Variant report

Variant	rs10408270
Chromosome Location	chr19:56960809-56960810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10408604	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413169	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10415307	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10416345	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10419332	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10421407	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10432288	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11084449	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11084450	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11667815	0.80[EUR][1000 genomes]
rs12460342	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12609819	0.81[EUR][1000 genomes]
rs12973407	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12981146	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12981443	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28373215	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2904017	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35027158	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35869148	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35914474	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3745826	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3760849	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810340	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4281830	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4801163	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4801319	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62121590	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62121593	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248278	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7250817	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7252607	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs728232	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8104319	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8104585	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8112531	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8112935	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917650	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs917651	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs917652	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9304776	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9749140	0.87[EUR][1000 genomes]
rs9789281	0.85[EUR][1000 genomes];0.81[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
rs10408270	ZNF582-AS1	cis	lung	GTEx
rs10408270	ZNF582-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:49 , 50 per page) page: 1

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	chr19:56957400-56961600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr19:56957400-56961600	ZNF genes & repeats	Brain Angular Gyrus	brain
5	chr19:56957400-56961800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
6	chr19:56957400-56961800	ZNF genes & repeats	Brain Germinal Matrix	brain
7	chr19:56957400-56962000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:56957400-56962000	ZNF genes & repeats	Fetal Brain Female	brain
9	chr19:56957400-56963000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
10	chr19:56957400-56963000	ZNF genes & repeats	Fetal Brain Male	brain
11	chr19:56957400-56963000	ZNF genes & repeats	Fetal Kidney	kidney
12	chr19:56957400-56963200	ZNF genes & repeats	Fetal Lung	lung
13	chr19:56957400-56964000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:56957400-56964200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr19:56957400-56968000	ZNF genes & repeats	Brain Hippocampus Middle	brain
16	chr19:56957400-56974200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:56957400-56976800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr19:56957400-56985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
19	chr19:56957400-56987400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr19:56957400-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:56957600-56961000	ZNF genes & repeats	Brain Substantia Nigra	brain
22	chr19:56957600-56961000	ZNF genes & repeats	Fetal Muscle Leg	muscle
23	chr19:56957600-56961200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
24	chr19:56957600-56961600	ZNF genes & repeats	Liver	Liver
25	chr19:56957600-56961600	ZNF genes & repeats	Colon Smooth Muscle	Colon
26	chr19:56957600-56962200	ZNF genes & repeats	Adipose Nuclei	Adipose
27	chr19:56957600-56962200	ZNF genes & repeats	Ovary	ovary
28	chr19:56957800-56961000	ZNF genes & repeats	Left Ventricle	heart
29	chr19:56957800-56961200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:56957800-56961600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:56957800-56961600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
32	chr19:56958000-56961000	ZNF genes & repeats	Aorta	Aorta
33	chr19:56958800-56961000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:56958800-56961200	ZNF genes & repeats	Fetal Stomach	stomach
35	chr19:56959400-56961000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:56959400-56961000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:56959400-56961000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:56959400-56961000	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr19:56959400-56961600	ZNF genes & repeats	Dnd41	blood
40	chr19:56959600-56961000	ZNF genes & repeats	Placenta Amnion	Placenta Amnion
41	chr19:56959800-56961000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:56960000-56961600	ZNF genes & repeats	Right Ventricle	heart
43	chr19:56960400-56963200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr19:56960400-56968400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr19:56960600-56968600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:56960600-56969200	Weak transcription	Thymus	Thymus
47	chr19:56960600-56973800	Weak transcription	HSMM	muscle
48	chr19:56960800-56967600	Weak transcription	HSMMtube	muscle
49	chr19:56960800-56968400	Weak transcription	Pancreas	Pancrea

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