Variant report

Variant	rs11666680
Chromosome Location	chr19:21681788-21681789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21680381..21683042-chr19:21685996..21688688,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF429-1	chr19:21681001-21682100	ENSG00000248094
2	lnc-ZNF429-1	chr19:21681001-21682695	NONHSAT063711
3	lnc-ZNF429-1	chr19:21681001-21682695	NONHSAT063715
4	lnc-ZNF429-1	chr19:21681001-21682100	ENSG00000268658.1

Variant related genes	Relation type
ENSG00000197013	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 27 )

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

rs_ID	r²[population]
rs11085456	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11667259	0.81[ASN][1000 genomes]
rs11668682	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11669130	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11671265	0.81[ASN][1000 genomes]
rs12461802	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12609768	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12609823	0.82[ASN][1000 genomes]
rs12610154	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973084	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12974329	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975424	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12985995	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1401926	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1879237	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1879238	0.86[AMR][1000 genomes]
rs2133822	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28498118	0.83[ASN][1000 genomes]
rs28898308	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34040704	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34497957	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35782355	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35994743	0.81[ASN][1000 genomes]
rs3973190	0.82[ASN][1000 genomes]
rs4462731	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56346453	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511255	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511259	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7245729	0.81[ASN][1000 genomes]
rs7246883	0.81[ASN][1000 genomes]
rs7247060	0.82[ASN][1000 genomes]
rs7250360	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7250838	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251540	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7251620	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252254	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253559	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7256389	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257186	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259317	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73017722	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8101089	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101900	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106840	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109536	0.86[AMR][1000 genomes]
rs8110814	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8111885	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs924487	0.82[ASN][1000 genomes]
rs951162	0.81[ASN][1000 genomes]
rs9789284	0.90[AMR][1000 genomes];0.89[EUR][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	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
10	nsv543941	chr19:21676223-21693215	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3434817	chr19:21681307-21684752	Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs11666680	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11666680	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs11666680	ZNF100	cis	Muscle Skeletal	GTEx
rs11666680	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs11666680	CTD-2561J22.5	cis	lung	GTEx
rs11666680	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs11666680	CTD-2561J22.5	cis	Thyroid	GTEx
rs11666680	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs11666680	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs11666680	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs11666680	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs11666680	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs11666680	RP11-678G14.2	cis	Whole Blood	GTEx
rs11666680	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs11666680	RP11-678G14.3	cis	lung	GTEx
rs11666680	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs11666680	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs11666680	RP11-678G14.2	cis	Thyroid	GTEx
rs11666680	RP11-678G14.3	cis	Whole Blood	GTEx
rs11666680	ZNF429	cis	Muscle Skeletal	GTEx
rs11666680	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs11666680	RP11-678G14.2	cis	lung	GTEx
rs11666680	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11666680	RP11-420K14.2	cis	Whole Blood	GTEx
rs11666680	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs11666680	ZNF429	cis	Whole Blood	GTEx
rs11666680	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21658200-21687800	Weak transcription	Brain Substantia Nigra	brain
2	chr19:21666800-21687600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:21669000-21687600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr19:21669800-21681800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:21672200-21681800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr19:21673400-21687800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:21674800-21687800	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:21675800-21681800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:21675800-21687200	Weak transcription	Primary T cells from cord blood	blood
10	chr19:21676000-21688000	Weak transcription	Fetal Stomach	stomach
11	chr19:21678000-21688000	Weak transcription	Thymus	Thymus
12	chr19:21678200-21684000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:21679200-21688200	Weak transcription	Brain Angular Gyrus	brain
14	chr19:21679600-21681800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr19:21680000-21687800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:21680000-21688200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:21680200-21687600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:21680200-21688200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr19:21680600-21683400	Weak transcription	Fetal Intestine Large	intestine
20	chr19:21681000-21681800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr19:21681200-21688400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:21681400-21688200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:21681600-21688200	Weak transcription	H9 Cell Line	embryonic stem cell

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