Variant report

Variant	rs11140309
Chromosome Location	chr9:86571834-86571835
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:271)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:271 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr9:86571699-86572019	K562	blood:	n/a	n/a
2	POLR2A	chr9:86570895-86571974	GM12878	blood:	n/a	n/a
3	PML	chr9:86570857-86572016	GM12878	blood:	n/a	n/a
4	EGR1	chr9:86571817-86572071	K562	blood:	n/a	n/a
5	ZNF143	chr9:86571300-86571992	Hela-S3	cervix:	n/a	n/a
6	GABPA	chr9:86571398-86571861	K562	blood:	n/a	n/a
7	PML	chr9:86571407-86571880	K562	blood:	n/a	n/a
8	UBTF	chr9:86571081-86572094	K562	blood:	n/a	n/a
9	GABPA	chr9:86571541-86571860	GM12878	blood:	n/a	n/a
10	MYC	chr9:86570808-86572117	K562	blood:	n/a	n/a
11	ZKSCAN1	chr9:86571260-86572044	Hela-S3	cervix:	n/a	n/a
12	YY1	chr9:86571461-86572151	SK-N-SH_RA	brain:	n/a	chr9:86571789-86571798
13	POLR2A	chr9:86570841-86572067	GM12892	blood:	n/a	n/a
14	POLR2A	chr9:86571256-86572274	U87	brain:	n/a	n/a
15	EP300	chr9:86571198-86571894	HepG2	liver:	n/a	chr9:86571652-86571659
16	TAF1	chr9:86571275-86572064	K562	blood:	n/a	n/a
17	TAF1	chr9:86571372-86572054	HepG2	liver:	n/a	n/a
18	GABPA	chr9:86570998-86572207	MCF-7	breast:	n/a	n/a
19	MAX	chr9:86570867-86572232	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr9:86571351-86571910	SK-N-MC	brain:	n/a	n/a
21	MYC	chr9:86570990-86572004	K562	blood:	n/a	n/a
22	JUND	chr9:86571344-86571905	A549	lung:	n/a	n/a
23	MAX	chr9:86570818-86572270	HepG2	liver:	n/a	n/a
24	POLR2A	chr9:86570928-86571947	GM12891	blood:	n/a	n/a
25	POLR2A	chr9:86570908-86572161	K562	blood:	n/a	n/a
26	POLR2A	chr9:86570840-86572132	K562	blood:	n/a	n/a
27	POLR2A	chr9:86570432-86572584	K562	blood:	n/a	n/a
28	POLR2A	chr9:86571173-86572131	PANC-1	pancreas:	n/a	n/a
29	ZNF384	chr9:86571135-86572132	K562	blood:	n/a	n/a
30	YY1	chr9:86570973-86572107	HepG2	liver:	n/a	chr9:86571789-86571798
31	MAX	chr9:86571229-86572289	MCF-7	breast:	n/a	n/a
32	POLR2A	chr9:86571053-86572087	MCF-7	breast:	n/a	n/a
33	NFIC	chr9:86571182-86571969	HepG2	liver:	n/a	n/a
34	POLR2A	chr9:86571024-86571924	GM12878	blood:	n/a	n/a
35	POLR2A	chr9:86571169-86571955	HepG2	liver:	n/a	n/a
36	TAF1	chr9:86571022-86571885	HepG2	liver:	n/a	n/a
37	POLR2A	chr9:86570960-86572079	A549	lung:	n/a	n/a
38	MXI1	chr9:86571568-86572137	K562	blood:	n/a	chr9:86571820-86571829
39	SRF	chr9:86571380-86572077	ECC-1	luminal epithelium:	n/a	chr9:86571590-86571608 chr9:86571592-86571609
40	E2F6	chr9:86571304-86571992	H1-hESC	embryonic stem cell:	n/a	chr9:86571899-86571906 chr9:86571899-86571906 chr9:86571445-86571457 chr9:86571899-86571906
41	POLR2A	chr9:86571403-86572032	A549	lung:	n/a	n/a
42	ELK1	chr9:86571400-86572040	Hela-S3	cervix:	n/a	chr9:86571704-86571713 chr9:86571704-86571713
43	POLR2A	chr9:86571018-86571856	GM12891	blood:	n/a	n/a
44	MAZ	chr9:86571074-86571875	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr9:86570946-86572090	Hela-S3	cervix:	n/a	n/a
46	YY1	chr9:86571368-86572174	ECC-1	luminal epithelium:	n/a	chr9:86571789-86571798
47	ZBTB7A	chr9:86570929-86572124	ECC-1	luminal epithelium:	n/a	n/a
48	SP1	chr9:86571249-86572120	A549	lung:	n/a	chr9:86571884-86571898 chr9:86571878-86571892
49	POLR2A	chr9:86570912-86571917	GM12892	blood:	n/a	n/a
50	POLR2A	chr9:86571256-86572269	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:86571814-86571864	GM06990	blood:	n/a
2	chr9:86571814-86571864	HEEpiC	esophagus:	n/a
3	chr9:86571814-86571864	NT2-D1	testis:	n/a
4	chr9:86571814-86571864	HEK293	kidney:	embryo
5	chr9:86571814-86571864	GM12892	blood:	n/a
6	chr9:86571814-86571864	SK-N-SH_RA	brain:	n/a
7	chr9:86571814-86571864	AG04450	lung:	fetal
8	chr9:86571814-86571864	NHBE	bronchial:	n/a
9	chr9:86571814-86571864	NB4	blood:	n/a
10	chr9:86571814-86571864	Jurkat	blood:	n/a
11	chr9:86571814-86571864	HCF	heart:	n/a
12	chr9:86571814-86571864	AoSMC	blood vessel:	n/a
13	chr9:86571814-86571864	HL-60	blood:	n/a
14	chr9:86571814-86571864	PrEC	prostate:	n/a
15	chr9:86571814-86571864	HepG2	liver:	n/a
16	chr9:86571814-86571864	HIPEpiC	eye:	n/a
17	chr9:86571814-86571864	MCF-7	breast:	n/a
18	chr9:86571814-86571864	RPTEC	kidney:	n/a
19	chr9:86571814-86571864	ECC-1	luminal epithelium:	n/a
20	chr9:86571814-86571864	SK-N-SH	brain:	n/a
21	chr9:86571814-86571864	BJ	skin:	n/a
22	chr9:86571814-86571864	LNCaP	prostate:	n/a
23	chr9:86571814-86571864	SAEC	small airway:	n/a
24	chr9:86571814-86571864	GM12891	blood:	n/a
25	chr9:86571814-86571864	HCT-116	colon:	n/a
26	chr9:86571814-86571864	GM12878	blood:	n/a
27	chr9:86571814-86571864	AG10803	skin:	n/a
28	chr9:86571814-86571864	HAEpiC	amniotic membrane:	n/a
29	chr9:86571814-86571864	HNPCEpiC	eye:	n/a
30	chr9:86571814-86571864	ProgFib	skin:	n/a
31	chr9:86571814-86571864	HPAEpiC	pulmonary alveolar:	n/a
32	chr9:86571814-86571864	PANC-1	pancreas:	n/a
33	chr9:86571814-86571864	PFSK-1	brain:	n/a
34	chr9:86571814-86571864	HUVEC	blood vessel:	n/a
35	chr9:86571814-86571864	Hela-S3	cervix:	n/a
36	chr9:86571814-86571864	SK-N-MC	brain:	n/a
37	chr9:86571814-86571864	HRPEpiC	eye:	n/a
38	chr9:86571814-86571864	T-47D	breast:	n/a
39	chr9:86571814-86571864	NHDF-neo	bronchial:	n/a
40	chr9:86571814-86571864	H1-hESC	embryonic stem cell:	embryo
41	chr9:86571814-86571864	U87	brain:	n/a
42	chr9:86571814-86571864	HCPEpiC	choroid plexus:	n/a
43	chr9:86571814-86571864	Caco-2	colon:	n/a
44	chr9:86571814-86571864	K562	blood:	n/a
45	chr9:86571814-86571864	CMK	blood:	n/a
46	chr9:86571814-86571864	HCM	heart:	n/a
47	chr9:86571814-86571864	Hepatocyte	liver:	n/a
48	chr9:86571814-86571864	HRE	kidney:	n/a
49	chr9:86571814-86571864	HMEC	breast:	n/a
50	chr9:86571814-86571864	AG09309	skin:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:98922926..98923573-chr9:86571634..86572370,2	Hela-S3	cervix:
2	chr3:73159959..73160592-chr9:86571618..86572404,2	Hela-S3	cervix:
3	chr9:86534561..86538164-chr9:86570673..86573880,3	K562	blood:
4	chr9:86237033..86239481-chr9:86571525..86573399,2	MCF-7	breast:
5	chr9:86534003..86537844-chr9:86570557..86574103,8	K562	blood:
6	chr9:86534503..86538702-chr9:86568820..86574555,7	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf64	TF binding region
C9orf64	CpG island
ENSG00000148057	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000241685	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10868067	0.93[EUR][1000 genomes]
rs11140269	0.85[EUR][1000 genomes]
rs11140270	0.85[EUR][1000 genomes]
rs11140271	1.00[EUR][1000 genomes]
rs11140274	0.92[EUR][1000 genomes]
rs11140275	0.92[EUR][1000 genomes]
rs11140280	1.00[EUR][1000 genomes]
rs11140288	1.00[EUR][1000 genomes]
rs11140290	0.86[EUR][1000 genomes]
rs11140292	1.00[EUR][1000 genomes]
rs11140294	1.00[EUR][1000 genomes]
rs11140296	1.00[EUR][1000 genomes]
rs11140308	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140310	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140312	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140313	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140314	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140316	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140318	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140321	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140322	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140337	1.00[EUR][1000 genomes]
rs11140338	1.00[EUR][1000 genomes]
rs11531847	1.00[EUR][1000 genomes]
rs11533022	1.00[EUR][1000 genomes]
rs11533047	0.93[EUR][1000 genomes]
rs11535577	1.00[EUR][1000 genomes]
rs11559387	0.85[EUR][1000 genomes]
rs12056961	1.00[EUR][1000 genomes]
rs12235653	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237056	1.00[EUR][1000 genomes]
rs12237297	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017558	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750407	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59409125	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60989495	0.86[EUR][1000 genomes]
rs73471357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9776332	0.93[EUR][1000 genomes]

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	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
2	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
3	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
4	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
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86570200-86572000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:86570400-86572000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:86570400-86572000	Active TSS	HepG2	liver
4	chr9:86570400-86572200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:86570400-86572200	Active TSS	Fetal Intestine Small	intestine
6	chr9:86570400-86572200	Active TSS	Psoas Muscle	Psoas
7	chr9:86570400-86572400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:86570400-86572400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr9:86570400-86572400	Active TSS	Right Ventricle	heart
10	chr9:86570400-86572400	Flanking Active TSS	NHEK	skin
11	chr9:86570400-86572600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr9:86570400-86572600	Active TSS	HSMMtube	muscle
13	chr9:86570600-86572000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr9:86570600-86572000	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr9:86570600-86572000	Active TSS	Thymus	Thymus
16	chr9:86570600-86572200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr9:86570600-86572200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:86570600-86572200	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr9:86570600-86572200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:86570600-86572200	Active TSS	HSMM	muscle
21	chr9:86570600-86572200	Active TSS	K562	blood
22	chr9:86570600-86572600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:86570800-86572000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:86570800-86572000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:86570800-86572000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:86570800-86572000	Active TSS	Fetal Lung	lung
27	chr9:86570800-86572000	Active TSS	Stomach Smooth Muscle	stomach
28	chr9:86570800-86572200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:86570800-86572200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:86570800-86572200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:86570800-86572200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:86570800-86572400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr9:86570800-86572400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:86570800-86572400	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr9:86570800-86572400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:86570800-86572400	Active TSS	GM12878-XiMat	blood
37	chr9:86570800-86572600	Active TSS	Colonic Mucosa	Colon
38	chr9:86571000-86572000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:86571000-86572000	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr9:86571000-86572000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:86571000-86572000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:86571000-86572000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr9:86571000-86572000	Active TSS	Brain Hippocampus Middle	brain
44	chr9:86571000-86572000	Active TSS	Duodenum Mucosa	Duodenum
45	chr9:86571000-86572000	Active TSS	A549	lung
46	chr9:86571000-86572000	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr9:86571000-86572200	Active TSS	H1 Cell Line	embryonic stem cell
48	chr9:86571000-86572200	Active TSS	H9 Cell Line	embryonic stem cell
49	chr9:86571000-86572200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:86571000-86572200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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