Variant report

Variant	rs3792694
Chromosome Location	chr17:46260442-46260443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46258902..46261655-chr17:46700087..46701863,2	K562	blood:
2	chr17:46252245..46255136-chr17:46259026..46261295,2	K562	blood:

Extended variants
information (count: 128 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1002330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1010228	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs10445339	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10445377	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853098	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079806	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079808	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079814	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651097	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11870056	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11872095	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150533	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12452956	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12603115	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12603380	0.81[AMR][1000 genomes]
rs12936369	0.84[ASN][1000 genomes]
rs12936731	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs12941830	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12947089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12948810	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12952670	0.83[EUR][1000 genomes]
rs1316657	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1377201	0.88[ASW][hapmap];0.88[MKK][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1452662	0.82[ASN][1000 genomes]
rs1452663	0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1452665	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1452666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1452667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468270	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs16951519	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs16953927	0.82[ASN][1000 genomes]
rs16953941	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs16954268	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs16954324	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs17620033	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[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17681336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1860862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1860863	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979897	0.85[CHB][hapmap]
rs2021752	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2021811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2041572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2051821	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2060876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072441	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs208005	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs208008	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs208009	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs208011	0.84[ASN][1000 genomes]
rs208012	0.84[ASN][1000 genomes]
rs208015	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208019	0.82[ASN][1000 genomes]
rs2109982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2109983	0.80[JPT][hapmap]
rs2109984	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2123341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229369	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2240120	0.85[CHB][hapmap]
rs2240121	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2240122	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2278868	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325784	0.81[ASN][1000 genomes]
rs2325804	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2325885	0.82[ASN][1000 genomes]
rs2924257	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2938483	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34949267	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34980108	0.82[ASN][1000 genomes]
rs36071506	0.82[ASN][1000 genomes]
rs3744346	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs3792692	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815472	0.82[ASN][1000 genomes]
rs3897986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3944039	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794447	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs4794451	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4794505	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794517	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794525	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55696440	0.84[ASN][1000 genomes]
rs55982346	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62066407	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62066447	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6504025	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs6504108	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs66683298	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67446770	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6847	0.81[JPT][hapmap]
rs71356521	0.80[ASN][1000 genomes]
rs7210149	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7212202	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7213876	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217496	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7219967	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7220619	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7220768	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7220922	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7222136	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7223867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7224014	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7225435	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7225550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7225865	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7501770	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs758999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8065670	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8066391	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8069064	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8069263	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]
rs8071199	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8071879	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8072282	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[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8075270	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077860	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8079616	0.82[ASN][1000 genomes]
rs875065	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs882380	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs954226	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs978263	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9899275	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs9899461	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs9903692	0.84[ASN][1000 genomes]
rs9909933	0.82[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3792694	CDK5RAP3	cis	parietal	SCAN
rs3792694	CDK5RAP3	cis	cerebellum	SCAN
rs3792694	EIF1	cis	cerebellum	SCAN
rs3792694	SNX11	cis	multi-tissue	Pritchard
rs3792694	SNX11	cis	Lymphoblastoid	GTEx
rs3792694	CBX1	cis	cerebellum	SCAN
rs3792694	PRAC	cis	parietal	SCAN
rs3792694	AARSD1	cis	parietal	SCAN
rs3792694	SNX11	cis	parietal	SCAN
rs3792694	HOXB2	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46251200-46267200	Strong transcription	Primary T cells from cord blood	blood
2	chr17:46251200-46277400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:46251800-46267400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr17:46252000-46271400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr17:46252600-46271000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr17:46253200-46270800	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr17:46253400-46260800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr17:46253600-46267000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
9	chr17:46253800-46266800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr17:46254000-46271000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:46254400-46266800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:46255000-46270800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:46255200-46270800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:46256800-46262000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:46256800-46268400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:46257000-46266200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:46257400-46262400	Weak transcription	HSMMtube	muscle
18	chr17:46257600-46262000	Weak transcription	Thymus	Thymus
19	chr17:46259400-46261800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:46259600-46261600	Weak transcription	GM12878-XiMat	blood
21	chr17:46260000-46261400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr17:46260200-46260600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr17:46260200-46260600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr17:46260200-46260600	Enhancers	HSMM	muscle
25	chr17:46260200-46261600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:46260200-46261600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr17:46260400-46261800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr17:46260400-46261800	Weak transcription	Fetal Thymus	thymus

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