Variant report

Variant	rs10961700
Chromosome Location	chr9:14776140-14776141
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	chr9:14775864-14776292	HepG2	liver:	n/a	n/a
2	POLR2A	chr9:14775915-14776275	HepG2	liver:	n/a	n/a
3	FOSL2	chr9:14775783-14776254	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:14775747-14776573	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:14775741-14777189	HepG2	liver:	n/a	n/a
6	POLR2A	chr9:14775852-14776252	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
FREM1	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10124839	0.87[GIH][hapmap]
rs10961702	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10961703	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10961704	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]
rs10961708	1.00[JPT][hapmap]
rs10961709	1.00[JPT][hapmap]
rs17292106	1.00[JPT][hapmap]
rs2291679	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2642406	1.00[YRI][hapmap]
rs2779507	1.00[YRI][hapmap]
rs2818939	1.00[YRI][hapmap]
rs4341240	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4740587	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv892615	chr9:14761260-14782367	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv892616	chr9:14762700-14780698	Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10961700	FREM1	cis	cerebellum	SCAN

Chromatin state (count:28 , 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	chr9:14767200-14779200	Weak transcription	Adipose Nuclei	Adipose
8	chr9:14767400-14779000	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:14768600-14808800	Weak transcription	Fetal Intestine Small	intestine
10	chr9:14768800-14780800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:14769000-14783000	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:14771000-14780200	Weak transcription	Left Ventricle	heart
13	chr9:14772600-14776400	Strong transcription	Fetal Lung	lung
14	chr9:14773200-14777400	Strong transcription	Fetal Kidney	kidney
15	chr9:14773400-14776200	Strong transcription	HepG2	liver
16	chr9:14773400-14796400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:14774400-14776200	Enhancers	Fetal Brain Male	brain
18	chr9:14774400-14779600	Weak transcription	Psoas Muscle	Psoas
19	chr9:14774600-14779200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:14775400-14776200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:14775600-14776200	Strong transcription	Fetal Stomach	stomach
22	chr9:14775600-14776400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:14775600-14779400	Weak transcription	Fetal Brain Female	brain
24	chr9:14775800-14776200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:14775800-14776200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:14775800-14776400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr9:14776000-14776200	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr9:14776000-14776200	Enhancers	Skeletal Muscle Female	skeletal muscle

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