Variant report

Variant	rs7020282
Chromosome Location	chr9:14866389-14866390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10810272	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810277	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810283	0.88[CEU][hapmap]
rs10961759	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17312753	0.89[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs1889048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889049	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889052	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996893	0.81[CEU][hapmap]
rs2065482	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2065484	0.83[ASN][1000 genomes]
rs2381975	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6474862	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6474863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6474865	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6474866	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6474868	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7019358	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7032309	0.83[AMR][1000 genomes]
rs7033932	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7045281	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7048511	0.82[CEU][hapmap]
rs7048783	0.88[CEU][hapmap]
rs73417624	0.84[ASN][1000 genomes]
rs7856810	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7862066	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7862716	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[ASN][1000 genomes]
rs7867761	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs7867927	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	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
5	nsv892617	chr9:14791348-14889834	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv892619	chr9:14821819-14866389	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1018416	chr9:14846753-14921247	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv613647	chr9:14852141-15016475	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3390567	chr9:14852461-14891880	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv521718	chr9:14866389-14867958	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7020282	FREM1	cis	parietal	SCAN
rs7020282	LOC93432	trans	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14807400-14868600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:14843400-14868800	Weak transcription	Pancreas	Pancrea
3	chr9:14849600-14869000	Weak transcription	Small Intestine	intestine
4	chr9:14850200-14869000	Weak transcription	Fetal Brain Male	brain
5	chr9:14853200-14868800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:14858200-14868600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:14859600-14868800	Weak transcription	Aorta	Aorta
8	chr9:14859600-14869600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:14859600-14876600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:14860000-14883800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:14863800-14870400	Enhancers	Colon Smooth Muscle	Colon
12	chr9:14864600-14866600	Enhancers	Fetal Kidney	kidney
13	chr9:14865000-14867600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:14865200-14866600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:14865400-14866400	Enhancers	Fetal Lung	lung
16	chr9:14865600-14867200	Active TSS	HepG2	liver
17	chr9:14865800-14866400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr9:14865800-14866400	Enhancers	Fetal Stomach	stomach
19	chr9:14865800-14866600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:14865800-14867000	Enhancers	Rectal Smooth Muscle	rectum
21	chr9:14866200-14867000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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