Variant report

Variant	rs8041781
Chromosome Location	chr15:49590114-49590115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10519230	0.91[CEU][hapmap];0.96[CHB][hapmap]
rs11070686	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070693	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11630629	0.84[CEU][hapmap]
rs11631040	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11636671	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11636795	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs11852524	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs12440534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12900001	1.00[CHB][hapmap]
rs12913745	0.82[CEU][hapmap]
rs16962243	0.83[JPT][hapmap]
rs16962490	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1904317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2243899	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs2413936	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2413939	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2413942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2580924	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2940747	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3098614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3105861	0.82[YRI][hapmap]
rs3105865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3105867	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs485182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs520949	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532209	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs568994	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs586758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs641077	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493369	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs8032650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8041823	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920772	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][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
rs8041781	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 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	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:49576400-49593600	Weak transcription	Stomach Mucosa	stomach
22	chr15:49576600-49605600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:49576800-49611800	Weak transcription	Thymus	Thymus
24	chr15:49577000-49605800	Weak transcription	A549	lung
25	chr15:49577200-49607000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:49577600-49605400	Weak transcription	Fetal Intestine Small	intestine
27	chr15:49577800-49596600	Weak transcription	HSMM	muscle
28	chr15:49577800-49611600	Weak transcription	Fetal Brain Female	brain
29	chr15:49578000-49596400	Weak transcription	Placenta	Placenta
30	chr15:49578200-49590400	Weak transcription	Brain Anterior Caudate	brain
31	chr15:49578200-49593600	Weak transcription	Osteobl	bone
32	chr15:49578200-49595800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:49578200-49604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:49578200-49611000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:49578400-49605400	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:49578400-49611200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:49579400-49612000	Weak transcription	HUVEC	blood vessel
38	chr15:49580600-49615600	Weak transcription	Fetal Brain Male	brain
39	chr15:49580800-49605600	Weak transcription	NHEK	skin
40	chr15:49581200-49607400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:49581400-49607600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:49582200-49611400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
44	chr15:49582800-49595600	Weak transcription	Aorta	Aorta
45	chr15:49583000-49606800	Weak transcription	Fetal Stomach	stomach
46	chr15:49583200-49595600	Weak transcription	Ovary	ovary
47	chr15:49583200-49600800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:49583200-49611400	Weak transcription	Small Intestine	intestine
49	chr15:49583400-49600800	Weak transcription	HSMMtube	muscle
50	chr15:49583800-49595600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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