Variant report

Variant	rs4239201
Chromosome Location	chr17:46464739-46464740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46462185..46466645-chr17:46467369..46472149,5	K562	blood:
2	chr17:46463272..46465978-chr17:46700470..46702463,2	K562	blood:
3	chr17:46461397..46463215-chr17:46464686..46466654,3	K562	blood:
4	chr17:46463565..46466806-chr17:46694501..46697815,3	K562	blood:
5	chr17:46464628..46466806-chr17:46694501..46697277,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12603827	0.84[ASN][1000 genomes]
rs12937347	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1396868	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1509635	0.87[JPT][hapmap]
rs1553750	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2123344	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2924250	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2924254	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2938470	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs3826397	0.94[YRI][hapmap]
rs4324172	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4423463	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4542696	0.82[AFR][1000 genomes]
rs4606751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4793816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6504160	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6504210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7209556	0.84[MEX][hapmap]
rs7211099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7211780	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs7212220	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7213149	0.88[ASN][1000 genomes]
rs7216202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7218287	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7218563	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7221510	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8072002	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];0.99[ASN][1000 genomes]
rs8073710	0.84[MEX][hapmap]
rs8077516	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8077763	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9303541	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9797269	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9898383	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9906658	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4239201	RND2	cis	parietal	SCAN
rs4239201	CDK5RAP3	cis	cerebellum	SCAN
rs4239201	CDK5RAP3	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46438400-46471800	Weak transcription	Thymus	Thymus
2	chr17:46457600-46464800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:46460400-46466400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:46460400-46471200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr17:46462000-46470400	Weak transcription	Fetal Thymus	thymus
6	chr17:46462200-46467000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:46462400-46474200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:46462600-46465000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr17:46462800-46465600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr17:46463200-46469000	Enhancers	Fetal Brain Male	brain
11	chr17:46463200-46469400	Weak transcription	GM12878-XiMat	blood
12	chr17:46463400-46466800	Weak transcription	K562	blood
13	chr17:46463400-46472200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:46463600-46471800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr17:46463800-46464800	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr17:46463800-46465000	Strong transcription	Primary T cells from cord blood	blood
17	chr17:46463800-46465000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:46463800-46465200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr17:46464200-46465400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr17:46464200-46469600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:46464400-46465000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:46464400-46465400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr17:46464600-46465000	Enhancers	Fetal Brain Female	brain
24	chr17:46464600-46466000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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