Variant report

Variant	rs17439752
Chromosome Location	chr9:72435713-72435714
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	SIX5	chr9:72435406-72435742	GM12878	blood:	n/a	n/a
2	ELF1	chr9:72435401-72435751	K562	blood:	n/a	n/a
3	NANOG	chr9:72435487-72435727	H1-hESC	embryonic stem cell:	n/a	n/a
4	EP300	chr9:72435432-72435856	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3AK20	chr9:72435473-72436009	H1-hESC	embryonic stem cell:	n/a	n/a
6	ATF3	chr9:72435327-72435740	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr9:72435524-72435936	H1-hESC	embryonic stem cell:	n/a	n/a
8	TCF12	chr9:72435193-72435865	A549	lung:	n/a	n/a
9	POLR2A	chr9:72435609-72435904	H1-hESC	embryonic stem cell:	n/a	n/a
10	ATF1	chr9:72435414-72435768	K562	blood:	n/a	n/a
11	SIX5	chr9:72435376-72435724	GM12878	blood:	n/a	n/a
12	SIX5	chr9:72435385-72435768	K562	blood:	n/a	n/a
13	MYC	chr9:72435454-72435721	K562	blood:	n/a	n/a
14	TCF12	chr9:72435477-72435848	H1-hESC	embryonic stem cell:	n/a	n/a
15	ETS1	chr9:72435300-72435869	A549	lung:	n/a	n/a
16	MAZ	chr9:72435414-72435770	K562	blood:	n/a	n/a
17	USF1	chr9:72435345-72435778	H1-hESC	embryonic stem cell:	n/a	n/a
18	YY1	chr9:72435371-72435907	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr9:72435298-72435913	H1-hESC	embryonic stem cell:	n/a	n/a
20	CREB1	chr9:72435434-72435885	K562	blood:	n/a	n/a
21	SIX5	chr9:72435329-72435812	H1-hESC	embryonic stem cell:	n/a	n/a
22	USF1	chr9:72435349-72435734	H1-hESC	embryonic stem cell:	n/a	n/a
23	CREB1	chr9:72435340-72435862	A549	lung:	n/a	n/a
24	ELF1	chr9:72435343-72435862	MCF-7	breast:	n/a	n/a
25	TBP	chr9:72435400-72435732	K562	blood:	n/a	n/a
26	JUND	chr9:72435440-72435739	K562	blood:	n/a	n/a
27	SIN3A	chr9:72435391-72436090	H1-hESC	embryonic stem cell:	n/a	chr9:72435973-72435982
28	IRF1	chr9:72435455-72435799	K562	blood:	n/a	chr9:72435678-72435692
29	SP1	chr9:72435273-72435798	A549	lung:	n/a	chr9:72435682-72435691 chr9:72435681-72435691 chr9:72435680-72435691 chr9:72435680-72435692 chr9:72435681-72435690 chr9:72435680-72435692 chr9:72435681-72435690
30	ZNF143	chr9:72435306-72435904	K562	blood:	n/a	n/a
31	USF1	chr9:72435324-72435736	A549	lung:	n/a	n/a
32	ETS1	chr9:72435338-72435787	A549	lung:	n/a	n/a
33	GATA3	chr9:72435571-72435818	MCF-7	breast:	n/a	chr9:72435703-72435710 chr9:72435701-72435711 chr9:72435703-72435710 chr9:72435701-72435710 chr9:72435698-72435714 chr9:72435703-72435710 chr9:72435696-72435717
34	SIX5	chr9:72435336-72435742	A549	lung:	n/a	n/a
35	CHD2	chr9:72435397-72435822	H1-hESC	embryonic stem cell:	n/a	n/a
36	CREB1	chr9:72435424-72435736	A549	lung:	n/a	n/a
37	ETS1	chr9:72435311-72435794	K562	blood:	n/a	n/a
38	TCF12	chr9:72435427-72436011	H1-hESC	embryonic stem cell:	n/a	n/a
39	RCOR1	chr9:72435434-72435850	K562	blood:	n/a	n/a
40	GABPA	chr9:72435434-72435790	A549	lung:	n/a	n/a
41	SIX5	chr9:72435176-72435938	A549	lung:	n/a	n/a
42	SIX5	chr9:72435386-72435744	K562	blood:	n/a	n/a
43	HDAC2	chr9:72435584-72435974	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr9:72435616-72435945	H1-hESC	embryonic stem cell:	n/a	n/a
45	SIN3AK20	chr9:72435535-72435936	H1-hESC	embryonic stem cell:	n/a	n/a
46	SP1	chr9:72435385-72435900	H1-hESC	embryonic stem cell:	n/a	chr9:72435682-72435691 chr9:72435681-72435691 chr9:72435680-72435691 chr9:72435680-72435692 chr9:72435681-72435690 chr9:72435680-72435692 chr9:72435681-72435690
47	GABPA	chr9:72435325-72435768	A549	lung:	n/a	n/a
48	GTF2F1	chr9:72435559-72435953	H1-hESC	embryonic stem cell:	n/a	n/a
49	CREB1	chr9:72435355-72435843	H1-hESC	embryonic stem cell:	n/a	n/a
50	ZNF143	chr9:72435397-72435741	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
C9orf135-AS1	TF binding region
C9orf135	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10521434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140470	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140833	1.00[CHB][hapmap]
rs11140836	1.00[CHB][hapmap]
rs11140842	1.00[CHB][hapmap]
rs11140890	1.00[CHB][hapmap]
rs12337927	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344550	1.00[CHB][hapmap]
rs12347511	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556208	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517599	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17518030	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029206	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723208	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72723215	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723218	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723219	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723223	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72434400-72437000	Weak transcription	Osteobl	bone
2	chr9:72434800-72436600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:72435000-72436200	Active TSS	A549	lung
4	chr9:72435200-72435800	Active TSS	Colonic Mucosa	Colon
5	chr9:72435200-72436000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:72435200-72436000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:72435200-72436000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:72435200-72436000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr9:72435200-72436000	Active TSS	Rectal Smooth Muscle	rectum
10	chr9:72435200-72436000	Active TSS	K562	blood
11	chr9:72435200-72436400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr9:72435200-72436400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr9:72435200-72437000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:72435400-72435800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:72435400-72435800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr9:72435400-72435800	Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr9:72435400-72435800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
18	chr9:72435400-72435800	Enhancers	Gastric	stomach
19	chr9:72435400-72435800	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr9:72435400-72435800	Enhancers	Spleen	Spleen
21	chr9:72435400-72435800	Flanking Active TSS	NH-A	brain
22	chr9:72435400-72435800	Active TSS	NHLF	lung
23	chr9:72435400-72436000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr9:72435400-72436000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr9:72435400-72436000	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr9:72435400-72436000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr9:72435400-72436000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr9:72435400-72436000	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr9:72435400-72436000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
30	chr9:72435400-72436000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:72435400-72436000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
32	chr9:72435400-72436000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
33	chr9:72435400-72436000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
34	chr9:72435400-72436000	Enhancers	Esophagus	oesophagus
35	chr9:72435400-72436000	Bivalent Enhancer	Fetal Brain Male	brain
36	chr9:72435400-72436000	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr9:72435400-72436000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
38	chr9:72435400-72436000	Active TSS	Fetal Kidney	kidney
39	chr9:72435400-72436000	Flanking Active TSS	Pancreas	Pancrea
40	chr9:72435400-72436000	Active TSS	Right Ventricle	heart
41	chr9:72435400-72436000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
42	chr9:72435400-72436000	Enhancers	Thymus	Thymus
43	chr9:72435400-72436000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
44	chr9:72435400-72436000	Active TSS	NHEK	skin
45	chr9:72435400-72436200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:72435400-72436200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:72435400-72436400	Active TSS	H9 Cell Line	embryonic stem cell
48	chr9:72435400-72436400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr9:72435400-72436400	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr9:72435400-72436400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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