Variant report

Variant	rs12909616
Chromosome Location	chr15:49328222-49328223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49327331..49331009-chr15:49336613..49340321,7	K562	blood:

Variant related genes	Relation type
ENSG00000138593	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1054307	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11638215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855740	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11858917	0.80[ASN][1000 genomes]
rs12903559	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16962017	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4284578	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4423366	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4536401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774536	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4775790	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4775792	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4775795	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4775796	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6493346	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7165264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167402	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7359317	0.80[EUR][1000 genomes]
rs8029751	0.82[ASN][1000 genomes]
rs8029914	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8037958	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs877007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920913	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12909616	GALK2	cis	Whole Blood	GTEx
rs12909616	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	chr15:49298000-49328400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:49298000-49328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:49298200-49329800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:49298600-49329600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:49301400-49329000	Weak transcription	K562	blood
10	chr15:49308800-49331800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:49308800-49334400	Weak transcription	Psoas Muscle	Psoas
12	chr15:49310000-49328400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:49313400-49335000	Weak transcription	Pancreas	Pancrea
14	chr15:49313800-49336400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:49314200-49329000	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:49315200-49330000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:49315800-49328600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:49317200-49329600	Strong transcription	Placenta	Placenta
19	chr15:49317800-49330200	Strong transcription	Primary B cells from cord blood	blood
20	chr15:49318000-49329200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:49318200-49330000	Strong transcription	Primary T cells from cord blood	blood
22	chr15:49319200-49329000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:49319200-49334600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:49319400-49329600	Weak transcription	Brain Germinal Matrix	brain
25	chr15:49320200-49336800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr15:49320800-49329800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:49320800-49336400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:49321000-49328400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:49321000-49336400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:49321200-49328400	Weak transcription	Colonic Mucosa	Colon
31	chr15:49321200-49329800	Weak transcription	Fetal Heart	heart
32	chr15:49321400-49338000	Weak transcription	Spleen	Spleen
33	chr15:49321800-49329000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:49321800-49336400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:49321800-49336800	Weak transcription	Thymus	Thymus
36	chr15:49322000-49336400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:49322600-49333600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:49322800-49328400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:49323000-49329800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr15:49324000-49328800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:49324400-49329000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:49324600-49328600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr15:49324800-49328400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr15:49325600-49328400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:49325800-49330000	Strong transcription	Fetal Lung	lung
46	chr15:49326400-49328400	Strong transcription	Hela-S3	cervix
47	chr15:49326400-49328600	Strong transcription	NHDF-Ad	bronchial
48	chr15:49326400-49329200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:49326400-49329200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:49326400-49329400	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links