Variant report

Variant	rs1424855
Chromosome Location	chr9:21078815-21078816
allele	C/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	CTCF	chr9:21078795-21078986	MCF-7	breast:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
2	CTCF	chr9:21078780-21078930	GM12870	blood:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
3	CTCF	chr9:21078800-21078950	GM12873	blood:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
4	ELF1	chr9:21078722-21079100	HepG2	liver:	n/a	chr9:21078945-21078956
5	CTCF	chr9:21078800-21078950	SAEC	small airway:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
6	MAX	chr9:21078700-21078900	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr9:21078800-21078950	HCT-116	colon:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
8	CTCF	chr9:21078813-21078984	Hela-S3	cervix:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
9	RAD21	chr9:21078738-21079190	HCT-116	colon:	n/a	n/a
10	CTCF	chr9:21078700-21078850	HepG2	liver:	n/a	n/a
11	SMC3	chr9:21078806-21079005	GM12878	blood:	n/a	n/a
12	ELF1	chr9:21078628-21079202	HCT-116	colon:	n/a	chr9:21078945-21078956
13	CTCF	chr9:21078700-21078850	RPTEC	kidney:	n/a	n/a
14	CTCF	chr9:21078728-21079154	MCF-7	breast:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
15	CTCF	chr9:21078748-21079142	MCF-7	breast:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
16	CTCF	chr9:21078776-21078987	GM12878	blood:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
17	CTCF	chr9:21078800-21078950	NHEK	skin:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
18	ELF1	chr9:21078725-21079156	A549	lung:	n/a	chr9:21078945-21078956
19	CTCF	chr9:21078740-21078890	GM12864	blood:	n/a	n/a
20	SPI1	chr9:21078776-21079138	HL-60	blood:	n/a	n/a
21	CTCF	chr9:21078760-21078910	HVMF	connective:	n/a	n/a
22	CTCF	chr9:21078800-21078950	HRE	kidney:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
23	CTCF	chr9:21078780-21078930	HPAF	blood vessel:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
24	CTCF	chr9:21078760-21078910	BE2_C	brain:	n/a	n/a
25	CTCF	chr9:21078800-21078950	HPAF	blood vessel:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
26	CTCF	chr9:21078780-21078930	GM12865	blood:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
27	CTCF	chr9:21078811-21079088	Lung_OC	lung:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
28	CTCF	chr9:21078780-21078930	AoAF	blood vessel:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
29	ZNF143	chr9:21078664-21079087	H1-hESC	embryonic stem cell:	n/a	n/a
30	WRNIP1	chr9:21078657-21078869	GM12878	blood:	n/a	n/a
31	CTCF	chr9:21078776-21079007	MCF-7	breast:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
32	CTCF	chr9:21078800-21078950	HUVEC	blood vessel:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
33	CTCF	chr9:21078760-21078910	GM12875	blood:	n/a	n/a
34	ELF1	chr9:21078797-21079057	HepG2	liver:	n/a	chr9:21078945-21078956
35	CTCF	chr9:21078808-21078992	T-47D	breast:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
36	CTCF	chr9:21078740-21078890	HFF-Myc	foreskin:	n/a	n/a
37	ELF1	chr9:21078588-21079165	MCF-7	breast:	n/a	chr9:21078945-21078956
38	CTCF	chr9:21078780-21078930	GM12871	blood:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
39	CTCF	chr9:21078800-21078950	GM12864	blood:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
40	CTCF	chr9:21078800-21078950	NHDF-neo	bronchial:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
41	ELF1	chr9:21078708-21079110	GM12878	blood:	n/a	chr9:21078945-21078956
42	CTCF	chr9:21078800-21078950	HEK293	kidney:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
43	RAD21	chr9:21078675-21079001	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr9:21078780-21078930	GM12872	blood:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
45	CTCF	chr9:21078760-21078910	AG04450	lung:	n/a	n/a
46	CTCF	chr9:21078800-21078950	AG04449	skin:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
47	RAD21	chr9:21078693-21079052	H1-hESC	embryonic stem cell:	n/a	n/a
48	ELF1	chr9:21078616-21079265	HCT-116	colon:	n/a	chr9:21078945-21078956
49	CTCF	chr9:21078780-21079010	NHEK	skin:	n/a	chr9:21078901-21078922 chr9:21078899-21078917 chr9:21078900-21078916
50	RAD21	chr9:21078671-21079093	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21076953..21079185-chr9:21106248..21108735,2	MCF-7	breast:
2	chr9:21078514..21079405-chr9:21110637..21111248,3	MCF-7	breast:

Variant related genes	Relation type
IFNB1	TF binding region
ENSG00000225027	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10481513	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738580	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1539740	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1539741	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1539744	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2161947	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2383176	1.00[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817218	chr9:20687769-21309177	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
3	nsv1017312	chr9:20892952-21122462	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv466293	chr9:21029330-21199680	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv613752	chr9:21029330-21199680	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv466294	chr9:21037771-21082814	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv613753	chr9:21037771-21082814	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1032466	chr9:21052069-21243756	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv540084	chr9:21052069-21243756	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv892732	chr9:21054806-21089434	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21071000-21082000	Weak transcription	Aorta	Aorta
2	chr9:21076200-21082000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:21076400-21082800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:21077400-21079200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr9:21077400-21079200	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr9:21077600-21081400	Weak transcription	Thymus	Thymus
7	chr9:21077800-21081400	Enhancers	Dnd41	blood
8	chr9:21078000-21081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:21078600-21079200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:21078600-21079200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:21078800-21079200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:21078800-21080600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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