Variant report

Variant	rs9897588
Chromosome Location	chr17:46488670-46488671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs11079818	0.92[EUR][1000 genomes]
rs11655672	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12449653	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12450014	0.91[EUR][1000 genomes]
rs12450081	0.91[EUR][1000 genomes]
rs12450786	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12450935	0.92[EUR][1000 genomes]
rs12451412	0.92[EUR][1000 genomes]
rs12452212	0.91[EUR][1000 genomes]
rs12452234	0.91[EUR][1000 genomes]
rs12453208	0.86[EUR][1000 genomes]
rs12937965	0.88[EUR][1000 genomes]
rs12938640	0.92[EUR][1000 genomes]
rs12940365	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12941926	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12944592	0.91[EUR][1000 genomes]
rs12945780	0.94[ASN][1000 genomes]
rs12946636	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12948017	0.91[EUR][1000 genomes]
rs12953245	0.89[EUR][1000 genomes]
rs1396870	0.94[ASN][1000 genomes]
rs1533057	0.89[ASN][1000 genomes]
rs1553749	0.91[EUR][1000 genomes]
rs1553751	0.91[EUR][1000 genomes]
rs1553752	0.91[EUR][1000 genomes]
rs1553753	0.91[EUR][1000 genomes]
rs16955397	0.91[EUR][1000 genomes]
rs1912153	0.91[EUR][1000 genomes]
rs1912154	0.91[EUR][1000 genomes]
rs2056458	0.91[EUR][1000 genomes]
rs2084881	0.87[EUR][1000 genomes]
rs2175158	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34771639	0.89[ASN][1000 genomes]
rs34791545	0.94[ASN][1000 genomes]
rs35387091	0.89[ASN][1000 genomes]
rs35680046	0.89[ASN][1000 genomes]
rs35767434	0.89[ASN][1000 genomes]
rs4131712	0.91[EUR][1000 genomes]
rs4261589	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4312351	0.88[EUR][1000 genomes]
rs4451990	0.91[EUR][1000 genomes]
rs4556829	0.87[EUR][1000 genomes]
rs4793846	0.89[ASN][1000 genomes]
rs5000249	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55682156	0.94[ASN][1000 genomes]
rs56655886	0.87[ASN][1000 genomes]
rs62064554	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6504158	0.88[EUR][1000 genomes]
rs6504172	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6504203	0.92[EUR][1000 genomes]
rs6504257	0.87[ASN][1000 genomes]
rs66529852	0.89[ASN][1000 genomes]
rs7207826	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7207928	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7209043	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7209522	0.91[EUR][1000 genomes]
rs7209855	0.89[EUR][1000 genomes]
rs7210445	0.91[EUR][1000 genomes]
rs7210708	0.90[EUR][1000 genomes]
rs7211712	0.94[ASN][1000 genomes]
rs7212149	0.89[EUR][1000 genomes]
rs7212930	0.87[EUR][1000 genomes]
rs7213513	0.90[EUR][1000 genomes]
rs7214269	0.92[ASN][1000 genomes]
rs7214589	0.91[EUR][1000 genomes]
rs7216971	0.91[EUR][1000 genomes]
rs7217025	0.91[EUR][1000 genomes]
rs7217120	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7218217	0.94[ASN][1000 genomes]
rs7218345	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7219816	0.91[EUR][1000 genomes]
rs7219985	0.88[EUR][1000 genomes]
rs7220387	0.94[ASN][1000 genomes]
rs7221770	0.91[EUR][1000 genomes]
rs7222452	0.91[EUR][1000 genomes]
rs7225998	0.85[EUR][1000 genomes]
rs8065385	0.87[EUR][1000 genomes]
rs8067953	0.91[EUR][1000 genomes]
rs8068128	0.91[EUR][1000 genomes]
rs8068397	0.87[EUR][1000 genomes]
rs8068623	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8072770	0.89[ASN][1000 genomes]
rs8073466	0.94[ASN][1000 genomes]
rs8073888	0.92[EUR][1000 genomes]
rs8074212	0.89[EUR][1000 genomes]
rs8074443	0.91[EUR][1000 genomes]
rs8078038	0.89[EUR][1000 genomes]
rs8082009	0.87[EUR][1000 genomes]
rs9303542	0.89[EUR][1000 genomes]
rs9747133	0.89[EUR][1000 genomes]
rs9890142	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9890488	0.89[EUR][1000 genomes]
rs9891073	0.91[EUR][1000 genomes]
rs9891635	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9894812	0.91[EUR][1000 genomes]
rs9895123	0.82[EUR][1000 genomes]
rs9895985	0.86[EUR][1000 genomes]
rs9897162	0.91[EUR][1000 genomes]
rs9898988	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9899213	0.86[EUR][1000 genomes]
rs9900511	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901279	0.87[EUR][1000 genomes]
rs9905220	0.86[EUR][1000 genomes]
rs9905961	0.86[EUR][1000 genomes]
rs9906193	0.87[EUR][1000 genomes]
rs9906651	0.88[EUR][1000 genomes]
rs9907699	0.91[EUR][1000 genomes]
rs9909002	0.91[EUR][1000 genomes]
rs9909872	0.86[EUR][1000 genomes]
rs9910535	0.87[EUR][1000 genomes]
rs9916227	0.90[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9897588	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs9897588	SKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46485000-46491200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:46485200-46488800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr17:46485400-46488800	Weak transcription	GM12878-XiMat	blood
4	chr17:46485800-46489800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr17:46486000-46489800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:46486200-46489200	Strong transcription	Fetal Thymus	thymus
7	chr17:46486800-46488800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:46486800-46489000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:46486800-46489800	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr17:46486800-46503000	Weak transcription	Thymus	Thymus
11	chr17:46487600-46501800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:46487800-46503600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:46488000-46488800	Weak transcription	Primary T cells from cord blood	blood
14	chr17:46488000-46488800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr17:46488000-46488800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr17:46488400-46488800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:46488400-46491600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:46488600-46488800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:46488600-46489600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr17:46488600-46491200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr17:46488600-46491200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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