rs56346453
Chromosome Location	chr19:21665484-21665485
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	CTCF	chr19:21665466-21666273	SK-N-SH	brain:	n/a	chr19:21665789-21665802 chr19:21665753-21665771 chr19:21665755-21665768 chr19:21665874-21665887 chr19:21665754-21665770 chr19:21665755-21665768
2	RAD21	chr19:21665474-21666078	ECC-1	luminal epithelium:	n/a	chr19:21665751-21665770
3	RAD21	chr19:21665454-21666092	SK-N-SH	brain:	n/a	chr19:21665751-21665770

No.	Distal block	Cell Line	Cell type
1	chr19:21665377..21666059-chr20:61799030..61799530,2	MCF-7	breast:
2	chr19:21664396..21666008-chr21:9825779..9827966,2	MCF-7	breast:
3	chr19:21665376..21665988-chr8:46940890..46941394,3	MCF-7	breast:
4	chr19:21665377..21666008-chr8:46940755..46941391,3	MCF-7	breast:

Variant related genes	Relation type
LINC00664	TF binding region
ENSG00000264063	Chromatin interaction
ENSG00000264462	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11085450	0.85[ASN][1000 genomes]
rs11085456	0.81[AMR][1000 genomes]
rs11666680	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11667259	0.88[ASN][1000 genomes]
rs11668682	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11669043	0.84[ASN][1000 genomes]
rs11669130	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11671265	0.87[ASN][1000 genomes]
rs12461802	0.80[AMR][1000 genomes]
rs12609768	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12609823	0.89[ASN][1000 genomes]
rs12610154	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12973084	0.81[AMR][1000 genomes]
rs12974329	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12985995	0.80[AMR][1000 genomes]
rs2133822	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28498118	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28898308	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34497957	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35782355	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35994743	0.88[ASN][1000 genomes]
rs3973190	0.89[ASN][1000 genomes]
rs4306654	0.82[ASN][1000 genomes]
rs4462731	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621113	0.81[ASN][1000 genomes]
rs6511255	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6511259	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7245729	0.87[ASN][1000 genomes]
rs7246883	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7247060	0.89[ASN][1000 genomes]
rs7248989	0.84[ASN][1000 genomes]
rs7250360	0.85[AMR][1000 genomes]
rs7250838	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7251082	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7251620	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7252254	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7253886	0.84[ASN][1000 genomes]
rs7256389	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7257186	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7259317	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73017722	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8101089	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8101900	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8106840	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110814	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8111549	0.81[ASN][1000 genomes]
rs924487	0.89[ASN][1000 genomes]
rs951162	0.87[ASN][1000 genomes]
rs9789284	0.81[AMR][1000 genomes]
rs9973240	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs56346453	CTD-2561J22.5	cis	lung	GTEx
rs56346453	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs56346453	CTD-2561J22.5	cis	Thyroid	GTEx
rs56346453	RP11-678G14.2	cis	Whole Blood	GTEx
rs56346453	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs56346453	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs56346453	RP11-678G14.2	cis	lung	GTEx
rs56346453	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs56346453	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs56346453	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs56346453	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs56346453	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs56346453	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs56346453	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs56346453	RP11-420K14.2	cis	Whole Blood	GTEx
rs56346453	ZNF429	cis	Whole Blood	GTEx
rs56346453	ZNF429	cis	Muscle Skeletal	GTEx
rs56346453	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs56346453	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs56346453	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs56346453	RP11-678G14.2	cis	Artery Tibial	GTEx
rs56346453	ZNF100	cis	Muscle Skeletal	GTEx
rs56346453	RP11-678G14.3	cis	lung	GTEx
rs56346453	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs56346453	RP11-678G14.3	cis	Whole Blood	GTEx
rs56346453	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs56346453	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs56346453	RP11-678G14.2	cis	Thyroid	GTEx
rs56346453	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21658000-21665600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:21658000-21665800	Weak transcription	Gastric	stomach
3	chr19:21658000-21665800	Weak transcription	Lung	lung
4	chr19:21658200-21665800	Weak transcription	Right Ventricle	heart
5	chr19:21658200-21667400	Weak transcription	Right Atrium	heart
6	chr19:21658200-21687800	Weak transcription	Brain Substantia Nigra	brain
7	chr19:21658400-21665800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:21658600-21665800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:21658800-21665600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:21658800-21665800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr19:21659000-21665800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:21659200-21665800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:21659200-21666000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:21659200-21668400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:21664200-21665800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:21664600-21665800	Weak transcription	Thymus	Thymus
17	chr19:21665200-21665600	Weak transcription	Placenta	Placenta
18	chr19:21665200-21665800	Weak transcription	Colonic Mucosa	Colon
19	chr19:21665400-21665600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr19:21665400-21665600	Enhancers	Stomach Smooth Muscle	stomach
21	chr19:21665400-21665800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:21665400-21666400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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