Variant report

Variant	rs587009
Chromosome Location	chr6:24947541-24947542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11760083	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs1410684	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16889798	0.89[CHB][hapmap]
rs6929465	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs6929680	0.89[ASN][1000 genomes]
rs9461081	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461082	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467355	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv275111	chr6:24946671-24951199	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs587009	SCGN	cis	cerebellum	SCAN
rs587009	PGBD1	cis	cerebellum	SCAN
rs587009	HIST1H2BF	cis	cerebellum	SCAN
rs587009	HIST1H3C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24942400-24948000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:24943800-24948000	ZNF genes & repeats	Dnd41	blood
3	chr6:24944800-24949200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:24946200-24949000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:24946400-24947600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr6:24946400-24951600	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:24946600-24947600	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr6:24946600-24947600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
9	chr6:24946600-24947800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr6:24946600-24948000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr6:24946600-24948000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:24946600-24949200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:24946800-24947600	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr6:24946800-24948000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:24946800-24948200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr6:24946800-24949200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:24947000-24947600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr6:24947000-24948000	ZNF genes & repeats	Primary B cells from cord blood	blood
19	chr6:24947000-24948400	Weak transcription	Fetal Thymus	thymus
20	chr6:24947200-24947600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:24947400-24947600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr6:24947400-24947600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr6:24947400-24947800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:24947400-24949400	Enhancers	Primary T cells from cord blood	blood

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