Variant report

Variant	rs28728368
Chromosome Location	chr15:49477476-49477477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10467992	0.83[EUR][1000 genomes]
rs1048975	0.86[ASN][1000 genomes]
rs11629547	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632063	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858114	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902875	0.81[ASN][1000 genomes]
rs1812926	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2086256	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2127241	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2127242	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2127244	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2169932	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2219812	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2263559	0.98[ASN][1000 genomes]
rs2413935	0.92[ASN][1000 genomes]
rs2413937	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2457228	0.96[ASN][1000 genomes]
rs2580923	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2580926	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2663088	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2663089	0.90[ASN][1000 genomes]
rs2663090	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28437582	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28479967	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28539950	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28731311	0.96[ASN][1000 genomes]
rs2899430	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919148	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940745	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2940746	0.98[ASN][1000 genomes]
rs3098615	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3098620	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105861	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3105863	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34854443	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4775804	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775805	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775807	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs490621	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs491277	0.88[AMR][1000 genomes]
rs500122	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736202	0.96[ASN][1000 genomes]
rs563533	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568726	0.96[ASN][1000 genomes]
rs600863	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603868	0.92[ASN][1000 genomes]
rs626855	0.96[ASN][1000 genomes]
rs6493361	0.83[EUR][1000 genomes]
rs6493363	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs671945	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679957	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs685172	0.96[ASN][1000 genomes]
rs7167338	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7167555	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176455	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs754165	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754166	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025952	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8034661	0.83[EUR][1000 genomes]
rs8040075	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9806748	0.84[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28728368	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463000-49479600	Weak transcription	Left Ventricle	heart
2	chr15:49463200-49479600	Weak transcription	Right Ventricle	heart
3	chr15:49463200-49479800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:49463200-49508200	Weak transcription	Ovary	ovary
5	chr15:49463400-49480000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:49463600-49479400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:49463600-49479600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:49463600-49494400	Weak transcription	Fetal Thymus	thymus
9	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:49463600-49527800	Weak transcription	HSMM	muscle
11	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
12	chr15:49463800-49479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:49463800-49479400	Weak transcription	Osteobl	bone
14	chr15:49464000-49482800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:49464000-49491600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:49464200-49479200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:49464200-49479400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:49464200-49481800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:49464400-49493800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:49464400-49493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:49464400-49500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:49464800-49479600	Weak transcription	NHLF	lung
23	chr15:49464800-49481800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:49465200-49494000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:49465400-49479600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:49465400-49508200	Weak transcription	Hela-S3	cervix
27	chr15:49466800-49482800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:49467600-49479400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:49467600-49494200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:49467800-49479600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:49468000-49479400	Weak transcription	Stomach Mucosa	stomach
32	chr15:49468400-49494400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:49468600-49479600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:49470200-49480000	Weak transcription	Fetal Intestine Small	intestine
35	chr15:49472800-49497200	Weak transcription	Brain Anterior Caudate	brain
36	chr15:49473000-49481600	Weak transcription	K562	blood
37	chr15:49473000-49483400	Weak transcription	Brain Hippocampus Middle	brain
38	chr15:49473600-49479800	Weak transcription	Lung	lung
39	chr15:49473600-49483200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:49474800-49490200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:49476400-49478600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:49476800-49483400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:49477200-49478000	Strong transcription	Primary hematopoietic stem cells	blood
44	chr15:49477400-49478000	ZNF genes & repeats	Primary T cells from cord blood	blood
45	chr15:49477400-49478000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr15:49477400-49478000	Enhancers	GM12878-XiMat	blood

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