Variant report

Variant	rs2413936
Chromosome Location	chr15:49468087-49468088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49467721..49470764-chr15:49484555..49487605,3	K562	blood:
2	chr15:49466906..49469875-chr15:49518141..49520157,2	K562	blood:
3	chr15:49461181..49463665-chr15:49466365..49468672,2	MCF-7	breast:
4	chr15:49457613..49460436-chr15:49466302..49469375,3	K562	blood:
5	chr15:49467463..49469165-chr15:49481019..49482745,2	K562	blood:

Variant related genes	Relation type
ENSG00000264210	Chromatin interaction
ENSG00000156958	Chromatin interaction

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

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

rs_ID	r²[population]
rs11070686	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636671	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12440534	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1904317	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243899	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246995	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2413939	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413942	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2580924	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2940747	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3098614	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105865	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3105867	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4468544	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4775803	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs485182	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs520949	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568994	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs586758	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641077	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493364	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7497114	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8032650	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041781	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8041823	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920772	0.81[AFR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2413936	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463000-49479600	Weak transcription	Left Ventricle	heart
2	chr15:49463200-49471800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr15:49463200-49472000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:49463200-49472000	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:49463200-49479600	Weak transcription	Right Ventricle	heart
6	chr15:49463200-49479800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:49463200-49508200	Weak transcription	Ovary	ovary
8	chr15:49463400-49469800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:49463400-49480000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:49463600-49471400	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:49463600-49472400	Weak transcription	HUVEC	blood vessel
12	chr15:49463600-49474200	Weak transcription	Fetal Stomach	stomach
13	chr15:49463600-49474400	Weak transcription	Primary B cells from cord blood	blood
14	chr15:49463600-49477200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:49463600-49479400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:49463600-49479600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:49463600-49494400	Weak transcription	Fetal Thymus	thymus
18	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:49463600-49527800	Weak transcription	HSMM	muscle
20	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
21	chr15:49463800-49471600	Weak transcription	HMEC	breast
22	chr15:49463800-49472400	Weak transcription	Fetal Brain Female	brain
23	chr15:49463800-49472600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:49463800-49472600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:49463800-49472800	Weak transcription	Fetal Lung	lung
26	chr15:49463800-49479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:49463800-49479400	Weak transcription	Osteobl	bone
28	chr15:49464000-49469600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:49464000-49474400	Weak transcription	NHDF-Ad	bronchial
30	chr15:49464000-49482800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr15:49464000-49491600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:49464200-49470400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr15:49464200-49470600	Weak transcription	Lung	lung
34	chr15:49464200-49470600	Weak transcription	Pancreas	Pancrea
35	chr15:49464200-49471600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr15:49464200-49471600	Weak transcription	NHEK	skin
37	chr15:49464200-49477400	Weak transcription	Fetal Intestine Large	intestine
38	chr15:49464200-49479200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:49464200-49479400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:49464200-49481800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:49464400-49470600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:49464400-49493800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:49464400-49493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:49464400-49500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:49464800-49470800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:49464800-49477400	Weak transcription	Primary T cells from cord blood	blood
47	chr15:49464800-49479600	Weak transcription	NHLF	lung
48	chr15:49464800-49481800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:49465200-49472200	Weak transcription	Dnd41	blood
50	chr15:49465200-49494000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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