Variant report

Variant	rs2938470
Chromosome Location	chr17:46330060-46330061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46317007..46319839-chr17:46328201..46331501,3	K562	blood:
2	chr17:46328637..46331168-chr17:46337351..46339869,2	K562	blood:
3	chr17:46328583..46331168-chr17:46336391..46339869,3	K562	blood:
4	chr17:46326654..46330395-chr17:46331839..46334091,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12603827	0.97[ASN][1000 genomes]
rs12937347	0.88[ASN][1000 genomes]
rs1396868	0.81[ASN][1000 genomes]
rs1553750	0.93[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2123344	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2924250	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2924254	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3826397	0.94[YRI][hapmap]
rs4239201	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]
rs4324172	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4423463	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4606751	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4793816	0.87[ASN][1000 genomes]
rs6504160	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6504210	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];0.88[ASN][1000 genomes]
rs7211099	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7211780	0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs7213149	0.94[ASN][1000 genomes]
rs7216202	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs7218563	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7221510	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs8072002	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs8077516	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8077763	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9303541	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9797269	0.85[ASN][1000 genomes]
rs9898383	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9906658	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2938470	PHOSPHO1	cis	cerebellum	SCAN
rs2938470	CCR10	cis	parietal	SCAN
rs2938470	CDK5RAP3	cis	cerebellum	SCAN
rs2938470	CDK5RAP3	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46306600-46335400	Weak transcription	Thymus	Thymus
2	chr17:46319600-46372000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:46322600-46341800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr17:46322600-46342200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:46322800-46356200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr17:46323000-46370800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:46323800-46330600	Weak transcription	GM12878-XiMat	blood
8	chr17:46324200-46355800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:46324200-46371600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:46324800-46337000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:46324800-46343000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr17:46326200-46330200	Weak transcription	Primary T cells from cord blood	blood
13	chr17:46326200-46335600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr17:46326200-46361200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr17:46327000-46330400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr17:46328200-46330600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr17:46328400-46332400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:46328400-46332800	Enhancers	A549	lung
19	chr17:46329000-46337000	Weak transcription	HUVEC	blood vessel
20	chr17:46329200-46332200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:46329600-46331800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr17:46329600-46335400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr17:46329800-46332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr17:46329800-46332200	Weak transcription	K562	blood
25	chr17:46330000-46332200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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