Variant report

Variant	rs2246995
Chromosome Location	chr15:49423357-49423358
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:49423236-49423620	K562	blood:	n/a	n/a

Variant related genes	Relation type
COPS2	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10519208	0.87[ASN][1000 genomes]
rs11070681	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11070686	0.80[AFR][1000 genomes]
rs11632976	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11636671	0.84[AFR][1000 genomes]
rs11637601	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12101442	0.86[ASN][1000 genomes]
rs12101599	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs12438357	0.86[ASN][1000 genomes]
rs12440534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898709	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12917024	0.85[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs1904317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2243899	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413930	0.86[ASN][1000 genomes]
rs2413936	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2413939	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2413942	0.84[AFR][1000 genomes]
rs2580924	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28505357	0.86[ASN][1000 genomes]
rs28575845	0.86[ASN][1000 genomes]
rs28790333	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2940747	0.91[EUR][1000 genomes]
rs3098614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3105861	0.86[YRI][hapmap]
rs3105865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3105867	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4468544	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4775803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs485182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs520949	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs532209	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs568994	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs641077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493364	0.84[AFR][1000 genomes]
rs7497114	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8032650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8041781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs8041823	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9920070	0.85[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2246995	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49388800-49434800	Weak transcription	Small Intestine	intestine
2	chr15:49395600-49426400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:49398600-49427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:49403000-49434600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:49403200-49423400	Weak transcription	Psoas Muscle	Psoas
6	chr15:49403400-49440200	Weak transcription	Pancreas	Pancrea
7	chr15:49403600-49423600	Weak transcription	Esophagus	oesophagus
8	chr15:49403600-49432200	Weak transcription	Fetal Stomach	stomach
9	chr15:49403600-49435200	Weak transcription	Aorta	Aorta
10	chr15:49403600-49435200	Weak transcription	Gastric	stomach
11	chr15:49403600-49435400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:49403800-49433200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:49404600-49424000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:49404800-49423400	Weak transcription	HepG2	liver
15	chr15:49404800-49425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:49404800-49434600	Weak transcription	Right Ventricle	heart
17	chr15:49404800-49435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:49405600-49441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:49411400-49432200	Weak transcription	Fetal Intestine Small	intestine
20	chr15:49413000-49427200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:49413400-49426200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:49413600-49447000	Weak transcription	Stomach Mucosa	stomach
23	chr15:49414000-49426400	Strong transcription	HSMM	muscle
24	chr15:49415200-49423600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr15:49415200-49433400	Weak transcription	Lung	lung
26	chr15:49415400-49427400	Strong transcription	Hela-S3	cervix
27	chr15:49415400-49427600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:49415600-49427400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:49415600-49437600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:49415800-49437400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:49416200-49427600	Weak transcription	Fetal Brain Male	brain
32	chr15:49416200-49437400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:49416400-49427800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:49416800-49423600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:49416800-49436800	Strong transcription	Liver	Liver
36	chr15:49416800-49437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:49417000-49437200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:49417200-49424400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:49417200-49424800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:49417200-49426600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:49417200-49436600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:49417200-49437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:49417200-49437200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:49417200-49437400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:49417200-49437400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:49417400-49427600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:49417400-49427600	Strong transcription	Placenta	Placenta
48	chr15:49417400-49437200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:49417600-49437200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:49417600-49437200	Strong transcription	Primary T cells fromperipheralblood	blood

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