Variant report

Variant	rs2663088
Chromosome Location	chr15:49528702-49528703
allele	A/G
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	chr15:49527148-49529664	SK-N-SH	brain:	n/a	chr15:49527963-49527982 chr15:49527968-49527980 chr15:49527967-49527976
2	SMC3	chr15:49527563-49529610	SK-N-SH	brain:	n/a	chr15:49527964-49527978

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49527986..49530632-chr15:49532231..49535128,2	K562	blood:
2	chr15:49527930..49530105-chr15:49533812..49536591,2	MCF-7	breast:

Variant related genes	Relation type
GALK2	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10467992	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1048975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10775139	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10851475	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs11070682	1.00[CHB][hapmap]
rs11070692	0.92[CEU][hapmap]
rs11629547	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632063	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11633810	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11858114	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12438777	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12904344	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1429556	0.92[CEU][hapmap]
rs1812926	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1864299	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1981995	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2086256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2127241	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];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127244	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2169932	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2219812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247517	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2263559	0.96[ASN][1000 genomes]
rs2413935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2413937	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413939	0.82[AMR][1000 genomes]
rs2413942	0.81[YRI][hapmap]
rs2457228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2580923	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2580926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2663089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2663090	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28437582	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28479967	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28539950	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28728368	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28731311	0.94[ASN][1000 genomes]
rs2899427	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2899430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2899431	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2919148	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940745	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2940746	0.96[ASN][1000 genomes]
rs3098613	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3098615	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098619	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3098620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3105863	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3105864	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3105866	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs34854443	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3907313	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4774537	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4775804	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775807	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs481466	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs489813	0.89[CHB][hapmap]
rs490621	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs500122	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55736202	0.94[ASN][1000 genomes]
rs563533	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs568726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs600863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs603868	0.90[ASN][1000 genomes]
rs604765	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs612803	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs626295	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs626855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs647118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs6493356	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6493357	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6493361	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]
rs6493363	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs671945	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs679957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs685172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7166847	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7167338	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7167555	0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7176455	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7179127	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs735495	0.89[CEU][hapmap]
rs754165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs754166	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]
rs8025952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8034661	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8034747	0.92[CEU][hapmap]
rs8039512	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs8040075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9806748	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2663088	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
2	chr15:49487200-49531200	Weak transcription	HMEC	breast
3	chr15:49492000-49530200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
5	chr15:49504200-49530800	Weak transcription	Fetal Thymus	thymus
6	chr15:49508800-49535800	Weak transcription	A549	lung
7	chr15:49510000-49541800	Weak transcription	NHEK	skin
8	chr15:49510200-49537000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:49510800-49534400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr15:49511400-49530600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:49511800-49531400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:49511800-49532200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:49516000-49531400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:49518000-49535400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:49518000-49541000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:49518200-49548600	Weak transcription	Aorta	Aorta
17	chr15:49518600-49532000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:49518600-49557600	Weak transcription	Esophagus	oesophagus
19	chr15:49518800-49539200	Weak transcription	Ovary	ovary
20	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
21	chr15:49520600-49531200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:49520800-49531400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:49522000-49534600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:49522000-49537800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:49522000-49538200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:49522000-49540400	Weak transcription	Stomach Mucosa	stomach
27	chr15:49522200-49531400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr15:49522200-49535000	Weak transcription	Left Ventricle	heart
29	chr15:49522400-49559400	Weak transcription	Pancreas	Pancrea
30	chr15:49522600-49534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:49522600-49535200	Weak transcription	Gastric	stomach
32	chr15:49522800-49531400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:49523800-49534800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:49523800-49540200	Weak transcription	Spleen	Spleen
35	chr15:49524400-49530800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:49524600-49531400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr15:49524600-49531400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:49524600-49531400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:49524600-49535200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:49524600-49535200	Weak transcription	Placenta	Placenta
41	chr15:49524600-49535200	Weak transcription	Thymus	Thymus
42	chr15:49524600-49539200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:49524600-49544800	Weak transcription	Lung	lung
44	chr15:49524800-49530200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:49524800-49530600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:49524800-49530600	Weak transcription	Liver	Liver
47	chr15:49524800-49531400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:49525000-49530200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:49525000-49531400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:49525000-49534600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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