Variant report

Variant	rs563533
Chromosome Location	chr15:49465581-49465582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:49465460-49465610	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:49462876..49466490-chr15:49481891..49484473,3	K562	blood:
2	chr15:49463826..49467662-chr15:49477786..49482554,6	K562	blood:
3	chr15:49464639..49466779-chr15:49488550..49492378,3	K562	blood:
4	chr15:49463856..49466607-chr15:49479734..49481312,2	K562	blood:
5	chr15:49446471..49449731-chr15:49460521..49465602,13	MCF-7	breast:
6	chr15:49464598..49467246-chr15:49506406..49508580,2	K562	blood:

No data

Variant related genes	Relation type
MIR4716	TF binding region
ENSG00000156958	Chromatin interaction
ENSG00000166200	Chromatin interaction
ENSG00000243338	Chromatin interaction
ENSG00000259467	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1048975	0.88[ASN][1000 genomes]
rs10775139	0.80[ASN][1000 genomes]
rs11629547	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632063	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858114	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12440709	0.80[ASN][1000 genomes]
rs12442679	0.81[ASN][1000 genomes]
rs12898691	0.80[ASN][1000 genomes]
rs12902875	0.83[ASN][1000 genomes]
rs1812926	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2086256	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2127241	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127242	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127244	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2169932	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2219812	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2263559	0.96[ASN][1000 genomes]
rs2413935	0.93[ASN][1000 genomes]
rs2413937	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2457228	0.98[ASN][1000 genomes]
rs2580923	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2580926	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2663088	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2663089	0.91[ASN][1000 genomes]
rs2663090	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437582	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28479967	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28539950	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28728368	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28731311	0.98[ASN][1000 genomes]
rs2899430	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2919148	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940745	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2940746	0.96[ASN][1000 genomes]
rs3098615	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098620	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3105861	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105863	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34854443	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775804	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775805	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4775807	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs490621	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs491277	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs500122	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55736202	0.98[ASN][1000 genomes]
rs568726	0.98[ASN][1000 genomes]
rs600863	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603868	0.93[ASN][1000 genomes]
rs626855	0.98[ASN][1000 genomes]
rs671945	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs679957	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs685172	0.98[ASN][1000 genomes]
rs7167338	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7167555	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7176455	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs754165	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs754166	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8025952	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8040075	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs563533	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs563533	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49462200-49465800	Active TSS	K562	blood
2	chr15:49463000-49466600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:49463000-49479600	Weak transcription	Left Ventricle	heart
4	chr15:49463200-49466400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:49463200-49467200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:49463200-49467200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:49463200-49467600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr15:49463200-49467600	Weak transcription	Stomach Mucosa	stomach
9	chr15:49463200-49471800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:49463200-49472000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:49463200-49472000	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:49463200-49479600	Weak transcription	Right Ventricle	heart
13	chr15:49463200-49479800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:49463200-49508200	Weak transcription	Ovary	ovary
15	chr15:49463400-49467400	Weak transcription	Fetal Intestine Small	intestine
16	chr15:49463400-49469800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:49463400-49480000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:49463600-49471400	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:49463600-49472400	Weak transcription	HUVEC	blood vessel
20	chr15:49463600-49474200	Weak transcription	Fetal Stomach	stomach
21	chr15:49463600-49474400	Weak transcription	Primary B cells from cord blood	blood
22	chr15:49463600-49477200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:49463600-49479400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:49463600-49479600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:49463600-49494400	Weak transcription	Fetal Thymus	thymus
26	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:49463600-49527800	Weak transcription	HSMM	muscle
28	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
29	chr15:49463800-49465600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr15:49463800-49465600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr15:49463800-49467000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:49463800-49467200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:49463800-49467200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:49463800-49468000	Weak transcription	Fetal Brain Male	brain
35	chr15:49463800-49471600	Weak transcription	HMEC	breast
36	chr15:49463800-49472400	Weak transcription	Fetal Brain Female	brain
37	chr15:49463800-49472600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:49463800-49472600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:49463800-49472800	Weak transcription	Fetal Lung	lung
40	chr15:49463800-49479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:49463800-49479400	Weak transcription	Osteobl	bone
42	chr15:49464000-49467000	Weak transcription	A549	lung
43	chr15:49464000-49469600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:49464000-49474400	Weak transcription	NHDF-Ad	bronchial
45	chr15:49464000-49482800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr15:49464000-49491600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:49464200-49466600	Weak transcription	Spleen	Spleen
48	chr15:49464200-49467200	Weak transcription	Gastric	stomach
49	chr15:49464200-49467200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr15:49464200-49467200	Weak transcription	HepG2	liver

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