Variant report

Variant	rs17518268
Chromosome Location	chr9:72435431-72435432
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	ELF1	chr9:72435381-72435694	A549	lung:	n/a	n/a
2	SIX5	chr9:72435406-72435742	GM12878	blood:	n/a	n/a
3	ELF1	chr9:72435401-72435751	K562	blood:	n/a	n/a
4	ATF3	chr9:72435327-72435740	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr9:72435193-72435865	A549	lung:	n/a	n/a
6	ATF1	chr9:72435414-72435768	K562	blood:	n/a	n/a
7	SIX5	chr9:72435376-72435724	GM12878	blood:	n/a	n/a
8	SIX5	chr9:72435385-72435768	K562	blood:	n/a	n/a
9	ETS1	chr9:72435300-72435869	A549	lung:	n/a	n/a
10	MAZ	chr9:72435414-72435770	K562	blood:	n/a	n/a
11	USF1	chr9:72435345-72435778	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr9:72435371-72435907	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZNF143	chr9:72435298-72435913	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIX5	chr9:72435329-72435812	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF1	chr9:72435349-72435734	H1-hESC	embryonic stem cell:	n/a	n/a
16	CREB1	chr9:72435340-72435862	A549	lung:	n/a	n/a
17	ELF1	chr9:72435343-72435862	MCF-7	breast:	n/a	n/a
18	TBP	chr9:72435400-72435732	K562	blood:	n/a	n/a
19	SIN3A	chr9:72435391-72436090	H1-hESC	embryonic stem cell:	n/a	chr9:72435973-72435982
20	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
21	ZNF143	chr9:72435306-72435904	K562	blood:	n/a	n/a
22	USF1	chr9:72435324-72435736	A549	lung:	n/a	n/a
23	ETS1	chr9:72435338-72435787	A549	lung:	n/a	n/a
24	EP300	chr9:72435387-72435690	K562	blood:	n/a	n/a
25	SIX5	chr9:72435336-72435742	A549	lung:	n/a	n/a
26	SIX5	chr9:72435388-72435665	K562	blood:	n/a	n/a
27	CHD2	chr9:72435397-72435822	H1-hESC	embryonic stem cell:	n/a	n/a
28	CREB1	chr9:72435424-72435736	A549	lung:	n/a	n/a
29	ETS1	chr9:72435311-72435794	K562	blood:	n/a	n/a
30	TCF12	chr9:72435427-72436011	H1-hESC	embryonic stem cell:	n/a	n/a
31	SIX5	chr9:72435176-72435938	A549	lung:	n/a	n/a
32	SIX5	chr9:72435386-72435744	K562	blood:	n/a	n/a
33	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
34	GABPA	chr9:72435325-72435768	A549	lung:	n/a	n/a
35	CTCF	chr9:72435400-72435550	A549	lung:	n/a	n/a
36	CREB1	chr9:72435355-72435843	H1-hESC	embryonic stem cell:	n/a	n/a
37	ZNF143	chr9:72435397-72435741	GM12878	blood:	n/a	n/a
38	SIX5	chr9:72435372-72435705	K562	blood:	n/a	n/a
39	SIX5	chr9:72435316-72435862	H1-hESC	embryonic stem cell:	n/a	n/a
40	HCFC1	chr9:72435329-72435832	K562	blood:	n/a	n/a
41	SP1	chr9:72435331-72435913	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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72425660..72428855-chr9:72433603..72435458,3	K562	blood:

Variant related genes	Relation type
C9orf135	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10521434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140470	0.86[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	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344550	1.00[CHB][hapmap]
rs12347511	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556208	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517599	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17518030	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029206	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036155	1.00[YRI][hapmap]
rs72723208	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72723215	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723218	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723219	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723223	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854014	1.00[YRI][hapmap]
rs7866489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72434200-72435600	Weak transcription	Fetal Lung	lung
2	chr9:72434400-72437000	Weak transcription	Osteobl	bone
3	chr9:72434800-72436600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:72435000-72436200	Active TSS	A549	lung
5	chr9:72435200-72435600	Active TSS	Primary T cells from cord blood	blood
6	chr9:72435200-72435600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:72435200-72435600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr9:72435200-72435600	Bivalent/Poised TSS	Placenta	Placenta
9	chr9:72435200-72435600	Enhancers	Fetal Thymus	thymus
10	chr9:72435200-72435800	Active TSS	Colonic Mucosa	Colon
11	chr9:72435200-72436000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:72435200-72436000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:72435200-72436000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:72435200-72436000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr9:72435200-72436000	Active TSS	Rectal Smooth Muscle	rectum
16	chr9:72435200-72436000	Active TSS	K562	blood
17	chr9:72435200-72436400	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr9:72435200-72436400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr9:72435200-72437000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr9:72435400-72435600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:72435400-72435600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:72435400-72435600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
23	chr9:72435400-72435600	Enhancers	Primary B cells from peripheral blood	blood
24	chr9:72435400-72435600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr9:72435400-72435600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr9:72435400-72435600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr9:72435400-72435600	Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr9:72435400-72435600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:72435400-72435600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:72435400-72435600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:72435400-72435600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:72435400-72435600	Bivalent Enhancer	Liver	Liver
33	chr9:72435400-72435600	Active TSS	Brain Anterior Caudate	brain
34	chr9:72435400-72435600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
35	chr9:72435400-72435600	Bivalent Enhancer	Brain Substantia Nigra	brain
36	chr9:72435400-72435600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr9:72435400-72435600	Bivalent Enhancer	Fetal Heart	heart
38	chr9:72435400-72435600	Bivalent Enhancer	Fetal Intestine Large	intestine
39	chr9:72435400-72435600	Bivalent Enhancer	Fetal Stomach	stomach
40	chr9:72435400-72435600	Bivalent Enhancer	Left Ventricle	heart
41	chr9:72435400-72435600	Enhancers	Right Atrium	heart
42	chr9:72435400-72435600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
43	chr9:72435400-72435600	Active TSS	Stomach Mucosa	stomach
44	chr9:72435400-72435600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
45	chr9:72435400-72435600	Bivalent Enhancer	HSMM	muscle
46	chr9:72435400-72435800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr9:72435400-72435800	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr9:72435400-72435800	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr9:72435400-72435800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
50	chr9:72435400-72435800	Enhancers	Gastric	stomach

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