Variant report

Variant	rs17696392
Chromosome Location	chr17:46427160-46427161
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46413464..46416314-chr17:46425869..46428355,2	MCF-7	breast:
2	chr17:46414525..46417047-chr17:46426098..46428962,2	K562	blood:
3	chr17:46423304..46425728-chr17:46426161..46428248,2	K562	blood:
4	chr17:46414525..46419119-chr17:46425524..46428962,4	K562	blood:
5	chr17:46427006..46429722-chr17:46617606..46619313,2	K562	blood:

Variant related genes	Relation type
ENSG00000141293	Chromatin interaction

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]
rs1472966	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]
rs16953235	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[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];0.83[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];0.94[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]
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
rs17696392	CDK5RAP3	cis	parietal	SCAN
rs17696392	NFE2L1	cis	cerebellum	SCAN
rs17696392	CDK5RAP3	cis	cerebellum	SCAN
rs17696392	DBF4B	cis	cerebellum	SCAN
rs17696392	NBR2	cis	parietal	SCAN
rs17696392	SNX11	cis	cerebellum	SCAN
rs17696392	C17orf57	cis	parietal	SCAN
rs17696392	PNPO	cis	parietal	SCAN
rs17696392	G6PC	cis	cerebellum	SCAN
rs17696392	AOC3	cis	parietal	SCAN
rs17696392	ABI3	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46390200-46429400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr17:46413800-46429400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:46414600-46450400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:46422400-46429400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:46423400-46429000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:46423400-46429400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr17:46423400-46441800	Weak transcription	GM12878-XiMat	blood
8	chr17:46423400-46451200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:46423600-46429200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:46423600-46429400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr17:46423600-46429400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:46423600-46438200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr17:46423600-46443400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr17:46423600-46453800	Weak transcription	Fetal Thymus	thymus
15	chr17:46423800-46439200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:46424400-46429400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:46426200-46427400	Strong transcription	Primary T cells from cord blood	blood
18	chr17:46426400-46427200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr17:46426400-46429400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:46426400-46435600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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