Variant report

Variant	rs2071520
Chromosome Location	chr9:117880792-117880793
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	STAT3	chr9:117880360-117880897	MCF10A-Er-Src	breast:	n/a	chr9:117880887-117880896 chr9:117880886-117880895
2	KAP1	chr9:117880315-117881746	HEK293	kidney:	n/a	chr9:117880934-117880942 chr9:117881309-117881318
3	TCF12	chr9:117880135-117881731	SK-N-SH	brain:	n/a	n/a
4	EGR1	chr9:117880194-117880840	ECC-1	luminal epithelium:	n/a	chr9:117880378-117880391 chr9:117880377-117880392 chr9:117880377-117880387 chr9:117880378-117880391 chr9:117880378-117880391 chr9:117880379-117880390 chr9:117880378-117880391 chr9:117880659-117880672 chr9:117880381-117880390 chr9:117880378-117880392
5	TCF12	chr9:117880033-117881711	SK-N-SH	brain:	n/a	n/a
6	EP300	chr9:117880149-117881594	ECC-1	luminal epithelium:	n/a	chr9:117880583-117880596 chr9:117881307-117881316
7	HDAC2	chr9:117880674-117881444	H1-hESC	embryonic stem cell:	n/a	chr9:117881215-117881229
8	POLR2A	chr9:117858058-117881674	U87	brain:	n/a	n/a
9	BACH1	chr9:117880260-117881471	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr9:117879558-117882145	SK-N-SH	brain:	n/a	n/a
11	SIN3A	chr9:117880344-117881393	H1-hESC	embryonic stem cell:	n/a	chr9:117881037-117881050
12	POLR2A	chr9:117879382-117881533	MCF10A-Er-Src	breast:	n/a	n/a
13	RAD21	chr9:117880205-117881517	SK-N-SH_RA	brain:	n/a	n/a
14	RAD21	chr9:117880187-117881557	ECC-1	luminal epithelium:	n/a	n/a
15	TCF12	chr9:117880442-117881541	A549	lung:	n/a	n/a
16	POLR2A	chr9:117877891-117881556	U87	brain:	n/a	n/a
17	YY1	chr9:117880296-117880932	SK-N-SH_RA	brain:	n/a	chr9:117880380-117880389
18	TEAD4	chr9:117880090-117881615	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr9:117880750-117880808	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr9:117877249-117881760	IMR90	lung:	n/a	n/a
21	CTBP2	chr9:117880363-117881420	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOSL2	chr9:117880155-117881664	SK-N-SH	brain:	n/a	chr9:117881308-117881316 chr9:117881307-117881317 chr9:117881309-117881316 chr9:117881306-117881318 chr9:117881308-117881316 chr9:117881307-117881317 chr9:117881307-117881317 chr9:117881307-117881317
23	TAF1	chr9:117880134-117881551	ECC-1	luminal epithelium:	n/a	n/a
24	TEAD4	chr9:117880479-117881249	H1-hESC	embryonic stem cell:	n/a	n/a
25	FOXM1	chr9:117880325-117881684	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr9:117880715-117881109	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr9:117877221-117881586	U87	brain:	n/a	n/a
28	ATF2	chr9:117880730-117881305	H1-hESC	embryonic stem cell:	n/a	n/a
29	REST	chr9:117880204-117880924	SK-N-SH	brain:	n/a	chr9:117880428-117880441
30	YY1	chr9:117880173-117881583	SK-N-SH	brain:	n/a	chr9:117880380-117880389
31	TAF1	chr9:117880180-117881517	SK-N-SH	brain:	n/a	n/a
32	TAF1	chr9:117880626-117881099	H1-hESC	embryonic stem cell:	n/a	n/a
33	ESR1	chr9:117880745-117881552	ECC-1	luminal epithelium:	n/a	n/a
34	EP300	chr9:117880738-117881264	H1-hESC	embryonic stem cell:	n/a	n/a
35	CHD2	chr9:117880781-117881392	H1-hESC	embryonic stem cell:	n/a	chr9:117881267-117881274
36	SP4	chr9:117880754-117881263	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr9:117880118-117881528	SK-N-SH	brain:	n/a	chr9:117880327-117880334 chr9:117880326-117880335 chr9:117880378-117880388 chr9:117880324-117880339
38	NFIC	chr9:117880078-117881569	ECC-1	luminal epithelium:	n/a	n/a
39	MYC	chr9:117880511-117880978	H1-hESC	embryonic stem cell:	n/a	n/a
40	NFIC	chr9:117880215-117881572	SK-N-SH	brain:	n/a	n/a
41	CEBPB	chr9:117880185-117881528	ECC-1	luminal epithelium:	n/a	n/a
42	JUND	chr9:117880784-117881119	H1-hESC	embryonic stem cell:	n/a	n/a
43	YY1	chr9:117880614-117881392	H1-hESC	embryonic stem cell:	n/a	n/a
44	TCF12	chr9:117880687-117881166	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr9:117880639-117881211	H1-hESC	embryonic stem cell:	n/a	n/a
46	MXI1	chr9:117879960-117881786	IMR90	lung:	n/a	n/a
47	RAD21	chr9:117880165-117881502	IMR90	lung:	n/a	n/a
48	GATA2	chr9:117880253-117881132	SH-SY5Y	brain:	n/a	chr9:117880890-117880907
49	GATA3	chr9:117880655-117881683	A549	lung:	n/a	chr9:117880890-117880907
50	NFIC	chr9:117880091-117881669	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10125663	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817713	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10982553	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1335332	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1414137	0.80[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1537015	0.88[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1537016	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1537720	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4979496	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7853883	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs884290	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs945256	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs945257	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117877200-117881400	Active TSS	Fetal Kidney	kidney
2	chr9:117877600-117881600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
3	chr9:117878000-117881600	Active TSS	Colon Smooth Muscle	Colon
4	chr9:117878200-117880800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:117878200-117881000	Active TSS	NHLF	lung
6	chr9:117878200-117881400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:117878200-117881600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr9:117878200-117881600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr9:117878400-117881000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:117878600-117881400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:117878600-117881400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:117878800-117880800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr9:117879000-117881400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr9:117879000-117881400	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr9:117879200-117880800	Active TSS	NHDF-Ad	bronchial
16	chr9:117879200-117881000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
17	chr9:117879200-117881000	Active TSS	Esophagus	oesophagus
18	chr9:117879400-117880800	Active TSS	NH-A	brain
19	chr9:117879600-117881200	Flanking Active TSS	Fetal Lung	lung
20	chr9:117879800-117880800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:117879800-117880800	Active TSS	Osteobl	bone
22	chr9:117879800-117881200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr9:117879800-117881200	Active TSS	Brain Substantia Nigra	brain
24	chr9:117879800-117881400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr9:117879800-117881800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr9:117879800-117881800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr9:117880000-117880800	Bivalent/Poised TSS	Fetal Brain Female	brain
28	chr9:117880000-117881000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:117880000-117881000	Bivalent Enhancer	Fetal Heart	heart
30	chr9:117880000-117881200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr9:117880000-117881400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr9:117880200-117880800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:117880200-117880800	Flanking Active TSS	Lung	lung
34	chr9:117880200-117880800	Enhancers	Ovary	ovary
35	chr9:117880200-117881000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
36	chr9:117880200-117881000	Enhancers	Psoas Muscle	Psoas
37	chr9:117880200-117881000	Flanking Active TSS	Right Ventricle	heart
38	chr9:117880200-117881000	Bivalent/Poised TSS	A549	lung
39	chr9:117880200-117881200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:117880200-117881200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr9:117880200-117881200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:117880200-117881200	Active TSS	Aorta	Aorta
43	chr9:117880200-117881200	Bivalent Enhancer	Fetal Brain Male	brain
44	chr9:117880200-117881200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
45	chr9:117880200-117881200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr9:117880200-117881200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr9:117880200-117881200	Enhancers	Pancreas	Pancrea
48	chr9:117880200-117881200	Flanking Active TSS	Hela-S3	cervix
49	chr9:117880200-117881200	Flanking Active TSS	HMEC	breast
50	chr9:117880200-117881200	Flanking Active TSS	HSMM	muscle

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