Variant report

Variant	rs12001014
Chromosome Location	chr9:8857245-8857246
allele	C/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	POLR2A	chr9:8857081-8859029	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr9:8857100-8857250	HAc	cerebellar:	n/a	n/a
3	CTBP2	chr9:8857170-8859227	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr9:8857180-8857330	HRE	kidney:	n/a	n/a
5	POLR2A	chr9:8857117-8858336	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr9:8856859-8857286	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr9:8857100-8857250	HRE	kidney:	n/a	n/a
8	JUND	chr9:8857092-8857369	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr9:8856850-8859316	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr9:8856879-8859283	H1-neurons	neurons:	n/a	n/a
11	CHD1	chr9:8857000-8858119	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr9:8857100-8857250	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr9:8857080-8857370	HRPEpiC	eye:	n/a	n/a
14	CTCF	chr9:8857100-8857250	HPAF	blood vessel:	n/a	n/a
15	CTCF	chr9:8857240-8857390	RPTEC	kidney:	n/a	n/a
16	GTF2F1	chr9:8857147-8857348	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr9:8857180-8857330	AoAF	blood vessel:	n/a	n/a
18	ZNF263	chr9:8856641-8860520	HEK293-T-REx	kidney:	n/a	chr9:8858101-8858122 chr9:8859812-8859821 chr9:8858020-8858029
19	TAF1	chr9:8857226-8859050	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr9:8857140-8857290	NHDF-neo	bronchial:	n/a	n/a
21	CTCF	chr9:8857220-8857370	HCPEpiC	choroid plexus:	n/a	n/a
22	TBP	chr9:8857074-8858817	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr9:8857180-8857330	BJ	skin:	n/a	n/a
24	REST	chr9:8854700-8859485	H1-neurons	neurons:	n/a	chr9:8858684-8858697 chr9:8858684-8858697 chr9:8858577-8858585 chr9:8858768-8858781 chr9:8854758-8854765 chr9:8858410-8858423
25	CTCF	chr9:8857180-8857330	HBMEC	blood vessel:	n/a	n/a
26	SIN3A	chr9:8856948-8858925	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr9:8856839-8857596	H1-neurons	neurons:	n/a	n/a
28	CTCF	chr9:8857100-8857250	HMF	breast:	n/a	n/a
29	YY1	chr9:8857062-8857583	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000225706	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12002381	1.00[ASN][1000 genomes]
rs2117099	1.00[ASN][1000 genomes]
rs55764273	1.00[ASN][1000 genomes]
rs56027406	1.00[ASN][1000 genomes]
rs57986047	1.00[ASN][1000 genomes]
rs58013521	1.00[ASN][1000 genomes]
rs58658598	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58887696	1.00[ASN][1000 genomes]
rs60125771	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018889	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73640958	1.00[ASN][1000 genomes]
rs7857477	1.00[ASN][1000 genomes]
rs7866882	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr9:8853200-8859000	Active TSS	Fetal Brain Female	brain
2	chr9:8853600-8858400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:8853600-8859200	Active TSS	Brain Cingulate Gyrus	brain
4	chr9:8853800-8859600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr9:8854200-8859200	Active TSS	Brain Substantia Nigra	brain
6	chr9:8854600-8859200	Active TSS	Brain Angular Gyrus	brain
7	chr9:8854600-8859400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:8854800-8858400	Active TSS	Fetal Brain Male	brain
9	chr9:8854800-8859000	Active TSS	Brain Anterior Caudate	brain
10	chr9:8855000-8858800	Bivalent/Poised TSS	Fetal Lung	lung
11	chr9:8855000-8859000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:8855200-8859000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:8855600-8859000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:8855600-8859000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr9:8855800-8858400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:8855800-8858800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:8855800-8858800	Active TSS	Right Atrium	heart
18	chr9:8855800-8859000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:8855800-8859000	Active TSS	Ovary	ovary
20	chr9:8856000-8858200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:8856000-8859000	Active TSS	Aorta	Aorta
22	chr9:8856200-8857600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:8856200-8858400	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr9:8856200-8858800	Active TSS	H1 Cell Line	embryonic stem cell
25	chr9:8856400-8857400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr9:8856400-8858200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr9:8856400-8858600	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr9:8856400-8858800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:8856400-8858800	Active TSS	Right Ventricle	heart
30	chr9:8856400-8859000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr9:8856400-8859200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
32	chr9:8856400-8859200	Active TSS	Fetal Kidney	kidney
33	chr9:8856600-8857400	Flanking Active TSS	Liver	Liver
34	chr9:8856600-8857400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
35	chr9:8856600-8857600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:8856600-8858200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:8856600-8858400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
38	chr9:8856600-8858600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
39	chr9:8856600-8858600	Active TSS	Lung	lung
40	chr9:8856600-8858800	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr9:8856600-8859000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr9:8856600-8859000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:8856600-8859000	Active TSS	Left Ventricle	heart
44	chr9:8856600-8859200	Active TSS	H9 Cell Line	embryonic stem cell
45	chr9:8856800-8857400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
46	chr9:8856800-8857400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
47	chr9:8856800-8857400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr9:8856800-8857400	Bivalent/Poised TSS	NHLF	lung
49	chr9:8856800-8857600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
50	chr9:8856800-8857600	Active TSS	Fetal Heart	heart

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