Variant report

Variant	rs2780109
Chromosome Location	chr9:86433103-86433104
allele	G/T
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	EBF1	chr9:86432887-86433119	GM12878	blood:	n/a	n/a
2	E2F6	chr9:86433001-86433129	K562	blood:	n/a	n/a
3	POLR2A	chr9:86432395-86433218	SK-N-MC	brain:	n/a	n/a
4	EBF1	chr9:86432889-86433148	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:86432121-86433131	A549	lung:	n/a	n/a
6	POLR2A	chr9:86432776-86433116	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr9:86432249-86433148	Hela-S3	cervix:	n/a	n/a
8	HA-E2F1	chr9:86431867-86433290	MCF-7	breast:	n/a	chr9:86432114-86432124 chr9:86432222-86432231 chr9:86432475-86432484 chr9:86432476-86432486
9	TAF1	chr9:86432758-86433393	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:86432103-86433547	H1-hESC	embryonic stem cell:	n/a	n/a
11	SP1	chr9:86432612-86433114	A549	lung:	n/a	chr9:86433049-86433059 chr9:86432664-86432678 chr9:86432668-86432677 chr9:86432669-86432678 chr9:86433049-86433059 chr9:86432667-86432679 chr9:86432669-86432678
12	FOXA2	chr9:86432617-86433161	A549	lung:	n/a	chr9:86432805-86432817
13	POLR2A	chr9:86432772-86433192	HepG2	liver:	n/a	n/a
14	HEY1	chr9:86432168-86433255	HepG2	liver:	n/a	chr9:86432474-86432489 chr9:86432783-86432798 chr9:86432672-86432687 chr9:86432829-86432844 chr9:86432790-86432805
15	POLR2A	chr9:86432096-86433143	A549	lung:	n/a	n/a
16	POLR2A	chr9:86432649-86433222	H1-hESC	embryonic stem cell:	n/a	n/a
17	USF1	chr9:86432815-86433169	GM12878	blood:	n/a	n/a
18	TAF1	chr9:86432767-86433197	HepG2	liver:	n/a	n/a
19	SIN3AK20	chr9:86432761-86433105	SK-N-SH	brain:	n/a	n/a
20	EGR1	chr9:86432606-86433117	K562	blood:	n/a	chr9:86433052-86433062 chr9:86432760-86432774 chr9:86432696-86432706 chr9:86433052-86433063
21	POLR2A	chr9:86432775-86433193	HepG2	liver:	n/a	n/a
22	HEY1	chr9:86432785-86433109	HepG2	liver:	n/a	chr9:86432829-86432844 chr9:86432790-86432805
23	ELF1	chr9:86432758-86433178	GM12878	blood:	n/a	n/a
24	PAX5	chr9:86432585-86433206	GM12878	blood:	n/a	n/a
25	POLR2A	chr9:86432248-86433328	HepG2	liver:	n/a	n/a
26	POLR2A	chr9:86432779-86433272	H1-hESC	embryonic stem cell:	n/a	n/a
27	RCOR1	chr9:86432598-86433127	IMR90	lung:	n/a	n/a
28	ZNF263	chr9:86431582-86433134	HEK293-T-REx	kidney:	n/a	chr9:86431870-86431879 chr9:86432456-86432477 chr9:86431867-86431876 chr9:86432467-86432476
29	ZNF143	chr9:86432926-86433109	GM12878	blood:	n/a	n/a
30	FOSL2	chr9:86432681-86433238	HepG2	liver:	n/a	chr9:86432696-86432705
31	POLR2A	chr9:86432757-86433252	GM12878	blood:	n/a	n/a
32	POLR2A	chr9:86432763-86433134	Hela-S3	cervix:	n/a	n/a
33	TCF3	chr9:86432769-86433224	GM12878	blood:	n/a	n/a
34	POLR2A	chr9:86432267-86433167	MCF-7	breast:	n/a	n/a
35	TAF1	chr9:86432743-86433222	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr9:86432159-86433124	Raji	blood:	n/a	n/a
37	POLR2A	chr9:86432786-86433292	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr9:86432766-86433266	H1-hESC	embryonic stem cell:	n/a	n/a
39	MYC	chr9:86432946-86433145	MCF-7	breast:	n/a	n/a
40	MAZ	chr9:86431918-86433112	IMR90	lung:	n/a	chr9:86432333-86432343 chr9:86432473-86432483
41	SP1	chr9:86432711-86433120	GM12878	blood:	n/a	chr9:86433049-86433059 chr9:86433049-86433059
42	POLR2A	chr9:86432061-86433134	GM12892	blood:	n/a	n/a
43	MXI1	chr9:86431775-86433216	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr9:86432773-86433192	GM12878	blood:	n/a	n/a
45	POU2F2	chr9:86432732-86433407	GM12878	blood:	n/a	n/a
46	USF1	chr9:86432785-86433105	A549	lung:	n/a	n/a
47	POLR2A	chr9:86433051-86433207	Gliobla	brain:	n/a	n/a
48	POLR2A	chr9:86432220-86433176	A549	lung:	n/a	n/a
49	POLR2A	chr9:86432766-86433128	HepG2	liver:	n/a	n/a
50	SP1	chr9:86432657-86433171	A549	lung:	n/a	chr9:86433049-86433059 chr9:86432664-86432678 chr9:86432668-86432677 chr9:86432669-86432678 chr9:86433049-86433059 chr9:86432667-86432679 chr9:86432669-86432678

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:86433081-86433131	NB4	blood:	n/a
2	chr9:86433081-86433131	HRCEpiC	kidney:	n/a
3	chr9:86433081-86433131	AoSMC	blood vessel:	n/a
4	chr9:86433081-86433131	HUVEC	blood vessel:	n/a
5	chr9:86433081-86433131	SK-N-SH	brain:	n/a
6	chr9:86433081-86433131	HepG2	liver:	n/a
7	chr9:86433081-86433131	HNPCEpiC	eye:	n/a
8	chr9:86433081-86433131	PFSK-1	brain:	n/a
9	chr9:86433081-86433131	GM12878	blood:	n/a
10	chr9:86433081-86433131	HCPEpiC	choroid plexus:	n/a
11	chr9:86433081-86433131	PrEC	prostate:	n/a
12	chr9:86433081-86433131	ovcar-3	ovarian:	n/a
13	chr9:86433081-86433131	HCT-116	colon:	n/a
14	chr9:86433081-86433131	U87	brain:	n/a
15	chr9:86433081-86433131	HEK293	kidney:	embryo
16	chr9:86433081-86433131	LNCaP	prostate:	n/a
17	chr9:86433081-86433131	HL-60	blood:	n/a
18	chr9:86433081-86433131	HRPEpiC	eye:	n/a
19	chr9:86433081-86433131	AG10803	skin:	n/a
20	chr9:86433081-86433131	IMR90	lung:	fetal
21	chr9:86433081-86433131	GM19239	blood:	n/a
22	chr9:86433081-86433131	PANC-1	pancreas:	n/a
23	chr9:86433081-86433131	AG09319	gingival:	n/a
24	chr9:86433081-86433131	BJ	skin:	n/a
25	chr9:86433081-86433131	A549	lung:	n/a
26	chr9:86433081-86433131	HCF	heart:	n/a
27	chr9:86433081-86433131	HAEpiC	amniotic membrane:	n/a
28	chr9:86433081-86433131	Caco-2	colon:	n/a
29	chr9:86433081-86433131	GM12892	blood:	n/a
30	chr9:86433081-86433131	NT2-D1	testis:	n/a
31	chr9:86433081-86433131	SAEC	small airway:	n/a
32	chr9:86433081-86433131	BE2_C	brain:	n/a
33	chr9:86433081-86433131	H1-hESC	embryonic stem cell:	embryo
34	chr9:86433081-86433131	SK-N-MC	brain:	n/a
35	chr9:86433081-86433131	Hepatocyte	liver:	n/a
36	chr9:86433081-86433131	HIPEpiC	eye:	n/a
37	chr9:86433081-86433131	Hela-S3	cervix:	n/a
38	chr9:86433081-86433131	HRE	kidney:	n/a
39	chr9:86433081-86433131	K562	blood:	n/a
40	chr9:86433081-86433131	AG04449	skin:	fetal
41	chr9:86433081-86433131	NHDF-neo	bronchial:	n/a
42	chr9:86433081-86433131	HMEC	breast:	n/a
43	chr9:86433081-86433131	HEEpiC	esophagus:	n/a
44	chr9:86433081-86433131	CMK	blood:	n/a
45	chr9:86433081-86433131	GM12891	blood:	n/a
46	chr9:86433081-86433131	GM06990	blood:	n/a
47	chr9:86433081-86433131	SK-N-SH_RA	brain:	n/a
48	chr9:86433081-86433131	AG04450	lung:	fetal
49	chr9:86433081-86433131	Jurkat	blood:	n/a
50	chr9:86433081-86433131	ECC-1	luminal epithelium:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86321555..86324208-chr9:86431445..86433817,2	MCF-7	breast:
2	chr9:86321469..86324662-chr9:86431245..86433854,3	MCF-7	breast:

Variant related genes	Relation type
GKAP1	TF binding region
GKAP1	CpG island
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2761538	chr9:86401015-86451943	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv982312	chr9:86424154-86490046	Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3331113	chr9:86431782-86433830	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86431000-86433200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:86431000-86433200	Active TSS	Aorta	Aorta
3	chr9:86431000-86433200	Active TSS	GM12878-XiMat	blood
4	chr9:86431000-86433200	Active TSS	Hela-S3	cervix
5	chr9:86431200-86433200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:86431200-86433400	Active TSS	Thymus	Thymus
7	chr9:86431400-86433200	Active TSS	Fetal Muscle Leg	muscle
8	chr9:86431400-86433200	Active TSS	HepG2	liver
9	chr9:86431400-86433400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:86431400-86433400	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr9:86431400-86433400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr9:86431600-86433200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:86431600-86433200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:86431600-86433200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:86431600-86433200	Active TSS	Brain Anterior Caudate	brain
16	chr9:86431600-86433200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr9:86431600-86433200	Active TSS	Fetal Intestine Large	intestine
18	chr9:86431600-86433200	Active TSS	Fetal Stomach	stomach
19	chr9:86431600-86433200	Active TSS	Ovary	ovary
20	chr9:86431600-86433200	Active TSS	Psoas Muscle	Psoas
21	chr9:86431600-86433200	Active TSS	Rectal Smooth Muscle	rectum
22	chr9:86431600-86433200	Active TSS	Right Atrium	heart
23	chr9:86431600-86433200	Active TSS	Right Ventricle	heart
24	chr9:86431600-86433200	Active TSS	K562	blood
25	chr9:86431600-86433400	Active TSS	H1 Cell Line	embryonic stem cell
26	chr9:86431600-86433400	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr9:86431600-86433400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr9:86431600-86433400	Active TSS	Colonic Mucosa	Colon
29	chr9:86431600-86433400	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr9:86431600-86433400	Active TSS	HSMMtube	muscle
31	chr9:86431600-86433800	Active TSS	Stomach Smooth Muscle	stomach
32	chr9:86431800-86433200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:86431800-86433200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:86431800-86433200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:86431800-86433200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr9:86431800-86433200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr9:86431800-86433200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr9:86431800-86433200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:86431800-86433200	Active TSS	Primary monocytes fromperipheralblood	blood
40	chr9:86431800-86433200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:86431800-86433200	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr9:86431800-86433200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr9:86431800-86433200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr9:86431800-86433200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:86431800-86433200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:86431800-86433200	Active TSS	Brain Angular Gyrus	brain
47	chr9:86431800-86433200	Active TSS	Brain Cingulate Gyrus	brain
48	chr9:86431800-86433200	Active TSS	Brain Germinal Matrix	brain
49	chr9:86431800-86433200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:86431800-86433200	Active TSS	Brain Substantia Nigra	brain

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