Variant report

Variant	rs1553750
Chromosome Location	chr17:46503958-46503959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46503026..46505286-chr17:46512719..46514914,2	K562	blood:
2	chr17:46503757..46506567-chr17:46674757..46677231,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1027895	0.83[ASN][1000 genomes]
rs12937347	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12942428	0.80[ASN][1000 genomes]
rs1396868	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509635	0.91[JPT][hapmap]
rs1858162	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2123344	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2924250	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2924254	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2938470	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]
rs3826397	0.82[LWK][hapmap];0.94[YRI][hapmap]
rs4239201	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]
rs4267363	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4324172	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4423463	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4606751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4793816	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4794674	0.82[ASN][1000 genomes]
rs4794678	0.83[ASN][1000 genomes]
rs6504160	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504210	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.92[ASN][1000 genomes]
rs6504256	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7209556	0.84[MEX][hapmap]
rs7211099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7211636	0.85[ASN][1000 genomes]
rs7211780	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7212220	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7212325	0.83[ASN][1000 genomes]
rs7213149	0.83[ASN][1000 genomes]
rs7216202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7218287	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7218563	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7221510	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8072002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8073326	0.88[ASN][1000 genomes]
rs8073710	0.84[MEX][hapmap]
rs8077516	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077763	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9303541	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs9797269	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9898383	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9906658	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1553750	SKAP1	Cis_1M	lymphoblastoid	RTeQTL
rs1553750	CDK5RAP3	cis	cerebellum	SCAN
rs1553750	RND2	cis	parietal	SCAN
rs1553750	CDK5RAP3	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46489800-46505000	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr17:46502200-46505200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr17:46502200-46505200	Enhancers	Fetal Thymus	thymus
4	chr17:46502800-46505000	Flanking Active TSS	GM12878-XiMat	blood
5	chr17:46503000-46504400	Enhancers	Thymus	Thymus
6	chr17:46503200-46504400	Enhancers	HUVEC	blood vessel
7	chr17:46503200-46507000	Enhancers	Primary hematopoietic stem cells	blood
8	chr17:46503400-46504200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr17:46503400-46505400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr17:46503400-46505600	Enhancers	Primary B cells from cord blood	blood
11	chr17:46503400-46506400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr17:46503600-46504000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:46503600-46504000	Flanking Active TSS	K562	blood
14	chr17:46503600-46504200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr17:46503600-46504200	Bivalent/Poised TSS	Fetal Brain Male	brain
16	chr17:46503600-46504400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr17:46503600-46504600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:46503600-46505200	Bivalent Enhancer	Fetal Lung	lung
19	chr17:46503600-46505400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr17:46503600-46505400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:46503600-46505400	Enhancers	A549	lung
22	chr17:46503600-46505600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:46503600-46506000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr17:46503600-46506600	Enhancers	Primary B cells from peripheral blood	blood
25	chr17:46503600-46506600	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr17:46503600-46506600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:46503800-46504000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr17:46503800-46504200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr17:46503800-46506400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr17:46503800-46507600	Active TSS	Primary T cells fromperipheralblood	blood

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