Variant report

Variant	rs17106995
Chromosome Location	chr5:147018084-147018085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10045944	0.90[EUR][1000 genomes]
rs10051794	0.90[EUR][1000 genomes]
rs10515588	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1106894	0.89[ASN][1000 genomes]
rs1106895	0.95[EUR][1000 genomes]
rs1159523	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1347137	0.81[ASW][hapmap]
rs1347138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1529685	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529686	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529687	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529688	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096666	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17106940	0.86[EUR][1000 genomes]
rs17106947	0.91[EUR][1000 genomes]
rs17106977	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17106994	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17107039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17107043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2116765	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2116768	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2116769	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2304036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34100034	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35416673	0.96[ASN][1000 genomes]
rs35502493	0.86[EUR][1000 genomes]
rs36119468	0.89[ASN][1000 genomes]
rs3763093	0.88[EUR][1000 genomes]
rs3763094	0.88[EUR][1000 genomes]
rs3765006	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382156	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382157	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577681	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4635925	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4705176	0.85[EUR][1000 genomes]
rs4705181	0.90[EUR][1000 genomes]
rs55851807	0.91[EUR][1000 genomes]
rs56295956	0.91[EUR][1000 genomes]
rs56384964	0.87[EUR][1000 genomes]
rs57061855	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58595614	0.91[EUR][1000 genomes]
rs59225792	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61508445	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580478	0.90[EUR][1000 genomes]
rs6580480	0.87[EUR][1000 genomes]
rs6860404	0.90[EUR][1000 genomes]
rs6887481	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6892958	0.87[EUR][1000 genomes]
rs73268153	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73268172	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7380570	0.90[EUR][1000 genomes]
rs7704474	0.90[EUR][1000 genomes]
rs7705148	0.90[EUR][1000 genomes]
rs7706575	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711029	0.91[EUR][1000 genomes]
rs7711042	0.90[EUR][1000 genomes]
rs7725758	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729949	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180519	0.91[EUR][1000 genomes]
rs8180520	0.82[EUR][1000 genomes]
rs9325047	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9686194	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9686196	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9686961	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981644	0.90[EUR][1000 genomes]
rs9918128	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999953	0.93[CEU][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17106995	CAMK2A	cis	cerebellum	SCAN
rs17106995	JAKMIP2	cis	cerebellum	SCAN
rs17106995	HTR4	cis	cerebellum	SCAN
rs17106995	JAKMIP2	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146957800-147038000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:146990600-147022600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:146991400-147022800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:146995800-147020200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr5:146997600-147018600	Weak transcription	Fetal Brain Male	brain
6	chr5:146999400-147025400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:146999800-147019800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:147006600-147022400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:147006800-147025200	Weak transcription	Fetal Intestine Small	intestine
10	chr5:147007200-147018200	Weak transcription	Fetal Thymus	thymus
11	chr5:147007800-147018600	Weak transcription	Fetal Lung	lung
12	chr5:147008400-147020400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:147009200-147019400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:147009400-147027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:147009400-147033200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:147009800-147051200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:147010800-147028600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:147013000-147027400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:147013000-147030200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:147013000-147038400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:147013200-147024600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:147013600-147025800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:147014000-147029800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:147014000-147030400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:147014200-147030400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:147015000-147030000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:147015200-147029000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr5:147015400-147025600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:147015400-147050000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:147015800-147018800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:147016000-147024400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:147016200-147024600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:147016400-147018200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:147016400-147018200	Weak transcription	Liver	Liver
35	chr5:147016400-147022400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:147016400-147052400	Weak transcription	Primary B cells from cord blood	blood
37	chr5:147016600-147018600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:147016600-147018800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:147016600-147019000	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:147016600-147020200	Weak transcription	Primary T cells from cord blood	blood
41	chr5:147016600-147022200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:147016600-147022200	Weak transcription	Thymus	Thymus
43	chr5:147016600-147022400	Weak transcription	Brain Substantia Nigra	brain
44	chr5:147016600-147022800	Weak transcription	Brain Anterior Caudate	brain
45	chr5:147016600-147037400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:147016600-147037800	Weak transcription	Fetal Stomach	stomach
47	chr5:147016600-147038200	Weak transcription	Brain Angular Gyrus	brain
48	chr5:147016600-147047400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:147016800-147019800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:147016800-147020200	Weak transcription	Brain Germinal Matrix	brain

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