Variant report

Variant	rs12609768
Chromosome Location	chr19:21677321-21677322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11085450	0.80[ASN][1000 genomes]
rs11085456	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11666680	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668682	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12461802	0.86[EUR][1000 genomes]
rs12610154	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12973084	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12974329	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12975424	0.83[EUR][1000 genomes]
rs12985995	0.85[EUR][1000 genomes]
rs2133822	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28498118	0.81[AMR][1000 genomes]
rs28898308	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34497957	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35782355	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4462731	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56346453	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511255	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511259	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250360	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7250838	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7251540	0.82[EUR][1000 genomes]
rs7251620	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7252254	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256389	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7257186	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7259317	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73017722	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8101089	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101900	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106840	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8110814	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111885	0.87[EUR][1000 genomes]
rs9789284	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs12609768	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs12609768	RP11-678G14.2	cis	lung	GTEx
rs12609768	CTD-2561J22.5	cis	Thyroid	GTEx
rs12609768	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs12609768	RP11-678G14.3	cis	lung	GTEx
rs12609768	RP11-678G14.2	cis	Nerve Tibial	GTEx
rs12609768	RP11-678G14.2	cis	Artery Tibial	GTEx
rs12609768	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12609768	RP11-678G14.3	cis	Whole Blood	GTEx
rs12609768	RP11-420K14.3	cis	Whole Blood	GTEx
rs12609768	RP11-678G14.2	cis	Thyroid	GTEx
rs12609768	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs12609768	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs12609768	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs12609768	RP11-678G14.2	cis	Whole Blood	GTEx
rs12609768	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs12609768	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs12609768	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12609768	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12609768	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs12609768	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs12609768	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs12609768	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs12609768	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs12609768	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs12609768	ZNF429	cis	Muscle Skeletal	GTEx
rs12609768	ZNF100	cis	Muscle Skeletal	GTEx
rs12609768	RP11-420K14.2	cis	Whole Blood	GTEx
rs12609768	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs12609768	ZNF429	cis	Whole Blood	GTEx
rs12609768	CTD-2561J22.5	cis	lung	GTEx

Chromatin state (count:22 , 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	chr19:21669000-21677600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:21669000-21687600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr19:21669800-21681800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:21672200-21681800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr19:21672800-21681000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:21673000-21680200	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr19:21673200-21680200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:21673400-21687800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:21674400-21678200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr19:21674800-21680000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:21674800-21687800	Weak transcription	Brain Hippocampus Middle	brain
14	chr19:21675800-21680200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
15	chr19:21675800-21681800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:21675800-21687200	Weak transcription	Primary T cells from cord blood	blood
17	chr19:21676000-21688000	Weak transcription	Fetal Stomach	stomach
18	chr19:21676200-21678200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:21676800-21677400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:21676800-21679600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:21677000-21677800	Enhancers	Placenta	Placenta
22	chr19:21677000-21680000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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