Variant report

Variant	rs4536401
Chromosome Location	chr15:49328668-49328669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49328431..49332105-chr15:49337151..49339977,3	MCF-7	breast:
2	chr15:49327331..49331009-chr15:49336613..49340321,7	K562	blood:

Variant related genes	Relation type
ENSG00000138593	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1054307	0.96[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10775139	0.82[CEU][hapmap]
rs11070682	0.88[CEU][hapmap]
rs11638215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855740	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12903559	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12904344	0.86[CHB][hapmap]
rs12909616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16962017	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2899427	0.88[CEU][hapmap]
rs4284578	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4423366	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4774536	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775790	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4775792	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4775795	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4775796	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164309	0.90[YRI][hapmap]
rs7165264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7167402	1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8029751	0.95[CHB][hapmap]
rs8029914	1.00[CEU][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8037958	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs877007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920913	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4536401	GALK2	cis	Whole Blood	GTEx
rs4536401	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49282800-49333400	Weak transcription	A549	lung
2	chr15:49283600-49337600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:49285000-49329000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:49289200-49336400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:49298000-49328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:49298200-49329800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:49298600-49329600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:49301400-49329000	Weak transcription	K562	blood
9	chr15:49308800-49331800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:49308800-49334400	Weak transcription	Psoas Muscle	Psoas
11	chr15:49313400-49335000	Weak transcription	Pancreas	Pancrea
12	chr15:49313800-49336400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:49314200-49329000	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:49315200-49330000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:49317200-49329600	Strong transcription	Placenta	Placenta
16	chr15:49317800-49330200	Strong transcription	Primary B cells from cord blood	blood
17	chr15:49318000-49329200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:49318200-49330000	Strong transcription	Primary T cells from cord blood	blood
19	chr15:49319200-49329000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:49319200-49334600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:49319400-49329600	Weak transcription	Brain Germinal Matrix	brain
22	chr15:49320200-49336800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:49320800-49329800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:49320800-49336400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:49321000-49336400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:49321200-49329800	Weak transcription	Fetal Heart	heart
27	chr15:49321400-49338000	Weak transcription	Spleen	Spleen
28	chr15:49321800-49329000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:49321800-49336400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:49321800-49336800	Weak transcription	Thymus	Thymus
31	chr15:49322000-49336400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:49322600-49333600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:49323000-49329800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr15:49324000-49328800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:49324400-49329000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:49325800-49330000	Strong transcription	Fetal Lung	lung
37	chr15:49326400-49329200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:49326400-49329200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:49326400-49329400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr15:49326600-49329800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:49326800-49328800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:49326800-49329200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:49326800-49329200	Strong transcription	Fetal Muscle Leg	muscle
44	chr15:49326800-49329200	Strong transcription	Fetal Thymus	thymus
45	chr15:49326800-49330000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr15:49327000-49329200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr15:49327000-49329200	Strong transcription	Adipose Nuclei	Adipose
48	chr15:49327000-49329400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:49327000-49329800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:49327200-49329400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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