Variant report

Variant	rs7180168
Chromosome Location	chr15:49582492-49582493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:49582379-49582670	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr15:49581820-49583032	SK-N-SH	brain:	n/a	chr15:49582892-49582906
3	RAD21	chr15:49582358-49582708	SK-N-SH_RA	brain:	n/a	n/a
4	TCF12	chr15:49582140-49582921	SK-N-SH	brain:	n/a	n/a
5	EP300	chr15:49582270-49582758	SK-N-SH_RA	brain:	n/a	n/a
6	GATA3	chr15:49582092-49582834	SK-N-SH	brain:	n/a	chr15:49582156-49582163 chr15:49582384-49582394
7	EP300	chr15:49582274-49582714	SK-N-SH_RA	brain:	n/a	n/a
8	POLR2A	chr15:49582293-49582704	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr15:49582288-49582845	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr15:49582272-49582786	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
GALK2	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10519224	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10519225	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11853969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11854039	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11854557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11855798	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11857515	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11858814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12591300	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12592508	0.92[CEU][hapmap]
rs12899422	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12900838	0.81[AFR][1000 genomes]
rs12901353	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12901929	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12902096	0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12902271	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12905094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12905203	0.85[CEU][hapmap]
rs12905477	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12914876	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12916839	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs17435932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17472989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17478694	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs17478785	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1961393	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34562714	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34748066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36023246	1.00[AFR][1000 genomes]
rs36100631	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4389093	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs4436732	0.84[AFR][1000 genomes]
rs4547278	0.84[AFR][1000 genomes]
rs4774538	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4775806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4775808	0.96[AFR][1000 genomes]
rs55979115	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62009834	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009977	0.84[AFR][1000 genomes]
rs6493372	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7497335	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8029687	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033184	0.91[EUR][1000 genomes]
rs8043493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9672848	0.81[AFR][1000 genomes]
rs9920722	0.85[CEU][hapmap]

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
rs7180168	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr15:49563800-49583200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:49564000-49586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:49564000-49593600	Weak transcription	HMEC	breast
14	chr15:49564200-49593600	Weak transcription	Lung	lung
15	chr15:49565400-49583600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:49565400-49602000	Weak transcription	Fetal Heart	heart
17	chr15:49565600-49583200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:49565800-49585200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:49566000-49585200	Weak transcription	GM12878-XiMat	blood
20	chr15:49566000-49586200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:49566200-49611800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:49566400-49595600	Weak transcription	Gastric	stomach
23	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr15:49572000-49583600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:49572000-49595800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:49572800-49600800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:49573400-49582800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:49573600-49613000	Weak transcription	Brain Germinal Matrix	brain
29	chr15:49573800-49588400	Weak transcription	Fetal Kidney	kidney
30	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:49574000-49588400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:49574200-49589000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:49574600-49588800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:49575600-49586800	Weak transcription	NH-A	brain
35	chr15:49575600-49587000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:49576400-49593600	Weak transcription	Stomach Mucosa	stomach
37	chr15:49576600-49583200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:49576600-49589600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:49576600-49605600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:49576800-49583800	Weak transcription	NHDF-Ad	bronchial
41	chr15:49576800-49584600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:49576800-49585200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:49576800-49611800	Weak transcription	Thymus	Thymus
44	chr15:49577000-49605800	Weak transcription	A549	lung
45	chr15:49577200-49607000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:49577400-49585200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:49577600-49605400	Weak transcription	Fetal Intestine Small	intestine
48	chr15:49577800-49596600	Weak transcription	HSMM	muscle
49	chr15:49577800-49611600	Weak transcription	Fetal Brain Female	brain
50	chr15:49578000-49582600	Weak transcription	Small Intestine	intestine

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