Variant report

Variant	rs2562417
Chromosome Location	chr19:21711202-21711203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10420016	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10854048	0.80[ASN][1000 genomes]
rs10854050	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10854051	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085462	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085465	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085468	0.81[EUR][1000 genomes]
rs11668606	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11671579	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12974758	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13346641	0.81[CEU][hapmap]
rs1879234	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1967182	0.85[CEU][hapmap]
rs2173727	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2359144	0.85[CEU][hapmap]
rs2359155	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562398	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562402	0.89[CHD][hapmap]
rs2562408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562428	0.90[AFR][1000 genomes]
rs2562435	0.89[CHD][hapmap]
rs2562456	0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562471	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562487	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2562507	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562508	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2650784	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2650793	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2650804	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2650805	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2650825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2650844	0.85[CEU][hapmap]
rs2681370	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681388	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2681389	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681391	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2681392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681395	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2946790	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968046	0.92[CHD][hapmap]
rs35008138	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35099594	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4321312	1.00[CEU][hapmap]
rs4359573	1.00[CEU][hapmap]
rs4638726	0.85[CEU][hapmap]
rs4809145	0.86[CHB][hapmap]
rs55771551	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58001930	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62110163	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511250	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511253	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511254	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511256	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6511258	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7252585	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259708	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7260065	0.95[CEU][hapmap]
rs9304986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9304987	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2562417	ZNF738	cis	cerebellum	SCAN
rs2562417	ZNF493	cis	cerebellum	SCAN
rs2562417	ZNF708	cis	lung	GTEx
rs2562417	ZNF826P	cis	parietal	SCAN
rs2562417	ZNF43	cis	parietal	SCAN
rs2562417	ZNF708	cis	cerebellum	SCAN
rs2562417	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2562417	ZNF708	cis	Muscle Skeletal	GTEx
rs2562417	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2562417	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2562417	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2562417	CTD-2561J22.5	cis	Thyroid	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21699600-21720800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:21699600-21727600	ZNF genes & repeats	Liver	Liver
3	chr19:21701000-21733400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:21701600-21712600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:21701600-21720400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr19:21702400-21721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:21702600-21713400	Weak transcription	Right Ventricle	heart
8	chr19:21702600-21713400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:21702600-21717200	Weak transcription	Psoas Muscle	Psoas
10	chr19:21702800-21713400	Weak transcription	Brain Angular Gyrus	brain
11	chr19:21702800-21717200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:21702800-21718600	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:21702800-21718600	Weak transcription	Fetal Heart	heart
14	chr19:21703000-21713400	Weak transcription	Brain Anterior Caudate	brain
15	chr19:21704000-21714600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:21704000-21717200	Weak transcription	NHDF-Ad	bronchial
17	chr19:21704400-21714400	Strong transcription	Primary T cells from cord blood	blood
18	chr19:21705000-21714200	Weak transcription	Fetal Thymus	thymus
19	chr19:21705000-21718600	Weak transcription	HSMM	muscle
20	chr19:21705200-21713200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:21705200-21713600	Weak transcription	Brain Substantia Nigra	brain
22	chr19:21705400-21713400	Weak transcription	Brain Hippocampus Middle	brain
23	chr19:21705800-21713600	Weak transcription	Fetal Stomach	stomach
24	chr19:21706000-21711600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:21706000-21713400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:21706000-21713400	Weak transcription	Fetal Kidney	kidney
27	chr19:21706000-21713400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:21706200-21713800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:21706400-21713600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:21706400-21714000	Weak transcription	Osteobl	bone
31	chr19:21706400-21717200	Weak transcription	K562	blood
32	chr19:21706600-21712000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:21706600-21713400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:21706600-21713400	Weak transcription	Thymus	Thymus
35	chr19:21706800-21713000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr19:21706800-21713400	Weak transcription	HSMMtube	muscle
37	chr19:21707000-21713000	Weak transcription	Fetal Lung	lung
38	chr19:21707000-21713400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:21707000-21713400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:21707000-21714000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr19:21707000-21719000	Weak transcription	Stomach Mucosa	stomach
42	chr19:21707200-21713400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:21707200-21713800	Weak transcription	Fetal Brain Male	brain
44	chr19:21708200-21716200	Strong transcription	Dnd41	blood
45	chr19:21708200-21717400	Strong transcription	Placenta	Placenta
46	chr19:21708800-21711400	ZNF genes & repeats	Primary B cells from cord blood	blood
47	chr19:21709000-21722800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:21709400-21712200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:21709600-21711400	ZNF genes & repeats	Fetal Muscle Leg	muscle
50	chr19:21709600-21716800	Strong transcription	H1 Cell Line	embryonic stem cell

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