Variant report

Variant	rs28373215
Chromosome Location	chr19:56954933-56954934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10408270	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10408604	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10413169	0.96[ASN][1000 genomes]
rs10415307	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10416345	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10419332	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10421407	0.94[ASN][1000 genomes]
rs10432288	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084446	0.82[EUR][1000 genomes]
rs11084449	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11084450	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11667815	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12460342	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12608966	0.82[EUR][1000 genomes]
rs12610115	0.86[EUR][1000 genomes]
rs12973407	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12981146	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12981443	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288860	0.84[EUR][1000 genomes]
rs2904016	0.84[EUR][1000 genomes]
rs2904017	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35027158	0.96[ASN][1000 genomes]
rs35869148	0.96[ASN][1000 genomes]
rs35914474	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745826	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3760849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810340	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4281830	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4801163	0.94[ASN][1000 genomes]
rs4801319	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56301546	0.84[EUR][1000 genomes]
rs59858465	0.84[EUR][1000 genomes]
rs62121590	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62121593	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248278	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250817	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252607	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7258010	0.82[EUR][1000 genomes]
rs728232	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104319	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104585	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8112531	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8112935	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs917650	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917651	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917652	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304776	0.93[ASN][1000 genomes]
rs9749140	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9789281	0.95[EUR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28373215	ZNF582-AS1	cis	lung	GTEx
rs28373215	ZNF582-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56916400-56956000	ZNF genes & repeats	Liver	Liver
2	chr19:56916600-56956000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:56946800-56956000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:56948200-56955800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
5	chr19:56948200-56956000	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:56949400-56955800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
7	chr19:56949400-56956000	ZNF genes & repeats	Brain Anterior Caudate	brain
8	chr19:56949400-56956000	ZNF genes & repeats	Brain Hippocampus Middle	brain
9	chr19:56949600-56955800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:56949800-56956000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:56950000-56955400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr19:56950200-56955800	ZNF genes & repeats	Fetal Brain Male	brain
13	chr19:56950200-56956000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:56950400-56955800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:56950400-56956000	ZNF genes & repeats	Fetal Brain Female	brain
16	chr19:56950600-56955800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr19:56950600-56956000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr19:56950800-56956000	ZNF genes & repeats	Brain Substantia Nigra	brain
19	chr19:56951000-56955800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
20	chr19:56951200-56956000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:56951600-56955400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:56951600-56955600	ZNF genes & repeats	Fetal Kidney	kidney
23	chr19:56951600-56958400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:56952000-56955800	ZNF genes & repeats	Psoas Muscle	Psoas
25	chr19:56952200-56955800	ZNF genes & repeats	Fetal Lung	lung
26	chr19:56952200-56956000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
27	chr19:56952200-56956000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr19:56952200-56956000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:56952200-56956000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:56952400-56955000	ZNF genes & repeats	Fetal Heart	heart
31	chr19:56952400-56955800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:56952400-56955800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
33	chr19:56952400-56955800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
34	chr19:56952400-56955800	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:56952400-56955800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
36	chr19:56952600-56955000	ZNF genes & repeats	HSMM	muscle
37	chr19:56952600-56955800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr19:56952600-56955800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:56952600-56955800	ZNF genes & repeats	Brain Angular Gyrus	brain
40	chr19:56952600-56955800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:56952600-56955800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
42	chr19:56952600-56955800	ZNF genes & repeats	Right Ventricle	heart
43	chr19:56952600-56956000	ZNF genes & repeats	Ovary	ovary
44	chr19:56952800-56956000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr19:56953000-56955600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:56953400-56955200	Weak transcription	Aorta	Aorta
47	chr19:56953600-56955200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr19:56953600-56955600	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:56953600-56955800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
50	chr19:56953800-56955200	Strong transcription	Brain Germinal Matrix	brain

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