Variant report

Variant	rs2116765
Chromosome Location	chr5:147024509-147024510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10045944	0.88[EUR][1000 genomes]
rs10051794	0.88[EUR][1000 genomes]
rs10515588	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1106895	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1159523	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12657682	0.81[AFR][1000 genomes]
rs12658788	0.80[YRI][hapmap]
rs12658834	0.80[YRI][hapmap]
rs1347137	0.94[ASW][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs1347138	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1347139	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs1347140	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1529685	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1529686	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1529687	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1529688	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17096666	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17106940	0.87[EUR][1000 genomes]
rs17106947	0.87[EUR][1000 genomes]
rs17106977	0.94[EUR][1000 genomes]
rs17106994	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17106995	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17107039	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17107043	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2053051	0.81[AFR][1000 genomes]
rs2116766	0.82[ASW][hapmap];0.96[LWK][hapmap];0.89[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs2116768	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2116769	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304036	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34100034	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35416673	0.81[AFR][1000 genomes]
rs35502493	0.89[EUR][1000 genomes]
rs3763093	0.89[EUR][1000 genomes]
rs3763094	0.89[EUR][1000 genomes]
rs3765006	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4382156	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4382157	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4577681	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4635925	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705176	0.84[EUR][1000 genomes]
rs4705181	0.88[EUR][1000 genomes]
rs55851807	0.87[EUR][1000 genomes]
rs56295956	0.87[EUR][1000 genomes]
rs56384964	0.88[EUR][1000 genomes]
rs57061855	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58595614	0.87[EUR][1000 genomes]
rs59225792	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61508445	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580478	0.88[EUR][1000 genomes]
rs6580480	0.90[EUR][1000 genomes]
rs6859329	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs6860404	0.88[EUR][1000 genomes]
rs6887481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6892958	0.86[EUR][1000 genomes]
rs73268153	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73268170	0.90[AFR][1000 genomes]
rs73268172	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7380570	0.88[EUR][1000 genomes]
rs7704474	0.88[EUR][1000 genomes]
rs7705148	0.88[EUR][1000 genomes]
rs7706575	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7711029	0.87[EUR][1000 genomes]
rs7711042	0.88[EUR][1000 genomes]
rs7725758	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7729949	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7735403	0.81[ASW][hapmap];0.96[YRI][hapmap]
rs8180519	0.87[EUR][1000 genomes]
rs9325047	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325048	0.80[YRI][hapmap]
rs9686194	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9686196	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9686961	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs981644	0.88[EUR][1000 genomes]
rs9918128	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs999953	0.93[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2116765	CAMK2A	cis	cerebellum	SCAN
rs2116765	UQCC	trans	parietal	SCAN
rs2116765	JAKMIP2	cis	cerebellum	SCAN
rs2116765	TNIP1	cis	parietal	SCAN
rs2116765	JAKMIP2	cis	parietal	SCAN

Chromatin state (count:59 , 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	chr5:146999400-147025400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:147006800-147025200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:147009400-147027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:147009400-147033200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:147009800-147051200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:147010800-147028600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:147013000-147027400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:147013000-147030200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:147013000-147038400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:147013200-147024600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:147013600-147025800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:147014000-147029800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:147014000-147030400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:147014200-147030400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:147015000-147030000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:147015200-147029000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr5:147015400-147025600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:147015400-147050000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:147016200-147024600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:147016400-147052400	Weak transcription	Primary B cells from cord blood	blood
22	chr5:147016600-147037400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:147016600-147037800	Weak transcription	Fetal Stomach	stomach
24	chr5:147016600-147038200	Weak transcription	Brain Angular Gyrus	brain
25	chr5:147016600-147047400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:147017800-147026000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:147018200-147025400	Strong transcription	Fetal Thymus	thymus
28	chr5:147018200-147025600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:147018600-147025000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:147018800-147025400	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr5:147019400-147024600	Weak transcription	Fetal Muscle Leg	muscle
32	chr5:147020000-147037000	Weak transcription	Fetal Brain Male	brain
33	chr5:147021000-147025400	Strong transcription	Primary T cells from cord blood	blood
34	chr5:147021400-147037200	Weak transcription	Fetal Brain Female	brain
35	chr5:147021400-147042800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:147022000-147025200	Strong transcription	Brain Hippocampus Middle	brain
37	chr5:147022200-147024600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:147022400-147024600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:147022400-147024800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr5:147022400-147025400	Strong transcription	Brain Substantia Nigra	brain
41	chr5:147022600-147024600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:147022800-147024600	Strong transcription	Brain Anterior Caudate	brain
43	chr5:147022800-147025400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr5:147022800-147037600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:147023200-147024600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr5:147023200-147037600	Weak transcription	Thymus	Thymus
47	chr5:147023200-147037800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr5:147023400-147036800	Weak transcription	Brain Germinal Matrix	brain
49	chr5:147023800-147024600	Flanking Active TSS	Liver	Liver
50	chr5:147023800-147029000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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