Variant report

Variant	rs6493361
Chromosome Location	chr15:49615952-49615953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10467992	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10851475	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11070692	0.88[CEU][hapmap]
rs11632063	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11858114	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12439429	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1429556	0.88[CEU][hapmap]
rs16962440	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1812926	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1904314	0.85[EUR][1000 genomes]
rs1904316	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2086256	0.96[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2127241	0.96[CEU][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2127242	0.96[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2127244	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2169932	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2219812	0.96[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2413937	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2413942	0.81[YRI][hapmap]
rs2580926	0.96[CEU][hapmap];0.80[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2663088	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28479967	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28728368	0.83[EUR][1000 genomes]
rs2899430	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2919148	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3098615	0.82[EUR][1000 genomes]
rs3098620	0.96[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3105861	0.96[CEU][hapmap]
rs4316697	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs4775804	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4775805	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4775807	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4775809	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs500122	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs568726	0.80[CHB][hapmap]
rs600863	0.96[CEU][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap]
rs626855	0.81[CHB][hapmap]
rs647118	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[YRI][hapmap]
rs6493363	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs679957	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs685172	0.84[CHB][hapmap]
rs7167555	0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7176455	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs735495	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs754165	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754166	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]
rs8025952	0.96[CEU][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8031480	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs8034661	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8034747	0.88[CEU][hapmap]
rs8040075	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8040134	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9806748	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[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
rs6493361	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs6493361	COPS2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
2	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
6	chr15:49586000-49617000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:49594000-49619400	Weak transcription	Stomach Mucosa	stomach
8	chr15:49596800-49620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:49597200-49622200	Weak transcription	NH-A	brain
10	chr15:49597200-49624800	Weak transcription	Fetal Kidney	kidney
11	chr15:49597400-49624200	Weak transcription	K562	blood
12	chr15:49599200-49636800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:49606400-49622200	Weak transcription	HSMM	muscle
14	chr15:49607000-49622200	Weak transcription	NHDF-Ad	bronchial
15	chr15:49607200-49623800	Weak transcription	Psoas Muscle	Psoas
16	chr15:49607600-49624400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:49607800-49622200	Weak transcription	Brain Substantia Nigra	brain
18	chr15:49608000-49631800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:49608600-49631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:49609600-49621200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:49610400-49622400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:49611000-49616000	Strong transcription	Primary T cells from cord blood	blood
23	chr15:49611000-49616200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:49611000-49616400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr15:49611800-49616000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:49612000-49624200	Weak transcription	Lung	lung
27	chr15:49612200-49623200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr15:49612200-49631600	Weak transcription	Fetal Intestine Small	intestine
29	chr15:49612200-49639000	Weak transcription	NHEK	skin
30	chr15:49612600-49620800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:49612600-49622200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:49612600-49639400	Weak transcription	Right Ventricle	heart
33	chr15:49612800-49620200	Weak transcription	Dnd41	blood
34	chr15:49612800-49626600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:49612800-49638000	Weak transcription	Brain Angular Gyrus	brain
36	chr15:49613000-49616000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:49613000-49617600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:49613000-49620000	Weak transcription	HSMMtube	muscle
39	chr15:49613000-49622600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:49613000-49622600	Weak transcription	Brain Anterior Caudate	brain
41	chr15:49613000-49624400	Weak transcription	GM12878-XiMat	blood
42	chr15:49613000-49627600	Weak transcription	HUVEC	blood vessel
43	chr15:49613000-49628200	Weak transcription	Ovary	ovary
44	chr15:49613000-49633200	Weak transcription	Gastric	stomach
45	chr15:49613200-49621600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:49613200-49623200	Weak transcription	HMEC	breast
47	chr15:49613200-49625000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:49613200-49625000	Weak transcription	Hela-S3	cervix
49	chr15:49613200-49633200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr15:49613600-49617600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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