Variant report

Variant	rs3817397
Chromosome Location	chr19:21776652-21776653
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF100-1	chr19:21776487-21776720	ENSG00000268240.1
2	lnc-ZNF100-1	chr19:21776485-21776704	NONHSAT063731

Extended variants
information (count: 106 )
Associated
traits (count: 65 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10854054	0.85[ASN][1000 genomes]
rs11085469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11667151	0.89[ASN][1000 genomes]
rs11673280	0.82[ASN][1000 genomes]
rs11879044	0.96[ASN][1000 genomes]
rs11881160	0.83[ASN][1000 genomes]
rs11881176	0.83[ASN][1000 genomes]
rs11881813	0.81[ASN][1000 genomes]
rs12150968	0.82[ASN][1000 genomes]
rs12327638	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs12459011	0.82[ASN][1000 genomes]
rs12459715	0.87[ASN][1000 genomes]
rs12463384	0.82[ASN][1000 genomes]
rs12608625	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12610221	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12972148	0.96[ASN][1000 genomes]
rs12973203	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12973209	0.87[ASN][1000 genomes]
rs12974817	0.96[ASN][1000 genomes]
rs12978060	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs12979255	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12981277	0.89[ASN][1000 genomes]
rs1520068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1520069	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1520070	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533674	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850937	0.87[ASN][1000 genomes]
rs2102920	0.96[ASN][1000 genomes]
rs2102922	0.87[ASN][1000 genomes]
rs2139530	0.87[ASN][1000 genomes]
rs2359157	0.87[ASN][1000 genomes]
rs34692125	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34835488	0.96[ASN][1000 genomes]
rs35092215	0.85[ASN][1000 genomes]
rs35229762	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35465051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35998933	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4435389	0.81[ASN][1000 genomes]
rs4809140	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4809141	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4809146	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809147	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4809148	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809151	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809153	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809154	0.82[ASN][1000 genomes]
rs55778393	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57229007	0.86[ASN][1000 genomes]
rs59054166	0.96[ASN][1000 genomes]
rs59803919	0.82[ASN][1000 genomes]
rs61137407	0.86[ASN][1000 genomes]
rs61461318	0.82[ASN][1000 genomes]
rs62108370	0.81[ASN][1000 genomes]
rs62108372	0.80[ASN][1000 genomes]
rs62110244	0.96[ASN][1000 genomes]
rs62110249	0.86[ASN][1000 genomes]
rs6511268	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs6511273	0.87[ASN][1000 genomes]
rs67854708	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67876192	0.81[EUR][1000 genomes]
rs68172713	0.85[AFR][1000 genomes]
rs71333832	0.82[ASN][1000 genomes]
rs7246154	0.87[ASN][1000 genomes]
rs7248367	0.87[ASN][1000 genomes]
rs7249639	0.81[ASN][1000 genomes]
rs7249775	0.82[ASN][1000 genomes]
rs7250457	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250663	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250960	0.89[ASN][1000 genomes]
rs7251076	0.82[ASN][1000 genomes]
rs7251111	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252205	0.82[ASN][1000 genomes]
rs7252706	0.82[ASN][1000 genomes]
rs7254018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255395	0.82[ASN][1000 genomes]
rs7255521	0.81[ASN][1000 genomes]
rs7257246	0.87[ASN][1000 genomes]
rs7259763	0.82[ASN][1000 genomes]
rs7259888	0.82[ASN][1000 genomes]
rs7260391	0.81[ASN][1000 genomes]
rs7260514	0.87[ASN][1000 genomes]
rs8100536	0.80[ASN][1000 genomes]
rs8101255	0.82[ASN][1000 genomes]
rs8101857	0.81[ASN][1000 genomes]
rs8109757	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110320	0.87[ASN][1000 genomes]
rs8111076	0.87[ASN][1000 genomes]
rs8111313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112158	0.87[ASN][1000 genomes]
rs8112960	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9749033	0.87[ASN][1000 genomes]
rs9749043	0.87[ASN][1000 genomes]
rs9749067	0.87[ASN][1000 genomes]
rs9749163	0.87[ASN][1000 genomes]
rs9749167	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1056332	chr19:21746555-21807647	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv960938	chr19:21766627-21785276	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:65)

SNP	Gene	Cis/trans	Tissue	Source
rs3817397	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs3817397	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs3817397	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs3817397	ZNF429	cis	Artery Tibial	GTEx
rs3817397	ZNF429	cis	Whole Blood	GTEx
rs3817397	ZNF493	cis	cerebellum	SCAN
rs3817397	RP11-678G14.3	cis	Esophagus Mucosa	GTEx
rs3817397	RP11-420K14.2	cis	lung	GTEx
rs3817397	ZNF43	cis	Esophagus Mucosa	GTEx
rs3817397	ZNF738	cis	cerebellum	SCAN
rs3817397	C19orf50	cis	cerebellum	SCAN
rs3817397	LINC00664	cis	Muscle Skeletal	GTEx
rs3817397	ZNF708	cis	cerebellum	SCAN
rs3817397	ZNF14	cis	cerebellum	SCAN
rs3817397	ZNF257	cis	parietal	SCAN
rs3817397	LINC00664	cis	Whole Blood	GTEx
rs3817397	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3817397	CTD-2561J22.5	cis	lung	GTEx
rs3817397	ZNF429	cis	cerebellum	SCAN
rs3817397	ZNF430	cis	cerebellum	SCAN
rs3817397	ZNF429	cis	Muscle Skeletal	GTEx
rs3817397	ZNF486	cis	cerebellum	SCAN
rs3817397	ZNF93	cis	cerebellum	SCAN
rs3817397	ZNF595	cis	Liver	GTEx
rs3817397	RP11-678G14.2	cis	Whole Blood	GTEx
rs3817397	CTD-2561J22.5	cis	Esophagus Mucosa	GTEx
rs3817397	ZNF429	cis	Esophagus Mucosa	GTEx
rs3817397	RP11-678G14.4	cis	Muscle Skeletal	GTEx
rs3817397	LINC00664	cis	Esophagus Mucosa	GTEx
rs3817397	ZNF429	cis	Skin Sun Exposed Lower leg	GTEx
rs3817397	ZNF708	cis	multi-tissue	Pritchard
rs3817397	RP11-420K14.2	cis	Whole Blood	GTEx
rs3817397	ZNF493	cis	parietal	SCAN
rs3817397	RP11-678G14.2	cis	lung	GTEx
rs3817397	ZNF708	cis	Whole Blood	GTEx
rs3817397	ZNF43	cis	parietal	SCAN
rs3817397	ZNF431	cis	cerebellum	SCAN
rs3817397	ZNF493	cis	multi-tissue	Pritchard
rs3817397	RP11-678G14.3	cis	lung	GTEx
rs3817397	RP11-678G14.3	cis	Whole Blood	GTEx
rs3817397	ZNF493	cis	Whole Blood	GTEx
rs3817397	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs3817397	ZNF826P	cis	parietal	SCAN
rs3817397	CTD-2561J22.5	cis	Thyroid	GTEx
rs3817397	RP11-678G14.3	cis	Stomach	GTEx
rs3817397	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs3817397	ZNF208	cis	parietal	SCAN
rs3817397	RP11-678G14.3	cis	Thyroid	GTEx
rs3817397	RP11-678G14.3	cis	Artery Aorta	GTEx
rs3817397	ZNF429	cis	parietal	SCAN
rs3817397	ZNF826P	cis	cerebellum	SCAN
rs3817397	CTD-2561J22.5	cis	Whole Blood	GTEx
rs3817397	RP11-678G14.2	cis	Thyroid	GTEx
rs3817397	ZNF493	cis	Esophagus Mucosa	GTEx
rs3817397	ZNF429	cis	lung	GTEx
rs3817397	ZNF429	cis	multi-tissue	Pritchard
rs3817397	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs3817397	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs3817397	ZNF43	cis	cerebellum	SCAN
rs3817397	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs3817397	ZNF100	cis	cerebellum	SCAN
rs3817397	ZNF100	cis	Muscle Skeletal	GTEx
rs3817397	ZNF430	cis	parietal	SCAN
rs3817397	ZNF257	cis	cerebellum	SCAN
rs3817397	LINC00664	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21770000-21786600	Weak transcription	Primary T cells from cord blood	blood
2	chr19:21770200-21786600	Weak transcription	Right Ventricle	heart
3	chr19:21771000-21786200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:21771200-21786200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:21771200-21786200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr19:21771400-21782200	Weak transcription	Fetal Intestine Large	intestine
7	chr19:21771400-21785000	Weak transcription	Fetal Intestine Small	intestine
8	chr19:21775400-21777600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:21775400-21779000	Enhancers	Pancreas	Pancrea
10	chr19:21775400-21779200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr19:21775600-21778000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr19:21775800-21777400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:21776000-21779600	Weak transcription	Dnd41	blood
14	chr19:21776200-21776800	Enhancers	Adipose Nuclei	Adipose
15	chr19:21776200-21777200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr19:21776400-21777200	Flanking Active TSS	K562	blood
17	chr19:21776400-21777600	Enhancers	Primary hematopoietic stem cells	blood
18	chr19:21776600-21776800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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