Variant report

Variant	rs11665965
Chromosome Location	chr19:42429833-42429834
allele	A/G
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	ZEB1	chr19:42429140-42430954	GM12878	blood:	n/a	chr19:42429510-42429521 chr19:42429391-42429398 chr19:42430209-42430220 chr19:42430212-42430219 chr19:42429666-42429673 chr19:42430066-42430075 chr19:42429859-42429871 chr19:42430435-42430442 chr19:42429663-42429675
2	ZEB1	chr19:42429258-42430867	HepG2	liver:	n/a	chr19:42429510-42429521 chr19:42429391-42429398 chr19:42430209-42430220 chr19:42430212-42430219 chr19:42429666-42429673 chr19:42430066-42430075 chr19:42429859-42429871 chr19:42430435-42430442 chr19:42429663-42429675
3	BCL3	chr19:42429353-42430191	A549	lung:	n/a	n/a
4	ZEB1	chr19:42429418-42430198	GM12878	blood:	n/a	chr19:42429510-42429521 chr19:42429666-42429673 chr19:42430066-42430075 chr19:42429859-42429871 chr19:42429663-42429675

No.	Distal block	Cell Line	Cell type
1	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
2	chr19:42378071..42380066-chr19:42429626..42432415,2	MCF-7	breast:
3	chr19:42364250..42366335-chr19:42427565..42430035,3	K562	blood:
4	chr19:42407163..42408726-chr19:42429541..42431369,2	K562	blood:
5	chr19:42382327..42390135-chr19:42429723..42437438,12	MCF-7	breast:
6	chr19:42365213..42368096-chr19:42429393..42431288,2	K562	blood:
7	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
8	chr19:42423745..42425832-chr19:42428186..42430705,2	MCF-7	breast:
9	chr19:42427829..42430659-chr19:42431382..42433888,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000076928	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10409822	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10411814	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10414709	0.83[ASN][1000 genomes]
rs10416501	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419731	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10420264	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10424013	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083642	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11667048	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668332	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669448	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11878287	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971376	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974044	0.83[MEX][hapmap]
rs12975677	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1864207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965727	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075751	0.83[MEX][hapmap]
rs2081999	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3786539	0.83[MEX][hapmap]
rs3826707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61007366	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246830	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247727	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs735571	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8109192	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9304600	0.86[EUR][1000 genomes]
rs9676662	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9749440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11665965	RABAC1	cis	multi-tissue	Pritchard
rs11665965	RABAC1	cis	lymphoblastoid	seeQTL
rs11665965	SLC1A5	cis	parietal	SCAN
rs11665965	CCDC114	cis	cerebellum	SCAN
rs11665965	TMEM143	cis	parietal	SCAN
rs11665965	PSG9	cis	multi-tissue	Pritchard
rs11665965	PVR	cis	parietal	SCAN
rs11665965	IGFL1	cis	parietal	SCAN
rs11665965	PSG3	cis	multi-tissue	Pritchard
rs11665965	ZNF230	cis	parietal	SCAN
rs11665965	CEACAM3	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42421000-42431000	Weak transcription	Dnd41	blood
2	chr19:42425600-42432400	Weak transcription	Gastric	stomach
3	chr19:42426600-42431600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:42426800-42431600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:42427800-42431200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr19:42427800-42431600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr19:42427800-42431600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr19:42428200-42430000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:42429000-42432400	Weak transcription	Pancreas	Pancrea

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