Variant report

Variant	rs6784495
Chromosome Location	chr3:178792604-178792605
allele	G/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	FOXM1	chr3:178792283-178792906	GM12878	blood:	n/a	n/a
2	RCOR1	chr3:178792437-178792751	K562	blood:	n/a	n/a
3	ZNF384	chr3:178792512-178792762	K562	blood:	n/a	n/a
4	SPI1	chr3:178792501-178792830	GM12878	blood:	n/a	chr3:178792678-178792691 chr3:178792749-178792762 chr3:178792572-178792585 chr3:178792681-178792688 chr3:178792680-178792689
5	POLR2A	chr3:178792505-178792688	GM12891	blood:	n/a	n/a
6	ZNF384	chr3:178792383-178792619	GM12878	blood:	n/a	n/a
7	RUNX3	chr3:178792407-178792934	GM12878	blood:	n/a	n/a
8	SPI1	chr3:178792450-178792824	GM12891	blood:	n/a	chr3:178792678-178792691 chr3:178792749-178792762 chr3:178792572-178792585 chr3:178792681-178792688 chr3:178792680-178792689
9	IKZF1	chr3:178792471-178792834	GM12878	blood:	n/a	n/a
10	SPI1	chr3:178792421-178792890	HL-60	blood:	n/a	chr3:178792678-178792691 chr3:178792749-178792762 chr3:178792572-178792585 chr3:178792681-178792688 chr3:178792680-178792689
11	SPI1	chr3:178792497-178792846	GM12891	blood:	n/a	chr3:178792678-178792691 chr3:178792749-178792762 chr3:178792572-178792585 chr3:178792681-178792688 chr3:178792680-178792689
12	CUX1	chr3:178792518-178792724	K562	blood:	n/a	n/a
13	RUNX3	chr3:178792461-178792896	GM12878	blood:	n/a	n/a
14	NFIC	chr3:178792229-178793001	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:178780519..178783087-chr3:178791350..178793561,2	MCF-7	breast:
2	chr3:178790486..178793046-chr3:179039770..179041541,2	K562	blood:

Variant related genes	Relation type
ZMAT3	TF binding region
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11711320	0.83[AMR][1000 genomes]
rs13082485	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13099856	0.91[ASN][1000 genomes]
rs1517586	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2677763	0.91[ASN][1000 genomes]
rs2677764	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2677770	0.95[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[ASN][1000 genomes]
rs2699887	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs2699891	0.82[ASN][1000 genomes]
rs2699893	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2699905	0.95[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs2699906	0.91[ASN][1000 genomes]
rs4245914	0.83[AMR][1000 genomes]
rs4279147	0.80[AMR][1000 genomes]
rs4377525	0.83[AMR][1000 genomes]
rs4395442	0.82[AMR][1000 genomes]
rs4417911	0.83[AMR][1000 genomes]
rs4469018	0.86[AMR][1000 genomes]
rs4552405	0.83[AMR][1000 genomes]
rs4579062	0.93[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs4607155	0.86[AMR][1000 genomes]
rs4632588	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4637331	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4955801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4955807	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs4955810	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs56115013	0.83[AMR][1000 genomes]
rs6443614	0.83[AMR][1000 genomes]
rs6443617	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6772028	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6790867	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs6793769	0.83[AMR][1000 genomes]
rs6793893	0.93[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs6794956	0.86[AMR][1000 genomes]
rs6795238	0.86[AMR][1000 genomes]
rs6800015	0.93[GIH][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6804084	0.85[CEU][hapmap]
rs73187259	0.91[ASN][1000 genomes]
rs7612363	0.83[AMR][1000 genomes]
rs7633318	0.83[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]
rs7639391	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs9830482	0.82[AMR][1000 genomes]
rs9835752	0.82[AMR][1000 genomes]
rs9835765	0.84[AMR][1000 genomes]
rs9860318	0.82[AMR][1000 genomes]
rs9860749	0.85[AMR][1000 genomes]
rs9880749	0.86[AMR][1000 genomes]
rs9968179	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6784495	YEATS2	cis	cerebellum	SCAN
rs6784495	ZMAT3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178790000-178806200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:178790200-178792800	Enhancers	Fetal Thymus	thymus
3	chr3:178790200-178793400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:178790200-178793400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:178790400-178792800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr3:178790400-178793200	Enhancers	Primary T cells from cord blood	blood
7	chr3:178790400-178793200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr3:178790400-178793400	Enhancers	Primary B cells from cord blood	blood
9	chr3:178790400-178797200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:178791000-178793200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:178791000-178794200	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:178791200-178792800	Enhancers	Thymus	Thymus
13	chr3:178791400-178793400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:178791600-178793200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:178791600-178793400	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:178792000-178792800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:178792000-178792800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:178792200-178793200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr3:178792200-178793400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:178792400-178792800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:178792400-178794200	Enhancers	GM12878-XiMat	blood
22	chr3:178792400-178794600	Weak transcription	K562	blood
23	chr3:178792600-178792800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr3:178792600-178793000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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