Variant report

Variant	rs1472966
Chromosome Location	chr17:46430145-46430146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10514938	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12452773	1.00[CHB][hapmap]
rs16953235	1.00[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes]
rs16953382	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs16953461	1.00[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes]
rs16953925	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs16954078	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16954204	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16954581	0.84[TSI][hapmap]
rs16955073	1.00[ASW][hapmap];0.81[TSI][hapmap]
rs17624626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs17625073	1.00[CHB][hapmap]
rs17695373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825584	1.00[AFR][1000 genomes]
rs72827814	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827830	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827839	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827876	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72827877	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72827882	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72827885	0.85[EUR][1000 genomes]
rs72827887	0.83[EUR][1000 genomes]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1472966	SNX11	cis	cerebellum	SCAN
rs1472966	NBR2	cis	parietal	SCAN
rs1472966	NFE2L1	cis	cerebellum	SCAN
rs1472966	C17orf57	cis	parietal	SCAN
rs1472966	CDK5RAP3	cis	cerebellum	SCAN
rs1472966	ABI3	cis	lymphoblastoid	seeQTL
rs1472966	PNPO	cis	parietal	SCAN
rs1472966	AOC3	cis	parietal	SCAN
rs1472966	CDK5RAP3	cis	parietal	SCAN
rs1472966	DBF4B	cis	cerebellum	SCAN
rs1472966	G6PC	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46414600-46450400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr17:46423400-46441800	Weak transcription	GM12878-XiMat	blood
3	chr17:46423400-46451200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:46423600-46438200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr17:46423600-46443400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr17:46423600-46453800	Weak transcription	Fetal Thymus	thymus
7	chr17:46423800-46439200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:46426400-46435600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr17:46427200-46442400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr17:46427400-46440600	Weak transcription	Primary T cells from cord blood	blood
11	chr17:46429200-46430200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:46429400-46430400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:46429400-46430400	Enhancers	HSMM	muscle
14	chr17:46429800-46435000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:46429800-46435200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:46429800-46435200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:46429800-46435800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:46429800-46435800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr17:46429800-46436000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:46429800-46439200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr17:46429800-46440600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr17:46430000-46435800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr17:46430000-46438000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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