Variant report

Variant	rs62009834
Chromosome Location	chr15:49588356-49588357
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10519224	1.00[AFR][1000 genomes]
rs10519225	1.00[AFR][1000 genomes]
rs11853969	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11854039	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11854557	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11855798	1.00[AFR][1000 genomes]
rs11857515	0.88[AFR][1000 genomes]
rs11858814	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12591300	0.96[AFR][1000 genomes]
rs12899422	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12900838	0.81[AFR][1000 genomes]
rs12901353	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12901929	1.00[AFR][1000 genomes]
rs12902096	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12902271	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12905094	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12905477	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12914876	0.88[AFR][1000 genomes]
rs12916839	0.88[AFR][1000 genomes]
rs17435932	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17472989	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17478694	0.92[AFR][1000 genomes]
rs17478785	0.92[AFR][1000 genomes]
rs1961393	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289389	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34562714	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34748066	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36023246	1.00[AFR][1000 genomes]
rs36100631	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4436732	0.84[AFR][1000 genomes]
rs4547278	0.84[AFR][1000 genomes]
rs4774538	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4775806	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4775808	0.96[AFR][1000 genomes]
rs55979115	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62009977	0.84[AFR][1000 genomes]
rs6493372	0.84[AFR][1000 genomes]
rs7180168	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7497335	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8029687	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033184	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8043493	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9672848	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62009834	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
2	chr15:49541600-49595800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:49557200-49611800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:49557800-49607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
6	chr15:49558200-49611800	Weak transcription	Colonic Mucosa	Colon
7	chr15:49561000-49600800	Weak transcription	Pancreas	Pancrea
8	chr15:49562000-49595800	Weak transcription	HepG2	liver
9	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:49563600-49611000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:49564000-49593600	Weak transcription	HMEC	breast
12	chr15:49564200-49593600	Weak transcription	Lung	lung
13	chr15:49565400-49602000	Weak transcription	Fetal Heart	heart
14	chr15:49566200-49611800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:49566400-49595600	Weak transcription	Gastric	stomach
16	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:49572000-49595800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:49572800-49600800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:49573600-49613000	Weak transcription	Brain Germinal Matrix	brain
20	chr15:49573800-49588400	Weak transcription	Fetal Kidney	kidney
21	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:49574000-49588400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:49574200-49589000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr15:49574600-49588800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:49576400-49593600	Weak transcription	Stomach Mucosa	stomach
26	chr15:49576600-49589600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:49576600-49605600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:49576800-49611800	Weak transcription	Thymus	Thymus
29	chr15:49577000-49605800	Weak transcription	A549	lung
30	chr15:49577200-49607000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:49577600-49605400	Weak transcription	Fetal Intestine Small	intestine
32	chr15:49577800-49596600	Weak transcription	HSMM	muscle
33	chr15:49577800-49611600	Weak transcription	Fetal Brain Female	brain
34	chr15:49578000-49596400	Weak transcription	Placenta	Placenta
35	chr15:49578200-49590400	Weak transcription	Brain Anterior Caudate	brain
36	chr15:49578200-49593600	Weak transcription	Osteobl	bone
37	chr15:49578200-49595800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:49578200-49604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:49578200-49611000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:49578400-49605400	Weak transcription	Colon Smooth Muscle	Colon
41	chr15:49578400-49611200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:49579400-49612000	Weak transcription	HUVEC	blood vessel
43	chr15:49580000-49588800	Strong transcription	Primary T cells from cord blood	blood
44	chr15:49580400-49588800	Strong transcription	Liver	Liver
45	chr15:49580600-49588400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:49580600-49615600	Weak transcription	Fetal Brain Male	brain
47	chr15:49580800-49605600	Weak transcription	NHEK	skin
48	chr15:49581000-49588600	Weak transcription	Brain Substantia Nigra	brain
49	chr15:49581200-49607400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:49581400-49607600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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