Variant report

Variant	rs12591659
Chromosome Location	chr15:49933823-49933824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49926653..49929623-chr15:49932386..49934262,2	K562	blood:
2	chr15:49925299..49927581-chr15:49932841..49935051,2	MCF-7	breast:
3	chr15:49932896..49934447-chr15:49935029..49936774,2	MCF-7	breast:
4	chr15:49922511..49924888-chr15:49932196..49934708,2	K562	blood:
5	chr15:49912557..49915525-chr15:49931219..49934406,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104047	Chromatin interaction
ENSG00000166262	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10851478	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10851479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070699	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11070706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11634947	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11637582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11852336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11853248	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11854671	0.83[ASN][1000 genomes]
rs11858411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12050614	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12050624	0.91[ASN][1000 genomes]
rs12148716	0.92[AFR][1000 genomes]
rs12148764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12232355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593151	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12595692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12901680	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12902960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12906134	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906972	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12907661	0.86[ASN][1000 genomes]
rs12907918	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12907944	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12908624	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12908635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912703	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916839	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1395901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1395903	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17402115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17404727	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17478694	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17478785	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17479589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1874616	0.82[JPT][hapmap]
rs1911612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1948975	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2202714	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2413956	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34002493	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34146550	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34246470	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34414487	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34694913	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34941109	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35698479	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4389093	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4436732	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4480740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4547278	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775816	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55904469	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62009977	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62021589	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62022665	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62022667	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62022700	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7162741	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7172906	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7180421	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs753857	0.82[JPT][hapmap]
rs8032688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033476	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs925104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9920722	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12591659	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49913600-49937400	Weak transcription	Spleen	Spleen
2	chr15:49914400-49936400	Weak transcription	Small Intestine	intestine
3	chr15:49914400-49938000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:49914600-49934400	Weak transcription	Stomach Mucosa	stomach
5	chr15:49914800-49937800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:49915000-49936600	Weak transcription	Pancreas	Pancrea
7	chr15:49915400-49937800	Weak transcription	Brain Anterior Caudate	brain
8	chr15:49916000-49936400	Weak transcription	Psoas Muscle	Psoas
9	chr15:49918000-49938600	Weak transcription	Right Ventricle	heart
10	chr15:49918000-49938800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:49918200-49934000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:49918200-49934000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:49918200-49935800	Weak transcription	Brain Germinal Matrix	brain
14	chr15:49918200-49936200	Weak transcription	Aorta	Aorta
15	chr15:49918200-49936600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:49918200-49936600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:49918200-49937200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:49918200-49938000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:49918200-49938400	Weak transcription	HepG2	liver
20	chr15:49918200-49942200	Weak transcription	GM12878-XiMat	blood
21	chr15:49918400-49938000	Weak transcription	Colonic Mucosa	Colon
22	chr15:49918600-49938800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:49919800-49940200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:49920000-49938200	Weak transcription	Brain Angular Gyrus	brain
25	chr15:49920000-49940400	Weak transcription	A549	lung
26	chr15:49920200-49936600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:49920800-49936400	Weak transcription	K562	blood
28	chr15:49920800-49937800	Weak transcription	NHEK	skin
29	chr15:49920800-49938000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:49920800-49940000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:49921000-49935600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:49921000-49937600	Weak transcription	HMEC	breast
33	chr15:49921400-49934400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:49922000-49934400	Strong transcription	Hela-S3	cervix
35	chr15:49924000-49936400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:49924400-49935400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:49925200-49936400	Weak transcription	NHLF	lung
38	chr15:49925400-49935200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:49926000-49938000	Weak transcription	NH-A	brain
40	chr15:49927000-49940000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:49927600-49938800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:49927800-49936800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:49927800-49938600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:49928000-49936600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:49928000-49940200	Weak transcription	Fetal Intestine Small	intestine
46	chr15:49928200-49936200	Weak transcription	Primary T cells from cord blood	blood
47	chr15:49928200-49936200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:49928200-49936200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:49928200-49936200	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:49928200-49936200	Weak transcription	HSMMtube	muscle

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