Variant report

Variant	rs6980307
Chromosome Location	chr7:69289357-69289358
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	TBL1XR1	chr7:69289335-69290433	GM12878	blood:	n/a	n/a
2	ATF2	chr7:69289244-69289926	GM12878	blood:	n/a	n/a
3	FOXM1	chr7:69289226-69289871	GM12878	blood:	n/a	n/a
4	RAD21	chr7:69289238-69290641	GM12878	blood:	n/a	n/a
5	EBF1	chr7:69289321-69289920	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:69289156-69289362	GM12891	blood:	n/a	n/a
7	BHLHE40	chr7:69289274-69289855	GM12878	blood:	n/a	n/a
8	NFIC	chr7:69289241-69290044	GM12878	blood:	n/a	chr7:69289834-69289851
9	RAD21	chr7:69289304-69291202	SK-N-SH	brain:	n/a	n/a
10	EP300	chr7:69286758-69291642	SK-N-SH	brain:	n/a	chr7:69291036-69291050 chr7:69290891-69290900 chr7:69287730-69287740 chr7:69288757-69288771 chr7:69290887-69290901
11	CHD2	chr7:69289157-69289885	GM12878	blood:	n/a	n/a
12	ATF2	chr7:69289249-69290030	GM12878	blood:	n/a	n/a
13	ZNF384	chr7:69289208-69289955	GM12878	blood:	n/a	n/a
14	NFATC1	chr7:69289295-69289951	GM12878	blood:	n/a	n/a
15	RCOR1	chr7:69289323-69290507	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:69288915-69290889	GM12878	blood:	n/a	n/a
17	SPI1	chr7:69289093-69289924	GM12878	blood:	n/a	n/a
18	PBX3	chr7:69289302-69289539	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:69288999-69289934	GM12878	blood:	n/a	n/a
20	TCF12	chr7:69289329-69289679	GM12878	blood:	n/a	chr7:69289503-69289510
21	TBP	chr7:69289235-69290674	GM12878	blood:	n/a	n/a
22	EP300	chr7:69289060-69289841	GM12878	blood:	n/a	n/a
23	RUNX3	chr7:69289252-69290053	GM12878	blood:	n/a	chr7:69289763-69289778
24	BCL11A	chr7:69289248-69289935	GM12878	blood:	n/a	n/a
25	SPI1	chr7:69289332-69289766	GM12878	blood:	n/a	n/a
26	STAT3	chr7:69289355-69289913	GM12878	blood:	n/a	chr7:69289501-69289512 chr7:69289443-69289457
27	POU2F2	chr7:69289241-69289953	GM12878	blood:	n/a	n/a
28	MXI1	chr7:69288979-69290699	GM12878	blood:	n/a	n/a
29	EP300	chr7:69289307-69289724	GM12878	blood:	n/a	n/a
30	EP300	chr7:69289168-69289868	GM12878	blood:	n/a	n/a
31	NFIC	chr7:69289237-69290407	GM12878	blood:	n/a	chr7:69289834-69289851
32	NFATC1	chr7:69289252-69289905	GM12878	blood:	n/a	n/a
33	IRF4	chr7:69289250-69289858	GM12878	blood:	n/a	chr7:69289499-69289513 chr7:69289501-69289515
34	ZBTB33	chr7:69289152-69289507	GM12878	blood:	n/a	n/a
35	MTA3	chr7:69289241-69290730	GM12878	blood:	n/a	n/a
36	EBF1	chr7:69289298-69290682	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:69288060-69289911	Raji	blood:	n/a	n/a
38	IRF4	chr7:69289240-69289829	GM12878	blood:	n/a	chr7:69289499-69289513 chr7:69289501-69289515
39	FOXM1	chr7:69289202-69289860	GM12878	blood:	n/a	n/a
40	RUNX3	chr7:69289244-69289944	GM12878	blood:	n/a	chr7:69289763-69289778
41	BCL11A	chr7:69289298-69289850	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
AUTS2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1008379	0.80[EUR][1000 genomes]
rs1014417	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10245786	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10259748	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11508453	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11763186	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11974201	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12333974	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12698813	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12698816	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12698825	0.81[AMR][1000 genomes]
rs13226538	0.81[AMR][1000 genomes]
rs17140933	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17140980	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17140982	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17353815	0.81[EUR][1000 genomes]
rs2865805	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34221396	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55990156	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60359704	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60739014	0.81[EUR][1000 genomes]
rs6460532	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6943309	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6955261	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6958981	0.81[AMR][1000 genomes]
rs6961164	0.82[AMR][1000 genomes]
rs6963882	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6966036	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6978134	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6979355	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs726372	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs763759	0.81[EUR][1000 genomes]
rs7779010	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7781403	0.82[EUR][1000 genomes]
rs7786073	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7796973	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7801117	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7808773	0.81[EUR][1000 genomes]
rs7809145	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7809934	0.81[AMR][1000 genomes]
rs877687	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9332399	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][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	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69279800-69289600	Weak transcription	Psoas Muscle	Psoas
2	chr7:69282800-69289400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:69282800-69289600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:69283200-69289600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:69283200-69289600	Weak transcription	HSMM	muscle
6	chr7:69283400-69289400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:69283400-69291800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:69283400-69292600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:69284400-69289600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:69284400-69289600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:69284400-69290400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:69284600-69289600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:69284600-69289600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:69284600-69289800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:69284600-69289800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:69284600-69290400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:69284600-69297400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr7:69284800-69289400	Weak transcription	HSMMtube	muscle
19	chr7:69284800-69289600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:69284800-69289600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:69284800-69291400	Weak transcription	Left Ventricle	heart
22	chr7:69285000-69295800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:69286000-69290400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:69287800-69289400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:69287800-69289400	Enhancers	Primary B cells from cord blood	blood
26	chr7:69287800-69289600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:69287800-69289600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:69287800-69289600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr7:69288000-69289400	Weak transcription	Adipose Nuclei	Adipose
30	chr7:69288000-69289600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:69288200-69289600	Weak transcription	Brain Substantia Nigra	brain
32	chr7:69288200-69290400	Weak transcription	Fetal Heart	heart
33	chr7:69288200-69304800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:69288400-69289600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:69288400-69289600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:69288400-69289600	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:69288400-69289600	Weak transcription	Fetal Stomach	stomach
38	chr7:69288400-69289800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:69288600-69289600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:69288600-69289600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:69288600-69289600	Weak transcription	Brain Angular Gyrus	brain
42	chr7:69288600-69289600	Weak transcription	Brain Anterior Caudate	brain
43	chr7:69288600-69289600	Weak transcription	Brain Germinal Matrix	brain
44	chr7:69288600-69289600	Weak transcription	Colon Smooth Muscle	Colon
45	chr7:69288600-69289600	Weak transcription	Fetal Brain Female	brain
46	chr7:69288600-69289600	Weak transcription	Right Atrium	heart
47	chr7:69288600-69291600	Enhancers	Fetal Brain Male	brain
48	chr7:69288600-69292000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr7:69288600-69304800	Weak transcription	Ovary	ovary
50	chr7:69288800-69289400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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