Variant report

Variant	rs2102920
Chromosome Location	chr19:21786807-21786808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10854054	0.89[ASN][1000 genomes]
rs11085469	0.97[ASN][1000 genomes]
rs11667151	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11673280	0.86[ASN][1000 genomes]
rs11879044	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[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	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12327638	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs12459011	0.86[ASN][1000 genomes]
rs12459715	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12463354	0.81[ASN][1000 genomes]
rs12463384	0.86[ASN][1000 genomes]
rs12608625	0.89[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs12610221	0.92[ASN][1000 genomes]
rs12972148	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973203	0.97[ASN][1000 genomes]
rs12973209	0.91[ASN][1000 genomes]
rs12974817	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978060	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12979255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12981277	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520068	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1520069	0.97[ASN][1000 genomes]
rs1520070	0.97[ASN][1000 genomes]
rs1533674	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1850937	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2102922	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2139530	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2359157	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34015922	0.83[ASN][1000 genomes]
rs34692125	0.97[ASN][1000 genomes]
rs34835488	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35092215	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	0.80[AMR][1000 genomes];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	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4809153	0.94[ASN][1000 genomes]
rs4809154	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55778393	0.93[ASN][1000 genomes]
rs57229007	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57235280	0.81[ASN][1000 genomes]
rs59054166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59803919	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61137407	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61461318	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62108370	0.84[ASN][1000 genomes]
rs62108372	0.84[ASN][1000 genomes]
rs62110244	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110249	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511268	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6511273	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511275	0.83[ASN][1000 genomes]
rs67854708	0.97[ASN][1000 genomes]
rs71333832	0.86[ASN][1000 genomes]
rs7246154	0.91[ASN][1000 genomes]
rs7248367	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7249639	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7249775	0.86[ASN][1000 genomes]
rs7250457	0.97[ASN][1000 genomes]
rs7250470	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7250663	0.97[ASN][1000 genomes]
rs7250960	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7251076	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7251111	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7252080	0.83[ASN][1000 genomes]
rs7252081	0.83[ASN][1000 genomes]
rs7252104	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7252205	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7252706	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7254018	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7254378	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7255081	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7255395	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7255521	0.85[ASN][1000 genomes]
rs7257246	0.91[ASN][1000 genomes]
rs7259763	0.86[ASN][1000 genomes]
rs7259888	0.86[ASN][1000 genomes]
rs7260016	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7260391	0.85[ASN][1000 genomes]
rs7260514	0.91[ASN][1000 genomes]
rs8100536	0.84[ASN][1000 genomes]
rs8101255	0.86[ASN][1000 genomes]
rs8101857	0.85[ASN][1000 genomes]
rs8109757	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8110320	0.91[ASN][1000 genomes]
rs8111076	0.91[ASN][1000 genomes]
rs8111313	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8112158	0.91[ASN][1000 genomes]
rs8112960	0.95[ASN][1000 genomes]
rs9749033	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749043	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749067	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749163	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749167	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2102920	ZNF429	cis	multi-tissue	Pritchard
rs2102920	RP11-420K14.2	cis	lung	GTEx
rs2102920	ZNF429	cis	lung	GTEx
rs2102920	ZNF493	cis	cerebellum	SCAN
rs2102920	CTD-2561J22.5	cis	Esophagus Mucosa	GTEx
rs2102920	ZNF208	cis	parietal	SCAN
rs2102920	NCAN	cis	parietal	SCAN
rs2102920	ZNF93	cis	parietal	SCAN
rs2102920	ZNF43	cis	cerebellum	SCAN
rs2102920	ZNF493	cis	parietal	SCAN
rs2102920	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2102920	RP11-678G14.3	cis	Whole Blood	GTEx
rs2102920	ZNF738	cis	cerebellum	SCAN
rs2102920	RP11-678G14.3	cis	Esophagus Mucosa	GTEx
rs2102920	RP11-420K14.2	cis	Whole Blood	GTEx
rs2102920	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs2102920	ZNF429	cis	Whole Blood	GTEx
rs2102920	ZNF429	cis	cerebellum	SCAN
rs2102920	ZNF493	cis	multi-tissue	Pritchard
rs2102920	ZNF43	cis	parietal	SCAN
rs2102920	ZNF708	cis	cerebellum	SCAN
rs2102920	RP11-678G14.3	cis	lung	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21783600-21787000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr19:21784600-21787200	Enhancers	Fetal Intestine Large	intestine
3	chr19:21784800-21788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:21785000-21787000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:21785000-21787000	Enhancers	Ovary	ovary
6	chr19:21785400-21787000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:21785400-21787000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr19:21785400-21787000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr19:21785400-21788200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:21785800-21787000	Enhancers	Fetal Intestine Small	intestine
11	chr19:21785800-21787000	Enhancers	Pancreas	Pancrea
12	chr19:21786000-21787000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr19:21786000-21787000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr19:21786000-21787000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr19:21786000-21787000	Enhancers	Brain Germinal Matrix	brain
16	chr19:21786000-21788000	Flanking Active TSS	K562	blood
17	chr19:21786000-21788200	Flanking Active TSS	Dnd41	blood
18	chr19:21786200-21787000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr19:21786200-21787000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:21786200-21787000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:21786200-21787000	Enhancers	Fetal Muscle Trunk	muscle
22	chr19:21786200-21787000	Enhancers	Fetal Muscle Leg	muscle
23	chr19:21786200-21787000	Enhancers	Placenta	Placenta
24	chr19:21786200-21787000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr19:21786200-21787000	Enhancers	Psoas Muscle	Psoas
26	chr19:21786200-21787000	Enhancers	Right Atrium	heart
27	chr19:21786200-21787000	Enhancers	Stomach Mucosa	stomach
28	chr19:21786200-21787200	Enhancers	Fetal Heart	heart
29	chr19:21786200-21787200	Enhancers	Gastric	stomach
30	chr19:21786200-21787800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:21786200-21787800	Enhancers	Spleen	Spleen
32	chr19:21786200-21788000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:21786200-21788200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr19:21786200-21788400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:21786400-21787000	Enhancers	Primary B cells from peripheral blood	blood
36	chr19:21786400-21787000	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr19:21786400-21787000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr19:21786400-21787000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr19:21786400-21787200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:21786400-21787400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr19:21786400-21788200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr19:21786600-21787000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:21786600-21787000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr19:21786600-21787000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr19:21786600-21787000	Weak transcription	Aorta	Aorta
46	chr19:21786600-21787000	Enhancers	Liver	Liver
47	chr19:21786600-21787000	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr19:21786600-21787000	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr19:21786600-21787000	Enhancers	Fetal Stomach	stomach
50	chr19:21786600-21787000	Enhancers	Right Ventricle	heart

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