Variant report

Variant	rs12974817
Chromosome Location	chr19:21786462-21786463
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21776789..21778695-chr19:21784881..21786729,2	K562	blood:

Variant related genes	Relation type
ENSG00000268240	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10854054	0.89[ASN][1000 genomes]
rs11085469	0.97[ASN][1000 genomes]
rs11667151	0.93[ASN][1000 genomes]
rs11673280	0.86[ASN][1000 genomes]
rs11879044	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881160	0.87[ASN][1000 genomes]
rs11881176	0.87[ASN][1000 genomes]
rs11881813	0.85[ASN][1000 genomes]
rs12150968	0.86[ASN][1000 genomes]
rs12459011	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12459715	0.91[ASN][1000 genomes]
rs12463354	0.81[ASN][1000 genomes]
rs12463384	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12608625	0.93[ASN][1000 genomes]
rs12610221	0.92[ASN][1000 genomes]
rs12972148	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973203	0.97[ASN][1000 genomes]
rs12973209	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12979255	0.97[ASN][1000 genomes]
rs12981277	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520068	0.97[ASN][1000 genomes]
rs1520069	0.97[ASN][1000 genomes]
rs1520070	0.97[ASN][1000 genomes]
rs1533674	0.96[ASN][1000 genomes]
rs1850937	0.91[ASN][1000 genomes]
rs2102920	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102922	0.91[ASN][1000 genomes]
rs2139530	0.91[ASN][1000 genomes]
rs2359157	0.91[ASN][1000 genomes]
rs34015922	0.83[ASN][1000 genomes]
rs34692125	0.97[ASN][1000 genomes]
rs34835488	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35092215	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35229762	0.97[ASN][1000 genomes]
rs35465051	0.95[ASN][1000 genomes]
rs35998933	0.92[ASN][1000 genomes]
rs3817397	0.96[ASN][1000 genomes]
rs4435389	0.84[ASN][1000 genomes]
rs4809140	0.82[ASN][1000 genomes]
rs4809141	0.82[ASN][1000 genomes]
rs4809146	0.94[ASN][1000 genomes]
rs4809147	0.93[ASN][1000 genomes]
rs4809148	0.94[ASN][1000 genomes]
rs4809151	0.97[ASN][1000 genomes]
rs4809152	0.97[ASN][1000 genomes]
rs4809153	0.94[ASN][1000 genomes]
rs4809154	0.86[ASN][1000 genomes]
rs55778393	0.93[ASN][1000 genomes]
rs57229007	0.90[ASN][1000 genomes]
rs57235280	0.81[ASN][1000 genomes]
rs59054166	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59803919	0.86[ASN][1000 genomes]
rs61137407	0.90[ASN][1000 genomes]
rs61461318	0.86[ASN][1000 genomes]
rs62108370	0.84[ASN][1000 genomes]
rs62108372	0.84[ASN][1000 genomes]
rs62110244	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110249	0.90[ASN][1000 genomes]
rs6511273	0.91[ASN][1000 genomes]
rs6511275	0.83[ASN][1000 genomes]
rs67854708	0.97[ASN][1000 genomes]
rs71333832	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7246154	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248367	0.91[ASN][1000 genomes]
rs7249639	0.85[ASN][1000 genomes]
rs7249775	0.86[ASN][1000 genomes]
rs7250457	0.97[ASN][1000 genomes]
rs7250470	0.97[ASN][1000 genomes]
rs7250663	0.97[ASN][1000 genomes]
rs7250960	0.93[ASN][1000 genomes]
rs7251076	0.86[ASN][1000 genomes]
rs7251111	0.97[ASN][1000 genomes]
rs7252080	0.83[ASN][1000 genomes]
rs7252081	0.83[ASN][1000 genomes]
rs7252104	0.83[ASN][1000 genomes]
rs7252205	0.86[ASN][1000 genomes]
rs7252706	0.86[ASN][1000 genomes]
rs7254018	0.97[ASN][1000 genomes]
rs7254378	0.97[ASN][1000 genomes]
rs7255081	0.97[ASN][1000 genomes]
rs7255395	0.86[ASN][1000 genomes]
rs7255521	0.85[ASN][1000 genomes]
rs7257246	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7259763	0.86[ASN][1000 genomes]
rs7259888	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7260016	0.81[ASN][1000 genomes]
rs7260391	0.85[ASN][1000 genomes]
rs7260514	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8100536	0.84[ASN][1000 genomes]
rs8101255	0.86[ASN][1000 genomes]
rs8101857	0.85[ASN][1000 genomes]
rs8109757	0.94[ASN][1000 genomes]
rs8110320	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111076	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111313	0.96[ASN][1000 genomes]
rs8112158	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8112960	0.95[ASN][1000 genomes]
rs9749033	0.91[ASN][1000 genomes]
rs9749043	0.91[ASN][1000 genomes]
rs9749067	0.91[ASN][1000 genomes]
rs9749163	0.91[ASN][1000 genomes]
rs9749167	0.91[ASN][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	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	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv911423	chr19:21783995-21858994	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs12974817	ZNF429	cis	lung	GTEx
rs12974817	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs12974817	RP11-678G14.3	cis	Esophagus Mucosa	GTEx
rs12974817	RP11-420K14.2	cis	lung	GTEx
rs12974817	CTD-2561J22.5	cis	Esophagus Mucosa	GTEx
rs12974817	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs12974817	RP11-678G14.3	cis	Thyroid	GTEx
rs12974817	RP11-420K14.2	cis	Whole Blood	GTEx
rs12974817	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs12974817	ZNF100	cis	Muscle Skeletal	GTEx
rs12974817	ZNF429	cis	Muscle Skeletal	GTEx
rs12974817	ZNF493	cis	Esophagus Mucosa	GTEx
rs12974817	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12974817	RP11-678G14.3	cis	Whole Blood	GTEx
rs12974817	RP11-678G14.3	cis	Artery Aorta	GTEx
rs12974817	ZNF429	cis	Whole Blood	GTEx
rs12974817	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs12974817	RP11-678G14.3	cis	lung	GTEx
rs12974817	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs12974817	ZNF429	cis	Esophagus Mucosa	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

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	chr19:21783600-21787000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr19:21784600-21787200	Enhancers	Fetal Intestine Large	intestine
5	chr19:21784800-21788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:21785000-21786600	Enhancers	Fetal Kidney	kidney
7	chr19:21785000-21787000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:21785000-21787000	Enhancers	Ovary	ovary
9	chr19:21785400-21787000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:21785400-21787000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr19:21785400-21787000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr19:21785400-21788200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:21785600-21786600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr19:21785800-21786800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:21785800-21786800	Enhancers	Fetal Lung	lung
16	chr19:21785800-21787000	Enhancers	Fetal Intestine Small	intestine
17	chr19:21785800-21787000	Enhancers	Pancreas	Pancrea
18	chr19:21786000-21786800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr19:21786000-21787000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr19:21786000-21787000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr19:21786000-21787000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr19:21786000-21787000	Enhancers	Brain Germinal Matrix	brain
23	chr19:21786000-21788000	Flanking Active TSS	K562	blood
24	chr19:21786000-21788200	Flanking Active TSS	Dnd41	blood
25	chr19:21786200-21786600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
26	chr19:21786200-21786600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:21786200-21786600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:21786200-21786600	Enhancers	Brain Anterior Caudate	brain
29	chr19:21786200-21786600	Active TSS	Brain Substantia Nigra	brain
30	chr19:21786200-21786600	Enhancers	Duodenum Mucosa	Duodenum
31	chr19:21786200-21786600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr19:21786200-21786600	Active TSS	Stomach Smooth Muscle	stomach
33	chr19:21786200-21786800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:21786200-21786800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
35	chr19:21786200-21786800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr19:21786200-21786800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr19:21786200-21786800	Enhancers	Brain Cingulate Gyrus	brain
38	chr19:21786200-21786800	Enhancers	Left Ventricle	heart
39	chr19:21786200-21786800	Enhancers	Thymus	Thymus
40	chr19:21786200-21787000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr19:21786200-21787000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:21786200-21787000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:21786200-21787000	Enhancers	Fetal Muscle Trunk	muscle
44	chr19:21786200-21787000	Enhancers	Fetal Muscle Leg	muscle
45	chr19:21786200-21787000	Enhancers	Placenta	Placenta
46	chr19:21786200-21787000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr19:21786200-21787000	Enhancers	Psoas Muscle	Psoas
48	chr19:21786200-21787000	Enhancers	Right Atrium	heart
49	chr19:21786200-21787000	Enhancers	Stomach Mucosa	stomach
50	chr19:21786200-21787200	Enhancers	Fetal Heart	heart

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