Variant report

Variant	rs12339346
Chromosome Location	chr9:3181013-3181014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr9:3180967-3182072	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr9:3180949-3181432	ECC-1	luminal epithelium:	n/a	n/a
3	E2F6	chr9:3180957-3181919	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr9:3180932-3182063	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr9:3180982-3182013	ECC-1	luminal epithelium:	n/a	n/a
6	ZNF263	chr9:3180978-3181925	HEK293-T-REx	kidney:	n/a	chr9:3181288-3181297
7	MAX	chr9:3180904-3182020	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr9:3180996-3182245	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:3181007-3181057	BE2_C	brain:	n/a
2	chr9:3181007-3181057	PANC-1	pancreas:	n/a
3	chr9:3181007-3181057	A549	lung:	n/a
4	chr9:3181007-3181057	BJ	skin:	n/a
5	chr9:3181007-3181057	Hepatocyte	liver:	n/a
6	chr9:3181007-3181057	AG09319	gingival:	n/a
7	chr9:3181007-3181057	GM12891	blood:	n/a
8	chr9:3181007-3181057	LNCaP	prostate:	n/a
9	chr9:3181007-3181057	ECC-1	luminal epithelium:	n/a
10	chr9:3181007-3181057	CMK	blood:	n/a
11	chr9:3181007-3181057	HCPEpiC	choroid plexus:	n/a
12	chr9:3181007-3181057	GM12878	blood:	n/a
13	chr9:3181007-3181057	AG04450	lung:	fetal
14	chr9:3181007-3181057	IMR90	lung:	fetal
15	chr9:3181007-3181057	AG04449	skin:	fetal
16	chr9:3181007-3181057	NHBE	bronchial:	n/a
17	chr9:3181007-3181057	U87	brain:	n/a
18	chr9:3181007-3181057	HNPCEpiC	eye:	n/a
19	chr9:3181007-3181057	PrEC	prostate:	n/a
20	chr9:3181007-3181057	HEEpiC	esophagus:	n/a
21	chr9:3181007-3181057	HCT-116	colon:	n/a
22	chr9:3181007-3181057	MCF-7	breast:	n/a
23	chr9:3181007-3181057	NHDF-neo	bronchial:	n/a
24	chr9:3181007-3181057	T-47D	breast:	n/a
25	chr9:3181007-3181057	HUVEC	blood vessel:	n/a
26	chr9:3181007-3181057	HL-60	blood:	n/a
27	chr9:3181007-3181057	PFSK-1	brain:	n/a
28	chr9:3181007-3181057	GM19239	blood:	n/a
29	chr9:3181007-3181057	NT2-D1	testis:	n/a
30	chr9:3181007-3181057	Caco-2	colon:	n/a
31	chr9:3181007-3181057	MCF10A-Er-Src	breast:	n/a
32	chr9:3181007-3181057	K562	blood:	n/a
33	chr9:3181007-3181057	AG09309	skin:	n/a
34	chr9:3181007-3181057	HPAEpiC	pulmonary alveolar:	n/a
35	chr9:3181007-3181057	HEK293	kidney:	embryo
36	chr9:3181007-3181057	GM06990	blood:	n/a
37	chr9:3181007-3181057	Jurkat	blood:	n/a
38	chr9:3181007-3181057	SK-N-MC	brain:	n/a
39	chr9:3181007-3181057	NH-A	brain:	n/a
40	chr9:3181007-3181057	RPTEC	kidney:	n/a
41	chr9:3181007-3181057	HRCEpiC	kidney:	n/a
42	chr9:3181007-3181057	GM12892	blood:	n/a
43	chr9:3181007-3181057	HMEC	breast:	n/a
44	chr9:3181007-3181057	SAEC	small airway:	n/a
45	chr9:3181007-3181057	HCM	heart:	n/a
46	chr9:3181007-3181057	SK-N-SH	brain:	n/a
47	chr9:3181007-3181057	HepG2	liver:	n/a
48	chr9:3181007-3181057	SKMC	muscle:	n/a
49	chr9:3181007-3181057	AoSMC	blood vessel:	n/a
50	chr9:3181007-3181057	Hela-S3	cervix:	n/a

No data

Variant related genes	Relation type
ENSG00000236511	TF binding region
ENSG00000236511	CpG island

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10511444	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340000	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7021876	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044133	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7860342	0.96[EUR][1000 genomes]
rs7874570	0.96[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	nsv892085	chr9:2937654-3215842	Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1017474	chr9:3019068-3247215	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892088	chr9:3019383-3215842	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1028668	chr9:3139007-3262791	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv539939	chr9:3139007-3262791	Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 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	chr9:3180600-3181400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:3180600-3181400	Active TSS	Brain Anterior Caudate	brain
3	chr9:3180600-3181800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
4	chr9:3180600-3182000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:3180600-3182200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:3180600-3182200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr9:3180600-3182200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:3180800-3181200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr9:3180800-3181200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr9:3180800-3181200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
11	chr9:3180800-3181200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
12	chr9:3180800-3181200	Bivalent Enhancer	Fetal Brain Male	brain
13	chr9:3180800-3181400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
14	chr9:3180800-3181400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:3180800-3181400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:3180800-3181600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:3180800-3181600	Active TSS	Colon Smooth Muscle	Colon
18	chr9:3180800-3181800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr9:3180800-3181800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
20	chr9:3180800-3181800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr9:3180800-3181800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
24	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr9:3180800-3181800	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr9:3180800-3181800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
30	chr9:3180800-3182000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:3180800-3182000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr9:3180800-3182000	Bivalent Enhancer	Fetal Heart	heart
33	chr9:3180800-3182200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr9:3181000-3181200	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:3181000-3181200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
36	chr9:3181000-3181200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr9:3181000-3181200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
38	chr9:3181000-3181200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
39	chr9:3181000-3181200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
40	chr9:3181000-3181200	Flanking Active TSS	Psoas Muscle	Psoas
41	chr9:3181000-3181200	Flanking Active TSS	Right Atrium	heart
42	chr9:3181000-3181200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
43	chr9:3181000-3181400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:3181000-3181400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:3181000-3181400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:3181000-3181400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
47	chr9:3181000-3181400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
48	chr9:3181000-3181400	Bivalent/Poised TSS	Fetal Kidney	kidney
49	chr9:3181000-3181400	Enhancers	Gastric	stomach
50	chr9:3181000-3181400	Bivalent/Poised TSS	NHLF	lung

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