Variant report

Variant	rs10421407
Chromosome Location	chr19:56976578-56976579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10408270	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10408604	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10413169	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415307	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10416345	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10419332	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10432288	0.90[ASN][1000 genomes]
rs11084449	0.89[ASN][1000 genomes]
rs11084450	0.89[ASN][1000 genomes]
rs12460342	0.89[ASN][1000 genomes]
rs12973407	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12981146	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12981443	0.88[ASN][1000 genomes]
rs1542038	0.91[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap]
rs1542039	0.91[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs2288860	0.88[CEU][hapmap]
rs28373215	0.94[ASN][1000 genomes]
rs2904016	0.88[CEU][hapmap]
rs2904017	0.89[ASN][1000 genomes]
rs35027158	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35869148	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35914474	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745826	0.99[ASN][1000 genomes]
rs3760849	0.89[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.94[ASN][1000 genomes]
rs3810340	0.89[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs4281830	0.89[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs4801163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801319	0.86[ASN][1000 genomes]
rs62121590	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121593	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248278	0.94[ASN][1000 genomes]
rs7250817	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7252607	0.88[ASN][1000 genomes]
rs728232	0.90[ASN][1000 genomes]
rs8104319	0.88[ASN][1000 genomes]
rs8104585	0.88[ASN][1000 genomes]
rs8112531	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8112935	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917650	0.89[CEU][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs917651	0.89[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs917652	0.88[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9304776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9749140	0.83[ASN][1000 genomes]
rs9789281	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10421407	ZNF582-AS1	cis	Artery Tibial	GTEx
rs10421407	ZNF329	cis	cerebellum	SCAN
rs10421407	ZNF582-AS1	cis	lung	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56957200-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:56957400-56976800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
3	chr19:56957400-56985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:56957400-56987400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr19:56957400-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:56965800-56977400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:56966400-56979800	ZNF genes & repeats	Ovary	ovary
8	chr19:56967200-56987600	Weak transcription	Fetal Heart	heart
9	chr19:56969400-56987600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:56970200-56981400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:56972800-56987600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:56973000-56981400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr19:56973000-56981600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:56973200-56981000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:56973400-56981600	Weak transcription	Psoas Muscle	Psoas
16	chr19:56973400-56983600	Weak transcription	Dnd41	blood
17	chr19:56973600-56981800	Weak transcription	Left Ventricle	heart
18	chr19:56973800-56976600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:56974000-56981000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr19:56974000-56981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:56974000-56981600	Weak transcription	Right Ventricle	heart
22	chr19:56974400-56976600	Weak transcription	Brain Anterior Caudate	brain
23	chr19:56974600-56976800	Weak transcription	Brain Angular Gyrus	brain
24	chr19:56974800-56976800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:56975600-56978200	ZNF genes & repeats	Liver	Liver
26	chr19:56975600-56978600	ZNF genes & repeats	Fetal Brain Female	brain
27	chr19:56975600-56979600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr19:56975600-56985200	ZNF genes & repeats	Brain Germinal Matrix	brain
29	chr19:56975600-56987200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:56975800-56978200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
31	chr19:56976000-56977000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
32	chr19:56976400-56979800	Weak transcription	Brain Cingulate Gyrus	brain

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