Variant report

Variant	rs58362069
Chromosome Location	chr6:24975063-24975064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:24974567-24975359	GM12891	blood:	n/a	n/a
2	RUNX3	chr6:24974496-24975348	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:24974453-24975379	GM12878	blood:	n/a	n/a
4	SPI1	chr6:24974477-24975507	GM12878	blood:	n/a	n/a
5	BATF	chr6:24974762-24975164	GM12878	blood:	n/a	n/a
6	MEF2C	chr6:24974665-24975195	GM12878	blood:	n/a	chr6:24974955-24974970
7	NFIC	chr6:24974579-24975224	GM12878	blood:	n/a	n/a
8	SPI1	chr6:24975020-24975340	GM12891	blood:	n/a	n/a
9	MEF2A	chr6:24974806-24975451	GM12878	blood:	n/a	n/a
10	GATA3	chr6:24974625-24975265	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr6:24974651-24975277	SK-N-SH	brain:	n/a	n/a
12	EP300	chr6:24974797-24975172	GM12878	blood:	n/a	n/a
13	EP300	chr6:24974822-24975331	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr6:24974833-24975226	GM12878	blood:	n/a	n/a
15	MTA3	chr6:24974225-24975250	GM12878	blood:	n/a	n/a
16	POU2F2	chr6:24974103-24975208	GM12891	blood:	n/a	n/a
17	FOS	chr6:24974533-24975135	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr6:24974883-24975142	MCF10A-Er-Src	breast:	n/a	n/a
19	ATF2	chr6:24974706-24975178	GM12878	blood:	n/a	n/a
20	FOXM1	chr6:24974714-24975233	GM12878	blood:	n/a	n/a
21	MEF2A	chr6:24974696-24975207	GM12878	blood:	n/a	n/a
22	EBF1	chr6:24974755-24975070	GM12878	blood:	n/a	n/a
23	CUX1	chr6:24974860-24975359	GM12878	blood:	n/a	n/a
24	POU2F2	chr6:24974620-24975094	GM12878	blood:	n/a	n/a
25	SPI1	chr6:24974645-24975434	HL-60	blood:	n/a	n/a
26	ATF2	chr6:24974592-24975244	GM12878	blood:	n/a	n/a
27	BCL11A	chr6:24974754-24975135	GM12878	blood:	n/a	n/a
28	PML	chr6:24974271-24975121	GM12878	blood:	n/a	n/a
29	SPI1	chr6:24975060-24975392	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PPIAP29	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs127486	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374675	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379206	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384411	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425081	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441572	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453666	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608943	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61555713	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs618383	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618393	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620115	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621558	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631693	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638321	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654285	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662608	0.96[EUR][1000 genomes];1.00[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	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24950400-24988600	Weak transcription	Dnd41	blood
2	chr6:24954400-24980800	Weak transcription	Thymus	Thymus
3	chr6:24966600-24976000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr6:24969200-24980800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:24969400-24980600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:24973200-24975200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr6:24973400-24979200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:24973600-24975200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:24973600-24976000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:24974000-24976000	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:24974200-24975200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:24974200-24975400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:24974200-24975600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr6:24974200-24975800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr6:24974200-24976000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:24974200-24976000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:24974400-24976000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr6:24974600-24975200	Flanking Active TSS	GM12878-XiMat	blood
19	chr6:24974600-24975400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:24974600-24975800	Enhancers	Primary B cells from cord blood	blood
21	chr6:24974600-24976000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:24974800-24975200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:24974800-24975400	Enhancers	Primary T cells from cord blood	blood
24	chr6:24975000-24976000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:24975000-24978800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:24975000-24979000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr6:24975000-24979200	Weak transcription	HSMM	muscle
28	chr6:24975000-24979400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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