Variant report

Variant	rs7445694
Chromosome Location	chr5:178286356-178286357
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	STAT3	chr5:178286259-178287163	MCF10A-Er-Src	breast:	n/a	chr5:178286890-178286913 chr5:178286905-178286913
2	MXI1	chr5:178286169-178287627	SK-N-SH	brain:	n/a	n/a
3	TBL1XR1	chr5:178286154-178287328	K562	blood:	n/a	n/a
4	MAFK	chr5:178286203-178286544	HepG2	liver:	n/a	chr5:178286375-178286390
5	SETDB1	chr5:178286288-178286902	U2OS	brain:	n/a	n/a
6	MAFK	chr5:178286280-178286850	IMR90	lung:	n/a	chr5:178286375-178286390
7	MYC	chr5:178286286-178287278	MCF10A-Er-Src	breast:	n/a	chr5:178287186-178287196 chr5:178286729-178286738
8	EGR1	chr5:178286350-178287317	HCT-116	colon:	n/a	chr5:178286728-178286738 chr5:178286722-178286744 chr5:178286897-178286921 chr5:178286728-178286739 chr5:178286728-178286737 chr5:178286727-178286740 chr5:178286724-178286738 chr5:178286726-178286741 chr5:178286728-178286739 chr5:178286727-178286740 chr5:178286728-178286738 chr5:178287212-178287222 chr5:178286726-178286740 chr5:178287157-178287167 chr5:178286727-178286740
9	MAFK	chr5:178286207-178287079	HepG2	liver:	n/a	chr5:178286375-178286390
10	MAZ	chr5:178286322-178287269	GM12878	blood:	n/a	chr5:178287186-178287196 chr5:178286729-178286738
11	MYC	chr5:178286255-178287164	MCF10A-Er-Src	breast:	n/a	chr5:178286729-178286738

No.	Distal block	Cell Line	Cell type
1	chr5:178154802..178159439-chr5:178284936..178288781,7	MCF-7	breast:
2	chr5:178053391..178055177-chr5:178285758..178288394,2	MCF-7	breast:
3	chr5:178285646..178289279-chr5:178321547..178324884,4	MCF-7	breast:
4	chr5:178156014..178158845-chr5:178285994..178289826,5	MCF-7	breast:

Variant related genes	Relation type
ZNF354B	TF binding region
ENSG00000169131	Chromatin interaction
ENSG00000198939	Chromatin interaction
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10040956	0.83[CHB][hapmap]
rs10050708	1.00[ASN][1000 genomes]
rs10050787	1.00[ASN][1000 genomes]
rs10067521	0.83[CHB][hapmap]
rs10077950	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10479515	0.83[CHB][hapmap]
rs10479516	0.83[CHB][hapmap]
rs11249598	0.99[ASN][1000 genomes]
rs11743869	0.83[CHB][hapmap]
rs11746144	0.99[ASN][1000 genomes]
rs11955586	0.83[CHB][hapmap]
rs12654964	0.98[ASN][1000 genomes]
rs12655480	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12658098	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13153458	1.00[ASN][1000 genomes]
rs13157348	0.86[EUR][1000 genomes]
rs13157356	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13168290	1.00[ASN][1000 genomes]
rs13185338	1.00[ASN][1000 genomes]
rs34489756	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3922929	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6858885	0.96[ASN][1000 genomes]
rs6859072	1.00[ASN][1000 genomes]
rs6864114	1.00[ASN][1000 genomes]
rs6869746	1.00[ASN][1000 genomes]
rs6869885	0.97[ASN][1000 genomes]
rs6870086	1.00[ASN][1000 genomes]
rs6870961	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874387	1.00[ASN][1000 genomes]
rs6875162	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6877198	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6878261	1.00[ASN][1000 genomes]
rs6889589	1.00[ASN][1000 genomes]
rs6891035	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs6898983	1.00[ASN][1000 genomes]
rs7446225	1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7447547	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7710019	1.00[ASN][1000 genomes]
rs7716970	1.00[ASN][1000 genomes]
rs7722977	0.90[EUR][1000 genomes]
rs7723868	1.00[ASN][1000 genomes]
rs9329056	1.00[ASN][1000 genomes]
rs9329057	1.00[ASN][1000 genomes]
rs9329058	1.00[ASN][1000 genomes]
rs9716846	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv823352	chr5:178279625-178296623	Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7445694	GFPT2	cis	parietal	SCAN
rs7445694	ZNF454	cis	parietal	SCAN
rs7445694	TMED9	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178263600-178286400	Weak transcription	Right Atrium	heart
2	chr5:178282000-178286400	Weak transcription	K562	blood
3	chr5:178282000-178286600	Weak transcription	Placenta	Placenta
4	chr5:178282400-178286600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:178284200-178286600	Weak transcription	HSMMtube	muscle
6	chr5:178285800-178286800	Flanking Active TSS	Dnd41	blood
7	chr5:178286000-178286600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:178286000-178287600	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr5:178286000-178288400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:178286200-178286400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:178286200-178286400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:178286200-178286400	Enhancers	Primary T cells from cord blood	blood
13	chr5:178286200-178286400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:178286200-178286400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr5:178286200-178286400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr5:178286200-178286400	Flanking Active TSS	HepG2	liver
17	chr5:178286200-178286400	Enhancers	HMEC	breast
18	chr5:178286200-178286400	Enhancers	HUVEC	blood vessel
19	chr5:178286200-178286600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:178286200-178286600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:178286200-178286600	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:178286200-178286800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr5:178286200-178286800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr5:178286200-178287600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:178286200-178287600	Active TSS	Stomach Mucosa	stomach
26	chr5:178286200-178287600	Active TSS	A549	lung
27	chr5:178286200-178287800	Active TSS	iPS-20b Cell Line	embryonic stem cell

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