Variant report

Variant	rs4284578
Chromosome Location	chr15:49305805-49305806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49287788..49289553-chr15:49304281..49306822,2	K562	blood:

Variant related genes	Relation type
ENSG00000138593	Chromatin interaction
ENSG00000207105	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1054307	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775139	0.82[CEU][hapmap]
rs11070682	0.88[CEU][hapmap]
rs11638215	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11855740	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12903559	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909616	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16962017	0.88[JPT][hapmap]
rs2899427	0.88[CEU][hapmap]
rs4390538	0.84[CHB][hapmap]
rs4435198	0.82[ASN][1000 genomes]
rs4536401	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4774536	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775790	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4775792	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4775795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775796	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493346	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7165264	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7167402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183756	0.81[ASN][1000 genomes]
rs7359317	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8029914	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033060	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs8037958	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs877007	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9920913	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4284578	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49268800-49309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:49282800-49333400	Weak transcription	A549	lung
3	chr15:49283600-49337600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:49285000-49329000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:49287200-49308000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:49287600-49308000	Weak transcription	HepG2	liver
7	chr15:49289200-49336400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:49289800-49317000	Weak transcription	Stomach Mucosa	stomach
9	chr15:49291400-49307400	Weak transcription	Gastric	stomach
10	chr15:49291400-49307400	Weak transcription	Pancreas	Pancrea
11	chr15:49291400-49308000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:49292200-49307800	Weak transcription	NHEK	skin
13	chr15:49292800-49308000	Weak transcription	Fetal Heart	heart
14	chr15:49292800-49308000	Weak transcription	Small Intestine	intestine
15	chr15:49297000-49309800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr15:49297200-49306000	Strong transcription	Fetal Intestine Large	intestine
17	chr15:49297200-49310000	Strong transcription	Liver	Liver
18	chr15:49297400-49310200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:49297400-49310800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:49297600-49309400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:49297800-49309800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:49298000-49308000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:49298000-49309800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:49298000-49311400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:49298000-49328400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:49298000-49328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:49298200-49306800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:49298200-49308800	Strong transcription	Fetal Thymus	thymus
29	chr15:49298200-49309600	Strong transcription	Primary T cells from cord blood	blood
30	chr15:49298200-49309600	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr15:49298200-49309600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr15:49298200-49309800	Strong transcription	Fetal Lung	lung
33	chr15:49298200-49309800	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:49298200-49310000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:49298200-49310200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:49298200-49310200	Strong transcription	Osteobl	bone
37	chr15:49298200-49314600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:49298200-49314600	Strong transcription	Adipose Nuclei	Adipose
39	chr15:49298200-49316200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr15:49298200-49316400	Strong transcription	Placenta	Placenta
41	chr15:49298200-49329800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr15:49298400-49306000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr15:49298400-49309800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr15:49298400-49314000	Strong transcription	HSMM	muscle
45	chr15:49298400-49322000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:49298400-49322000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr15:49298600-49325200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:49298600-49329600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:49299000-49309800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:49299200-49310200	Strong transcription	Monocytes-CD14+_RO01746	blood

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