Variant report

Variant	rs754166
Chromosome Location	chr15:49596962-49596963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49591113..49594727-chr15:49595411..49597840,3	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10467992	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1048975	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10851475	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11070692	0.92[CEU][hapmap]
rs11629547	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11632063	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11633810	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs11858114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12438777	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1429556	0.92[CEU][hapmap]
rs1812926	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864299	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs1904314	0.85[EUR][1000 genomes]
rs1981995	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2086256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2127242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2127244	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2169932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2219812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2247517	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2263559	0.85[ASN][1000 genomes]
rs2413935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2413937	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2413939	0.81[AMR][1000 genomes]
rs2457228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2580923	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2580926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2663088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2663089	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2663090	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28479967	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28539950	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28728368	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28731311	0.84[ASN][1000 genomes]
rs2899430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2899431	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2919148	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2940746	0.85[ASN][1000 genomes]
rs3098613	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs3098615	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3098619	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs3098620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3098621	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3105858	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3105861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3105863	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3105864	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs3105866	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs34854443	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3907313	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4316697	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4774537	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4775804	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775805	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4775807	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775809	0.87[EUR][1000 genomes]
rs481466	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs489813	0.89[CHB][hapmap]
rs490621	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs500122	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55736202	0.84[ASN][1000 genomes]
rs563533	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs568726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs600863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs604765	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs612803	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs626295	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs626855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs647118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6493356	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6493357	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6493361	0.96[CEU][hapmap];0.80[CHB][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493363	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs671945	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs679957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs685172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7166847	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7167338	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7167555	0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7176455	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179127	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs735495	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs754165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034661	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034747	0.92[CEU][hapmap]
rs8039512	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs8040075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9806748	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs754166	COPS2	Cis_1M	lymphoblastoid	RTeQTL
rs754166	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49557200-49611800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:49557800-49607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
4	chr15:49558200-49611800	Weak transcription	Colonic Mucosa	Colon
5	chr15:49561000-49600800	Weak transcription	Pancreas	Pancrea
6	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:49563600-49611000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:49565400-49602000	Weak transcription	Fetal Heart	heart
9	chr15:49566200-49611800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:49572800-49600800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:49573600-49613000	Weak transcription	Brain Germinal Matrix	brain
13	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:49576600-49605600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:49576800-49611800	Weak transcription	Thymus	Thymus
16	chr15:49577000-49605800	Weak transcription	A549	lung
17	chr15:49577200-49607000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:49577600-49605400	Weak transcription	Fetal Intestine Small	intestine
19	chr15:49577800-49611600	Weak transcription	Fetal Brain Female	brain
20	chr15:49578200-49604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:49578200-49611000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:49578400-49605400	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:49578400-49611200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:49579400-49612000	Weak transcription	HUVEC	blood vessel
25	chr15:49580600-49615600	Weak transcription	Fetal Brain Male	brain
26	chr15:49580800-49605600	Weak transcription	NHEK	skin
27	chr15:49581200-49607400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:49581400-49607600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:49582200-49611400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
31	chr15:49583000-49606800	Weak transcription	Fetal Stomach	stomach
32	chr15:49583200-49600800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:49583200-49611400	Weak transcription	Small Intestine	intestine
34	chr15:49583400-49600800	Weak transcription	HSMMtube	muscle
35	chr15:49584000-49605800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:49584000-49607400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:49584000-49607400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:49584800-49600600	Weak transcription	Hela-S3	cervix
39	chr15:49585600-49607200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:49585600-49612800	Weak transcription	Fetal Thymus	thymus
41	chr15:49585800-49600800	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:49586000-49617000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:49586200-49611200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:49588800-49607400	Weak transcription	Brain Substantia Nigra	brain
45	chr15:49588800-49611200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:49588800-49611600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:49589200-49607400	Weak transcription	Brain Angular Gyrus	brain
48	chr15:49591400-49600800	Weak transcription	Psoas Muscle	Psoas
49	chr15:49593000-49601400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr15:49593200-49599400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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