Variant report

Variant	rs16953941
Chromosome Location	chr17:46296204-46296205
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46294391..46296638-chr17:46307664..46310420,2	K562	blood:
2	chr17:46288806..46291737-chr17:46295119..46298079,2	MCF-7	breast:
3	chr17:46296129..46298208-chr17:46360954..46363694,2	K562	blood:
4	chr17:46287226..46289688-chr17:46295233..46297657,2	K562	blood:
5	chr17:46289301..46291903-chr17:46294657..46296456,2	K562	blood:

Extended variants
information (count: 154 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs1002330	0.80[ASN][1000 genomes]
rs1010228	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1010230	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10445377	0.80[ASN][1000 genomes]
rs10514944	0.89[TSI][hapmap]
rs10853097	0.81[ASN][1000 genomes]
rs10853098	0.80[ASN][1000 genomes]
rs11079806	1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs11079808	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11079809	0.89[ASN][1000 genomes]
rs11079814	0.82[ASN][1000 genomes]
rs11651097	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs11872095	0.82[ASN][1000 genomes]
rs12150533	0.84[ASN][1000 genomes]
rs12452956	0.82[ASN][1000 genomes]
rs12600980	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12936369	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12936731	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12939334	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12941295	0.81[ASN][1000 genomes]
rs12941830	0.80[ASN][1000 genomes]
rs12943543	0.81[ASN][1000 genomes]
rs12946208	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12946679	0.82[YRI][hapmap]
rs12947089	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs12948214	1.00[YRI][hapmap]
rs12950402	0.81[ASN][1000 genomes]
rs12950437	0.82[YRI][hapmap]
rs1316657	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1452662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452663	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]
rs1452665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1452666	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1452667	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1468270	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs16951519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16952687	1.00[YRI][hapmap]
rs16953927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16954324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16955960	0.89[TSI][hapmap]
rs17620033	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs17623518	0.84[TSI][hapmap]
rs17681336	0.80[ASN][1000 genomes]
rs17694092	0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs17694404	0.95[TSI][hapmap]
rs1860862	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1860866	0.89[ASN][1000 genomes]
rs1979897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2021752	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2023885	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2041572	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2051821	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs2060876	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208005	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs208008	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs208009	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];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs208011	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs208012	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs208015	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs208019	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2109982	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2109983	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2109984	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2123341	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2229369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2240119	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2240120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2240121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2240122	1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs2278868	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2305433	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2325784	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2325804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2325885	1.00[ASN][1000 genomes]
rs34949267	0.80[ASN][1000 genomes]
rs34980108	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35688835	0.81[ASN][1000 genomes]
rs36071506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744346	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs3785737	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3792692	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs3792694	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs3805370	0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3805371	0.82[ASN][1000 genomes]
rs3815472	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3897789	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3897986	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4793779	0.83[CHB][hapmap]
rs4794441	0.81[ASN][1000 genomes]
rs4794447	0.83[CHB][hapmap]
rs4794448	0.81[ASN][1000 genomes]
rs4794449	0.81[ASN][1000 genomes]
rs4794451	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs4794453	0.81[ASN][1000 genomes]
rs4794505	0.84[ASN][1000 genomes]
rs4794517	0.84[ASN][1000 genomes]
rs4794525	0.82[ASN][1000 genomes]
rs55696440	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55982346	0.84[ASN][1000 genomes]
rs62064953	0.81[ASN][1000 genomes]
rs62066447	0.84[ASN][1000 genomes]
rs6504025	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6504031	0.81[ASN][1000 genomes]
rs6504108	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs67345313	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6847	0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs71356520	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71356521	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7209585	0.81[ASN][1000 genomes]
rs7209730	0.89[ASN][1000 genomes]
rs7210149	0.84[ASN][1000 genomes]
rs7212202	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7213876	0.82[ASN][1000 genomes]
rs7217496	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs7218700	0.85[ASN][1000 genomes]
rs7219967	0.84[ASN][1000 genomes]
rs7220520	0.95[CHD][hapmap];0.80[JPT][hapmap]
rs7220768	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7220922	0.80[ASN][1000 genomes]
rs7222136	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs7223867	0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs7224014	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7224461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7225550	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs72825596	0.80[EUR][1000 genomes]
rs741058	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757353	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs758999	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs8065670	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs8065993	0.81[ASN][1000 genomes]
rs8066049	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8066391	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs8069064	0.84[ASN][1000 genomes]
rs8069263	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs8071199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8071879	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];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8072282	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs8075270	0.82[ASN][1000 genomes]
rs8076380	0.81[ASN][1000 genomes]
rs8077860	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs8079616	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8080662	0.81[ASN][1000 genomes]
rs875065	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs882380	0.84[ASN][1000 genomes]
rs978263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9807087	0.89[ASN][1000 genomes]
rs9889470	0.91[ASN][1000 genomes]
rs9890691	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9899275	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs9899461	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs9903692	0.98[ASN][1000 genomes]
rs9909933	1.00[ASN][1000 genomes]
rs9910516	0.81[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16953941	CDK5RAP3	cis	parietal	SCAN
rs16953941	HSPB9	cis	parietal	SCAN
rs16953941	HOXB7	cis	cerebellum	SCAN
rs16953941	DHX58	cis	parietal	SCAN
rs16953941	TUBG1	cis	parietal	SCAN
rs16953941	CBX1	cis	cerebellum	SCAN
rs16953941	CDK5RAP3	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46266800-46298600	Weak transcription	Thymus	Thymus
2	chr17:46266800-46318200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr17:46273200-46302800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr17:46273200-46314000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr17:46274200-46297200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:46283600-46314000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:46286800-46297400	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr17:46288400-46307000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr17:46292800-46298600	Strong transcription	Primary T cells from cord blood	blood
10	chr17:46293000-46297200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:46293200-46297600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr17:46293600-46297000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:46293800-46301000	Weak transcription	HUVEC	blood vessel
14	chr17:46294000-46318000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr17:46295000-46296800	Weak transcription	GM12878-XiMat	blood
16	chr17:46295000-46301600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr17:46295000-46304400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:46295200-46303000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:46295400-46297400	Enhancers	A549	lung
20	chr17:46295400-46297600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:46295600-46296800	Enhancers	K562	blood
22	chr17:46295800-46297200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr17:46295800-46303200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr17:46295800-46314200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr17:46296000-46300600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr17:46296200-46296400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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