Variant report

Variant	rs10125667
Chromosome Location	chr9:79030827-79030828
allele	A/G
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	FOS	chr9:79030697-79030989	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr9:79030793-79030875	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr9:79030705-79030870	MCF10A-Er-Src	breast:	n/a	chr9:79030735-79030742
4	FOS	chr9:79029506-79030918	HUVEC	blood vessel:	n/a	chr9:79030251-79030262 chr9:79030647-79030659
5	USF1	chr9:79030740-79030932	SK-N-SH_RA	brain:	n/a	n/a
6	JUN	chr9:79030093-79030981	HUVEC	blood vessel:	n/a	chr9:79030647-79030659
7	EP300	chr9:79030678-79030957	SK-N-SH_RA	brain:	n/a	chr9:79030736-79030745
8	STAT3	chr9:79030733-79030864	MCF10A-Er-Src	breast:	n/a	chr9:79030735-79030742
9	SPI1	chr9:79030553-79030874	HL-60	blood:	n/a	chr9:79030736-79030745 chr9:79030735-79030748
10	USF1	chr9:79030715-79030930	SK-N-SH_RA	brain:	n/a	n/a
11	STAT3	chr9:79030665-79030994	MCF10A-Er-Src	breast:	n/a	chr9:79030674-79030682 chr9:79030735-79030742
12	STAT3	chr9:79030662-79031002	MCF10A-Er-Src	breast:	n/a	chr9:79030674-79030682 chr9:79030735-79030742
13	EP300	chr9:79030668-79030980	SK-N-SH_RA	brain:	n/a	chr9:79030736-79030745
14	FOS	chr9:79029609-79030990	MCF10A-Er-Src	breast:	n/a	chr9:79030251-79030262 chr9:79030647-79030659

Variant related genes	Relation type
GCNT1	TF binding region
ENSG00000233814	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10116800	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118954	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119732	0.95[ASN][1000 genomes]
rs10125012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781358	1.00[ASN][1000 genomes]
rs10781359	0.95[ASN][1000 genomes]
rs10781360	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869770	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869774	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144870	1.00[ASN][1000 genomes]
rs11144875	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144878	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144881	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144887	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144894	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144897	0.95[ASN][1000 genomes]
rs1129399	1.00[ASN][1000 genomes]
rs11548954	0.89[ASN][1000 genomes]
rs11791951	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793613	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794019	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12156473	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375735	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12377856	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377878	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380332	0.84[ASN][1000 genomes]
rs12380522	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1324213	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951910	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251604	0.84[AFR][1000 genomes]
rs2377640	0.89[AMR][1000 genomes]
rs2377641	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3187236	0.90[ASN][1000 genomes]
rs4571791	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55740812	0.94[ASN][1000 genomes]
rs57339182	0.84[ASN][1000 genomes]
rs57480680	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58136435	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59424752	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61334567	0.89[AMR][1000 genomes]
rs62564441	0.90[ASN][1000 genomes]
rs62564442	0.90[ASN][1000 genomes]
rs62564446	0.84[ASN][1000 genomes]
rs62565109	0.83[ASN][1000 genomes]
rs62567918	0.94[ASN][1000 genomes]
rs62567919	0.89[ASN][1000 genomes]
rs62568690	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62568692	1.00[ASN][1000 genomes]
rs6560513	0.89[AMR][1000 genomes]
rs6560515	0.89[AMR][1000 genomes]
rs6560516	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023191	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025942	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7026067	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029439	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035385	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037345	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7038009	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7038056	0.90[ASN][1000 genomes]
rs7040138	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041690	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047489	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7049245	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851616	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7852884	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7853410	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7854540	0.84[ASN][1000 genomes]
rs7859327	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875575	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv3451027	chr9:79021447-79056132	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79029000-79031600	Enhancers	HUVEC	blood vessel
2	chr9:79029200-79031200	Enhancers	NH-A	brain
3	chr9:79029200-79031400	Enhancers	Hela-S3	cervix
4	chr9:79029600-79031200	Enhancers	Osteobl	bone
5	chr9:79029600-79031400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:79029600-79031600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:79029600-79032800	Enhancers	Stomach Mucosa	stomach
8	chr9:79029800-79031000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:79029800-79031600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr9:79029800-79031600	Enhancers	Pancreas	Pancrea
11	chr9:79029800-79032600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:79030000-79031200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:79030000-79032200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:79030000-79032600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:79030200-79031200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:79030200-79031200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:79030200-79031400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:79030200-79031600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:79030200-79032000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:79030400-79031000	Enhancers	Duodenum Mucosa	Duodenum
21	chr9:79030400-79031600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:79030400-79032600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:79030400-79038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:79030600-79031000	Enhancers	Primary T cells from cord blood	blood
25	chr9:79030600-79031000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:79030600-79031200	Enhancers	Primary T cells fromperipheralblood	blood
27	chr9:79030600-79031600	Enhancers	Brain Germinal Matrix	brain
28	chr9:79030800-79031000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:79030800-79031200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr9:79030800-79031400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:79030800-79031600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:79030800-79031600	Enhancers	Lung	lung
33	chr9:79030800-79032200	Weak transcription	HepG2	liver

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