Variant report

Variant	rs10961704
Chromosome Location	chr9:14782934-14782935
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	CEBPB	chr9:14782789-14783062	MCF-7	breast:	n/a	n/a
2	FOS	chr9:14782746-14783090	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr9:14782726-14783009	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr9:14782750-14782992	MCF10A-Er-Src	breast:	n/a	n/a
5	FOSL2	chr9:14782715-14783076	HepG2	liver:	n/a	n/a
6	FOS	chr9:14782705-14783068	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr9:14782705-14782969	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr9:14782746-14783089	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr9:14782753-14783051	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:14782176-14783833	HepG2	liver:	n/a	n/a
11	MYC	chr9:14782800-14783004	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr9:14782325-14783308	HepG2	liver:	n/a	n/a
13	CEBPB	chr9:14782745-14783078	MCF-7	breast:	n/a	n/a
14	JUND	chr9:14782847-14782948	HepG2	liver:	n/a	n/a
15	CEBPB	chr9:14782802-14783000	Hela-S3	cervix:	n/a	n/a
16	FOS	chr9:14782748-14783075	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr9:14782806-14783054	HepG2	liver:	n/a	n/a
18	STAT3	chr9:14782835-14782990	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FREM1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10124839	0.87[GIH][hapmap]
rs10961700	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10961702	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10961703	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10961708	1.00[JPT][hapmap]
rs10961709	1.00[JPT][hapmap]
rs17292106	1.00[JPT][hapmap]
rs2291679	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4341240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4740587	0.89[CEU][hapmap]

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	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025566	chr9:14687088-14791199	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1023955	chr9:14754010-14800259	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2761502	chr9:14757877-14827373	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv831518	chr9:14760638-14953501	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10961704	FREM1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14745000-14809800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr9:14748800-14790000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:14755800-14812400	Weak transcription	Pancreas	Pancrea
4	chr9:14758400-14793400	Weak transcription	Aorta	Aorta
5	chr9:14764800-14809600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:14766600-14787400	Weak transcription	Fetal Intestine Large	intestine
7	chr9:14768600-14808800	Weak transcription	Fetal Intestine Small	intestine
8	chr9:14769000-14783000	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:14773400-14796400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:14776200-14794000	Weak transcription	Fetal Stomach	stomach
11	chr9:14779200-14798600	Strong transcription	Fetal Kidney	kidney
12	chr9:14779800-14789000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:14779800-14853200	Weak transcription	Placenta	Placenta
14	chr9:14780400-14795800	Weak transcription	Left Ventricle	heart
15	chr9:14780400-14843200	Weak transcription	Fetal Heart	heart
16	chr9:14780800-14783400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:14780800-14785200	Strong transcription	Fetal Lung	lung
18	chr9:14781200-14784400	Weak transcription	Psoas Muscle	Psoas
19	chr9:14782000-14783800	Genic enhancers	Fetal Muscle Leg	muscle
20	chr9:14782000-14822000	Weak transcription	Fetal Brain Male	brain
21	chr9:14782200-14790400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:14782400-14783000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr9:14782400-14783000	Strong transcription	HepG2	liver
24	chr9:14782400-14783200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr9:14782400-14783400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr9:14782400-14784600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr9:14782400-14784600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr9:14782400-14785200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:14782600-14783000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr9:14782600-14785200	Strong transcription	Adipose Nuclei	Adipose
31	chr9:14782800-14785400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr9:14782800-14822000	Weak transcription	Rectal Smooth Muscle	rectum

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