Variant report

Variant	rs7209556
Chromosome Location	chr17:46466163-46466164
allele	C/T
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	chr17:46465145..46467421-chr17:46468565..46471661,3	K562	blood:
3	chr17:46461397..46463215-chr17:46464686..46466654,3	K562	blood:
4	chr17:46450687..46453048-chr17:46465448..46467594,2	K562	blood:
5	chr17:46463565..46466806-chr17:46694501..46697815,3	K562	blood:
6	chr17:46464628..46466806-chr17:46694501..46697277,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs11079818	0.83[ASN][1000 genomes]
rs11655672	0.83[ASN][1000 genomes]
rs12150117	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12449653	0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12450014	0.81[ASN][1000 genomes]
rs12450081	0.85[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12450786	0.81[ASN][1000 genomes]
rs12450935	0.83[ASN][1000 genomes]
rs12451412	0.83[ASN][1000 genomes]
rs12452212	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs12452234	0.81[ASN][1000 genomes]
rs12940365	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12944592	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs12946636	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs12948017	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs12948128	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs12953245	0.81[ASN][1000 genomes]
rs1553749	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1553750	0.84[MEX][hapmap]
rs1553751	0.83[ASN][1000 genomes]
rs1553752	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1553753	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs16955397	0.81[ASN][1000 genomes]
rs17621199	0.82[JPT][hapmap]
rs17623154	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs17694192	0.83[JPT][hapmap]
rs17694895	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1912153	0.83[ASN][1000 genomes]
rs1912154	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1973575	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2056458	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2084881	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs2175158	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4131712	0.81[ASN][1000 genomes]
rs4239201	0.84[MEX][hapmap]
rs4312351	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4451990	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4556829	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs5000249	0.83[JPT][hapmap]
rs62064554	0.81[ASN][1000 genomes]
rs6504135	0.83[JPT][hapmap]
rs6504145	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6504158	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs6504160	0.84[MEX][hapmap]
rs6504172	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs6504203	0.83[ASN][1000 genomes]
rs6504210	0.84[MEX][hapmap]
rs7206951	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs7207826	0.83[JPT][hapmap]
rs7207928	0.81[ASN][1000 genomes]
rs7209043	0.82[JPT][hapmap]
rs7209522	0.83[ASN][1000 genomes]
rs7209855	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7210445	0.81[ASN][1000 genomes]
rs7210708	0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7211614	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7212149	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7212930	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs7213513	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7214589	0.81[ASN][1000 genomes]
rs7216202	0.94[ASW][hapmap];0.84[MEX][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs7216971	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7217025	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7217120	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7218848	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs7219816	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7219985	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs7221510	0.94[ASW][hapmap];0.84[MEX][hapmap];0.95[YRI][hapmap]
rs7221770	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7222452	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs7222593	0.83[JPT][hapmap]
rs7225998	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs8065115	0.83[JPT][hapmap]
rs8065385	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs8065535	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8067953	0.83[ASN][1000 genomes]
rs8068128	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8068397	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs8068623	0.81[ASN][1000 genomes]
rs8073710	0.94[ASW][hapmap];0.89[CEU][hapmap];0.93[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];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8073888	0.83[ASN][1000 genomes]
rs8074443	0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs8076655	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs8078038	0.83[ASN][1000 genomes]
rs8081754	0.83[JPT][hapmap]
rs9303542	0.81[ASN][1000 genomes]
rs9747133	0.81[ASN][1000 genomes]
rs9890142	0.81[ASN][1000 genomes]
rs9890488	0.81[ASN][1000 genomes]
rs9891073	0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9894812	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs9897162	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9905961	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9906193	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9906651	0.83[ASN][1000 genomes]
rs9907699	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9909002	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9909872	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9910535	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs9913760	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9916227	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7209556	NFE2L1	cis	cerebellum	SCAN
rs7209556	DGKH	trans	parietal	SCAN
rs7209556	NFE2L1	cis	parietal	SCAN
rs7209556	RND2	cis	parietal	SCAN
rs7209556	CCDC56	cis	cerebellum	SCAN
rs7209556	HOXB6	cis	cerebellum	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	chr17:46460400-46466400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:46460400-46471200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:46462000-46470400	Weak transcription	Fetal Thymus	thymus
5	chr17:46462200-46467000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr17:46462400-46474200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:46463200-46469000	Enhancers	Fetal Brain Male	brain
8	chr17:46463200-46469400	Weak transcription	GM12878-XiMat	blood
9	chr17:46463400-46466800	Weak transcription	K562	blood
10	chr17:46463400-46472200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:46463600-46471800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr17:46464200-46469600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:46464800-46466200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr17:46465000-46466400	Weak transcription	Primary T cells from cord blood	blood
15	chr17:46465000-46467000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr17:46465000-46467400	Weak transcription	Fetal Brain Female	brain
17	chr17:46465000-46472200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr17:46465400-46466200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:46465400-46470200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr17:46465600-46466600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr17:46465600-46471800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr17:46465800-46470200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr17:46466000-46467200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr17:46466000-46474600	Strong transcription	Primary T cells fromperipheralblood	blood

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