Variant report

Variant	rs7026624
Chromosome Location	chr9:95724550-95724551
allele	A/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	chr9:95724264-95724568	GM12878	blood:	n/a	n/a
2	ATF2	chr9:95724099-95724602	GM12878	blood:	n/a	n/a
3	RUNX3	chr9:95724190-95724647	GM12878	blood:	n/a	n/a
4	SPI1	chr9:95724216-95724570	GM12891	blood:	n/a	n/a
5	RUNX3	chr9:95724192-95724694	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95722390..95724791-chr9:95916678..95919347,2	MCF-7	breast:

Variant related genes	Relation type
FGD3	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10121340	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10121856	0.95[GIH][hapmap];0.81[MEX][hapmap]
rs10124112	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739940	0.95[GIH][hapmap]
rs10761182	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10761189	1.00[YRI][hapmap]
rs10821046	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992564	0.95[GIH][hapmap]
rs12346994	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3936098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3936099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4237217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744161	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6479440	0.88[CEU][hapmap]
rs6479441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6479445	1.00[YRI][hapmap]
rs7021090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023321	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7023602	0.81[ASN][1000 genomes]
rs7032953	0.83[EUR][1000 genomes]
rs7039741	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7869421	0.95[GIH][hapmap]
rs9942965	0.95[GIH][hapmap]

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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7026624	SUSD3	cis	multi-tissue	Pritchard
rs7026624	ZNF484	cis	parietal	SCAN
rs7026624	ZNF484	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95715400-95732200	Weak transcription	Fetal Brain Female	brain
2	chr9:95717000-95725600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr9:95717200-95724800	Enhancers	Primary T cells fromperipheralblood	blood
4	chr9:95717200-95725800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:95719600-95725800	Weak transcription	HepG2	liver
6	chr9:95720000-95731400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:95721600-95725800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr9:95721800-95725800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:95722200-95726000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr9:95722400-95725600	Weak transcription	Thymus	Thymus
11	chr9:95723000-95725600	Enhancers	Primary T cells from cord blood	blood
12	chr9:95723200-95726000	Enhancers	Primary B cells from peripheral blood	blood
13	chr9:95723400-95724600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr9:95723800-95724600	ZNF genes & repeats	Fetal Muscle Leg	muscle
15	chr9:95723800-95724800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:95723800-95725600	Enhancers	Primary B cells from cord blood	blood
17	chr9:95724000-95724600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:95724000-95724600	Enhancers	Fetal Thymus	thymus
19	chr9:95724000-95724800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr9:95724200-95724600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr9:95724200-95724600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:95724200-95724800	Enhancers	Brain Germinal Matrix	brain
23	chr9:95724200-95725400	Enhancers	Spleen	Spleen
24	chr9:95724200-95726000	Weak transcription	Pancreas	Pancrea
25	chr9:95724200-95726200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:95724400-95724600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr9:95724400-95724600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:95724400-95724600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr9:95724400-95724600	Flanking Active TSS	GM12878-XiMat	blood
30	chr9:95724400-95725400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr9:95724400-95726000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr9:95724400-95726600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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