Variant report

Variant	rs10408604
Chromosome Location	chr19:56960743-56960744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10408270	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413169	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415307	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421407	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]
rs10432288	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11084449	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11084450	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11667815	0.83[EUR][1000 genomes]
rs12460342	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12609819	0.83[EUR][1000 genomes]
rs12610115	0.80[EUR][1000 genomes]
rs12973407	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12981146	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981443	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1542038	0.86[JPT][hapmap]
rs1542039	0.86[JPT][hapmap]
rs2288860	0.96[CEU][hapmap]
rs28373215	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2904016	0.96[CEU][hapmap]
rs2904017	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35027158	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35869148	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35914474	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3745826	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3760849	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810340	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4281830	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4801163	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801319	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62121590	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62121593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248278	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7250817	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252607	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7258010	0.88[CEU][hapmap]
rs728232	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104319	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8104585	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8112531	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8112935	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917650	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917651	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917652	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9304776	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9749140	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9789281	0.88[EUR][1000 genomes];0.90[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
rs10408604	ZNF582-AS1	cis	lung	GTEx
rs10408604	ZNF582-AS1	cis	Artery Tibial	GTEx
rs10408604	ZNF582-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56957200-56962200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:56957200-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:56957400-56960800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
4	chr19:56957400-56960800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:56957400-56960800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:56957400-56960800	ZNF genes & repeats	Brain Anterior Caudate	brain
7	chr19:56957400-56960800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
8	chr19:56957400-56960800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:56957400-56960800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
10	chr19:56957400-56960800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
11	chr19:56957400-56961600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
12	chr19:56957400-56961600	ZNF genes & repeats	Brain Angular Gyrus	brain
13	chr19:56957400-56961800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
14	chr19:56957400-56961800	ZNF genes & repeats	Brain Germinal Matrix	brain
15	chr19:56957400-56962000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:56957400-56962000	ZNF genes & repeats	Fetal Brain Female	brain
17	chr19:56957400-56963000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
18	chr19:56957400-56963000	ZNF genes & repeats	Fetal Brain Male	brain
19	chr19:56957400-56963000	ZNF genes & repeats	Fetal Kidney	kidney
20	chr19:56957400-56963200	ZNF genes & repeats	Fetal Lung	lung
21	chr19:56957400-56964000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:56957400-56964200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
23	chr19:56957400-56968000	ZNF genes & repeats	Brain Hippocampus Middle	brain
24	chr19:56957400-56974200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr19:56957400-56976800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
26	chr19:56957400-56985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr19:56957400-56987400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr19:56957400-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:56957600-56960800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
30	chr19:56957600-56961000	ZNF genes & repeats	Brain Substantia Nigra	brain
31	chr19:56957600-56961000	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr19:56957600-56961200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
33	chr19:56957600-56961600	ZNF genes & repeats	Liver	Liver
34	chr19:56957600-56961600	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:56957600-56962200	ZNF genes & repeats	Adipose Nuclei	Adipose
36	chr19:56957600-56962200	ZNF genes & repeats	Ovary	ovary
37	chr19:56957800-56961000	ZNF genes & repeats	Left Ventricle	heart
38	chr19:56957800-56961200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:56957800-56961600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:56957800-56961600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
41	chr19:56958000-56961000	ZNF genes & repeats	Aorta	Aorta
42	chr19:56958800-56961000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:56958800-56961200	ZNF genes & repeats	Fetal Stomach	stomach
44	chr19:56959200-56960800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr19:56959400-56960800	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr19:56959400-56960800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
47	chr19:56959400-56960800	ZNF genes & repeats	Pancreas	Pancrea
48	chr19:56959400-56960800	ZNF genes & repeats	HSMMtube	muscle
49	chr19:56959400-56961000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:56959400-56961000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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