Variant report

Variant	rs2309517
Chromosome Location	chr9:72287026-72287027
allele	A/C
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	chr9:72286960-72287110	HUVEC	blood vessel:	n/a	n/a
2	MAX	chr9:72286708-72288222	SK-N-SH	brain:	n/a	chr9:72287424-72287434
3	CTCF	chr9:72286920-72287070	AG04449	skin:	n/a	n/a
4	YY1	chr9:72286772-72287303	ECC-1	luminal epithelium:	n/a	chr9:72287253-72287264 chr9:72287080-72287094
5	CTBP2	chr9:72286573-72287153	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:72286150-72288240	H1-neurons	neurons:	n/a	n/a
7	CTCF	chr9:72286940-72287090	RPTEC	kidney:	n/a	n/a
8	CTCF	chr9:72286900-72287050	SAEC	small airway:	n/a	n/a
9	TAF1	chr9:72286695-72287270	H1-neurons	neurons:	n/a	n/a
10	CTCF	chr9:72287000-72287150	GM12871	blood:	n/a	n/a
11	CTCF	chr9:72286001-72288515	SK-N-SH	brain:	n/a	chr9:72287629-72287642 chr9:72288204-72288214 chr9:72287510-72287523 chr9:72287953-72287962 chr9:72288010-72288019
12	SIN3AK20	chr9:72286942-72287244	SK-N-SH	brain:	n/a	n/a
13	YY1	chr9:72287017-72287351	SK-N-SH_RA	brain:	n/a	chr9:72287253-72287264 chr9:72287080-72287094
14	CTCF	chr9:72286900-72287050	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr9:72286920-72287070	SK-N-SH_RA	brain:	n/a	n/a
16	YY1	chr9:72286996-72287284	SK-N-SH_RA	brain:	n/a	chr9:72287253-72287264 chr9:72287080-72287094
17	CTCF	chr9:72287008-72287196	Fibrobl	skin:	n/a	n/a
18	CTCF	chr9:72286900-72287050	GM12864	blood:	n/a	n/a
19	SMC3	chr9:72286221-72288597	SK-N-SH	brain:	n/a	chr9:72286908-72286918 chr9:72287103-72287113
20	ZBTB7A	chr9:72286742-72287140	ECC-1	luminal epithelium:	n/a	n/a
21	CTCF	chr9:72286920-72287070	HMF	breast:	n/a	n/a
22	YY1	chr9:72286995-72287260	K562	blood:	n/a	chr9:72287080-72287094
23	CTCF	chr9:72286880-72287030	HFF	foreskin:	n/a	n/a
24	CTCF	chr9:72286746-72287153	IMR90	lung:	n/a	n/a
25	RAD21	chr9:72286790-72287141	SK-N-SH_RA	brain:	n/a	chr9:72286908-72286918
26	CTCF	chr9:72286880-72287030	HMEC	breast:	n/a	n/a
27	CTCF	chr9:72286900-72287050	AG09319	gingival:	n/a	n/a
28	YY1	chr9:72286976-72287432	HepG2	liver:	n/a	chr9:72287253-72287264 chr9:72287080-72287094
29	CTCF	chr9:72287020-72287170	HBMEC	blood vessel:	n/a	n/a
30	MYC	chr9:72286880-72287178	MCF-7	breast:	n/a	n/a
31	REST	chr9:72286572-72287295	H1-neurons	neurons:	n/a	chr9:72287119-72287126
32	MAZ	chr9:72286272-72288380	IMR90	lung:	n/a	chr9:72287424-72287434 chr9:72286293-72286302
33	POLR2A	chr9:72286082-72288205	H1-neurons	neurons:	n/a	n/a
34	YY1	chr9:72286809-72287219	H1-hESC	embryonic stem cell:	n/a	chr9:72287080-72287094
35	EP300	chr9:72286883-72288192	ECC-1	luminal epithelium:	n/a	chr9:72288031-72288047
36	CTCF	chr9:72287020-72287170	WERI-Rb-1	eye:	n/a	n/a
37	SIN3A	chr9:72286562-72287271	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr9:72286946-72287117	HepG2	liver:	n/a	n/a
39	RAD21	chr9:72285926-72288545	SK-N-SH	brain:	n/a	chr9:72287629-72287643 chr9:72286908-72286918 chr9:72287509-72287523 chr9:72287335-72287348
40	CTCF	chr9:72286900-72287050	HA-sp	spinal cord:	n/a	n/a
41	CTCF	chr9:72287000-72287150	HPAF	blood vessel:	n/a	n/a
42	CTCF	chr9:72287008-72287197	MCF-7	breast:	n/a	n/a
43	TAF1	chr9:72286580-72288270	H1-neurons	neurons:	n/a	n/a
44	CTCF	chr9:72286899-72287238	MCF-7	breast:	n/a	n/a
45	CTCF	chr9:72286920-72287070	HRPEpiC	eye:	n/a	n/a
46	CTCF	chr9:72287020-72287170	AG04449	skin:	n/a	n/a
47	YY1	chr9:72286885-72287301	H1-hESC	embryonic stem cell:	n/a	chr9:72287253-72287264 chr9:72287080-72287094
48	REST	chr9:72286012-72288556	H1-neurons	neurons:	n/a	chr9:72287119-72287126 chr9:72288032-72288045 chr9:72287792-72287806

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72286195..72289118-chr9:72373474..72376010,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261447	TF binding region
ENSG00000188647	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10780551	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10867853	0.93[EUR][1000 genomes]
rs10867859	0.93[EUR][1000 genomes]
rs10867877	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4629937	0.89[EUR][1000 genomes]
rs4744576	0.93[EUR][1000 genomes]
rs4744928	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4744932	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6559671	0.92[EUR][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	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3389299	chr9:72286157-72289005	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3321912	chr9:72286882-72288180	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72285400-72288400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:72286000-72287600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr9:72286000-72288200	Active TSS	Brain Substantia Nigra	brain
4	chr9:72286200-72287200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
5	chr9:72286200-72287200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr9:72286200-72287600	Active TSS	Osteobl	bone
7	chr9:72286200-72288000	Active TSS	Colonic Mucosa	Colon
8	chr9:72286200-72288200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr9:72286200-72288200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr9:72286200-72288600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:72286400-72287200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr9:72286400-72287200	Flanking Active TSS	Placenta	Placenta
13	chr9:72286400-72287600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr9:72286400-72287600	Active TSS	Primary T cells from cord blood	blood
15	chr9:72286400-72287800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr9:72286400-72288000	Active TSS	Rectal Smooth Muscle	rectum
17	chr9:72286400-72288000	Active TSS	HSMM	muscle
18	chr9:72286400-72288200	Active TSS	Brain Cingulate Gyrus	brain
19	chr9:72286400-72288200	Active TSS	Brain Hippocampus Middle	brain
20	chr9:72286400-72288400	Active TSS	Aorta	Aorta
21	chr9:72286400-72288400	Active TSS	HSMMtube	muscle
22	chr9:72286400-72288600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr9:72286600-72287200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr9:72286600-72287200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:72286600-72287200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
26	chr9:72286600-72287200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:72286600-72287200	Bivalent/Poised TSS	Fetal Stomach	stomach
28	chr9:72286600-72287200	Flanking Active TSS	HMEC	breast
29	chr9:72286600-72287600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:72286600-72287600	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr9:72286600-72287600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:72286600-72287600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:72286600-72287600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:72286600-72287600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:72286600-72287600	Active TSS	Fetal Brain Male	brain
36	chr9:72286600-72287800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
37	chr9:72286600-72288000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:72286600-72288000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:72286600-72288000	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr9:72286600-72288000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:72286600-72288000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:72286600-72288000	Active TSS	Gastric	stomach
43	chr9:72286600-72288000	Active TSS	NHDF-Ad	bronchial
44	chr9:72286600-72288200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr9:72286600-72288200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:72286600-72288200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr9:72286600-72288200	Active TSS	Brain Angular Gyrus	brain
48	chr9:72286600-72288200	Active TSS	Fetal Lung	lung
49	chr9:72286600-72288200	Active TSS	Left Ventricle	heart
50	chr9:72286600-72288200	Bivalent/Poised TSS	Thymus	Thymus

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