Variant report

Variant	rs28566064
Chromosome Location	chr15:49416462-49416463
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49414952..49417698-chr15:49422729..49425461,2	K562	blood:
2	chr15:49414600..49417536-chr15:49446435..49449033,2	MCF-7	breast:
3	chr15:49404329..49407457-chr15:49414444..49416690,3	K562	blood:

Variant related genes	Relation type
ENSG00000156958	Chromatin interaction
ENSG00000166200	Chromatin interaction
ENSG00000259467	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1048975	0.83[AMR][1000 genomes]
rs11630937	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632386	0.83[EUR][1000 genomes]
rs11633810	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12437486	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12438777	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12899761	0.80[AMR][1000 genomes]
rs16962111	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1864299	0.81[AMR][1000 genomes]
rs1981995	0.80[AMR][1000 genomes]
rs2247003	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2247517	0.81[AMR][1000 genomes]
rs2264508	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2289390	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413935	0.81[AMR][1000 genomes]
rs2413941	0.80[AMR][1000 genomes]
rs2439133	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2457229	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2663089	0.81[AMR][1000 genomes]
rs28653543	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2899431	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3098613	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3098619	0.85[EUR][1000 genomes]
rs3098621	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3105858	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3105864	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3105866	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4393519	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4774537	0.81[AMR][1000 genomes]
rs481466	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs489813	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs507054	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs520495	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58851861	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs603868	0.81[AMR][1000 genomes]
rs604765	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs609434	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs612803	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs619045	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62009779	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs626295	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs633333	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6493356	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493357	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66499252	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs672777	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs694882	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7168201	0.81[AMR][1000 genomes]
rs7169443	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7179127	0.80[AMR][1000 genomes]
rs8182081	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28566064	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49388800-49418800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:49388800-49434800	Weak transcription	Small Intestine	intestine
3	chr15:49395400-49419000	Weak transcription	Fetal Kidney	kidney
4	chr15:49395600-49426400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:49396000-49419600	Weak transcription	NHEK	skin
6	chr15:49396400-49418800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:49398600-49427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:49403000-49417200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:49403000-49434600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:49403200-49423400	Weak transcription	Psoas Muscle	Psoas
11	chr15:49403400-49419600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:49403400-49440200	Weak transcription	Pancreas	Pancrea
13	chr15:49403600-49423600	Weak transcription	Esophagus	oesophagus
14	chr15:49403600-49432200	Weak transcription	Fetal Stomach	stomach
15	chr15:49403600-49435200	Weak transcription	Aorta	Aorta
16	chr15:49403600-49435200	Weak transcription	Gastric	stomach
17	chr15:49403600-49435400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:49403800-49417400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:49403800-49419400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:49403800-49433200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:49404000-49419800	Weak transcription	NHLF	lung
22	chr15:49404400-49419800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:49404600-49424000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:49404800-49417200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:49404800-49417600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr15:49404800-49419000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:49404800-49419000	Weak transcription	Primary T cells from cord blood	blood
28	chr15:49404800-49419000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:49404800-49419200	Weak transcription	Brain Angular Gyrus	brain
30	chr15:49404800-49419400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:49404800-49419400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:49404800-49419400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:49404800-49419600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:49404800-49419600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:49404800-49419600	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:49404800-49419600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:49404800-49419600	Weak transcription	Ovary	ovary
38	chr15:49404800-49419600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:49404800-49419800	Weak transcription	Left Ventricle	heart
40	chr15:49404800-49419800	Weak transcription	Thymus	Thymus
41	chr15:49404800-49423400	Weak transcription	HepG2	liver
42	chr15:49404800-49425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:49404800-49434600	Weak transcription	Right Ventricle	heart
44	chr15:49404800-49435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:49405000-49416800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:49405000-49417000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:49405000-49417400	Weak transcription	Adipose Nuclei	Adipose
48	chr15:49405000-49417400	Weak transcription	Placenta	Placenta
49	chr15:49405000-49417400	Weak transcription	K562	blood
50	chr15:49405000-49418600	Weak transcription	Fetal Thymus	thymus

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